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Sample records for variable binding regions

SCOWLP classification: Structural comparison and analysis of protein binding regions

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Anders Gerd

2008-01-01

. The hierarchical classification of PBRs is implemented into the SCOWLP database and extends the SCOP classification with three additional family sub-levels: Binding Region, Interface and Contacting Domains. SCOWLP contains 9,334 binding regions distributed within 2,561 families. In 65% of the cases we observe families containing more than one binding region. Besides, 22% of the regions are forming complex with more than one different protein family. Conclusion The current SCOWLP classification and its web application represent a framework for the study of protein interfaces and comparative analysis of protein family binding regions. This comparison can be performed at atomic level and allows the user to study interactome conservation and variability. The new SCOWLP classification may be of great utility for reconstruction of protein complexes, understanding protein networks and ligand design. SCOWLP will be updated with every SCOP release. The web application is available at http://www.scowlp.org.
A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding

DEFF Research Database (Denmark)

Olsen, Lars Rønn; Simon, Christian; Kudahl, Ulrich J.

2015-01-01

Background: Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte antigen molecules. However, experimental studies have shown that T cells often...... target diverse regions in highly variable viral pathogens and this diversity may need to be addressed through redefinition of suitable peptide targets. Methods: We have developed a method for antigen assessment and target selection for polyvalent vaccines, with which we identified immune epitopes from...... variable regions, where all variants bind HLA. These regions, although variable, can thus be considered stable in terms of HLA binding and represent valuable vaccine targets. Results: We applied this method to predict CD8+ T-cell targets in influenza A H7N9 hemagglutinin and significantly increased...
The necessity of connection structures in neural models of variable binding.

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van der Velde, Frank; de Kamps, Marc

2015-08-01

In his review of neural binding problems, Feldman (Cogn Neurodyn 7:1-11, 2013) addressed two types of models as solutions of (novel) variable binding. The one type uses labels such as phase synchrony of activation. The other ('connectivity based') type uses dedicated connections structures to achieve novel variable binding. Feldman argued that label (synchrony) based models are the only possible candidates to handle novel variable binding, whereas connectivity based models lack the flexibility required for that. We argue and illustrate that Feldman's analysis is incorrect. Contrary to his conclusion, connectivity based models are the only viable candidates for models of novel variable binding because they are the only type of models that can produce behavior. We will show that the label (synchrony) based models analyzed by Feldman are in fact examples of connectivity based models. Feldman's analysis that novel variable binding can be achieved without existing connection structures seems to result from analyzing the binding problem in a wrong frame of reference, in particular in an outside instead of the required inside frame of reference. Connectivity based models can be models of novel variable binding when they possess a connection structure that resembles a small-world network, as found in the brain. We will illustrate binding with this type of model with episode binding and the binding of words, including novel words, in sentence structures.
Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

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Waqasuddin Khan

Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.
Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry

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Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibo...
Identification and therapeutic potential of a vitronectin binding region of meningococcal msf.

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Hill, Darryl J; Griffiths, Natalie J; Borodina, Elena; Andreae, Clio A; Sessions, Richard B; Virji, Mumtaz

2015-01-01

The human pathogen Neisseria meningitides (Nm) attains serum resistance via a number of mechanisms, one of which involves binding to the host complement regulator protein vitronectin. We have shown previously that the Meningococcal surface fibril (Msf), a trimeric autotransporter, binds to the activated form of vitronectin (aVn) to increase Nm survival in human serum. In this study, we aimed to identify the aVn-binding region of Msf to assess its potential as an antigen which can elicit antibodies that block aVn binding and/or possess bactericidal properties. Using several recombinant Msf fragments spanning its surface-exposed region, the smallest aVn-binding recombinants were found to span residues 1-86 and 39-124. The use of further deletion constructs and overlapping recombinant Msf fragments suggested that a region of Msf comprising residues 39-82 may be primarily important for aVn binding and that other regions may also be involved but to a lesser extent. Molecular modelling implicated K66 and K68, conserved in all available Msf sequences, to be involved in the interaction. Recombinant fragments which bound to aVn were able to reduce the survival advantage conveyed by aVn-interaction in serum bactericidal assays. Antibodies raised against one such fragment inhibited aVn binding to Msf. In addition, the antibodies enhanced specific killing of Msf-expressing Nm in a dose-dependent manner. Overall, this study identifies an aVn-binding region of Msf, an adhesin known to impart serum resistance properties to the pathogen; and shows that this region of Msf can elicit antibodies with dual properties which reduce pathogen survival within the host and thus has potential as a vaccine antigen.
Identification and therapeutic potential of a vitronectin binding region of meningococcal msf.

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Darryl J Hill

Full Text Available The human pathogen Neisseria meningitides (Nm attains serum resistance via a number of mechanisms, one of which involves binding to the host complement regulator protein vitronectin. We have shown previously that the Meningococcal surface fibril (Msf, a trimeric autotransporter, binds to the activated form of vitronectin (aVn to increase Nm survival in human serum. In this study, we aimed to identify the aVn-binding region of Msf to assess its potential as an antigen which can elicit antibodies that block aVn binding and/or possess bactericidal properties. Using several recombinant Msf fragments spanning its surface-exposed region, the smallest aVn-binding recombinants were found to span residues 1-86 and 39-124. The use of further deletion constructs and overlapping recombinant Msf fragments suggested that a region of Msf comprising residues 39-82 may be primarily important for aVn binding and that other regions may also be involved but to a lesser extent. Molecular modelling implicated K66 and K68, conserved in all available Msf sequences, to be involved in the interaction. Recombinant fragments which bound to aVn were able to reduce the survival advantage conveyed by aVn-interaction in serum bactericidal assays. Antibodies raised against one such fragment inhibited aVn binding to Msf. In addition, the antibodies enhanced specific killing of Msf-expressing Nm in a dose-dependent manner. Overall, this study identifies an aVn-binding region of Msf, an adhesin known to impart serum resistance properties to the pathogen; and shows that this region of Msf can elicit antibodies with dual properties which reduce pathogen survival within the host and thus has potential as a vaccine antigen.
Extreme sequence divergence but conserved ligand-binding specificity in Streptococcus pyogenes M protein.

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2006-05-01

Full Text Available Many pathogenic microorganisms evade host immunity through extensive sequence variability in a protein region targeted by protective antibodies. In spite of the sequence variability, a variable region commonly retains an important ligand-binding function, reflected in the presence of a highly conserved sequence motif. Here, we analyze the limits of sequence divergence in a ligand-binding region by characterizing the hypervariable region (HVR of Streptococcus pyogenes M protein. Our studies were focused on HVRs that bind the human complement regulator C4b-binding protein (C4BP, a ligand that confers phagocytosis resistance. A previous comparison of C4BP-binding HVRs identified residue identities that could be part of a binding motif, but the extended analysis reported here shows that no residue identities remain when additional C4BP-binding HVRs are included. Characterization of the HVR in the M22 protein indicated that two relatively conserved Leu residues are essential for C4BP binding, but these residues are probably core residues in a coiled-coil, implying that they do not directly contribute to binding. In contrast, substitution of either of two relatively conserved Glu residues, predicted to be solvent-exposed, had no effect on C4BP binding, although each of these changes had a major effect on the antigenic properties of the HVR. Together, these findings show that HVRs of M proteins have an extraordinary capacity for sequence divergence and antigenic variability while retaining a specific ligand-binding function.
Structural Fingerprints of Transcription Factor Binding Site Regions

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Peter Willett

2009-03-01

Full Text Available Fourier transforms are a powerful tool in the prediction of DNA sequence properties, such as the presence/absence of codons. We have previously compiled a database of the structural properties of all 32,896 unique DNA octamers. In this work we apply Fourier techniques to the analysis of the structural properties of human chromosomes 21 and 22 and also to three sets of transcription factor binding sites within these chromosomes. We find that, for a given structural property, the structural property power spectra of chromosomes 21 and 22 are strikingly similar. We find common peaks in their power spectra for both Sp1 and p53 transcription factor binding sites. We use the power spectra as a structural fingerprint and perform similarity searching in order to find transcription factor binding site regions. This approach provides a new strategy for searching the genome data for information. Although it is difficult to understand the relationship between specific functional properties and the set of structural parameters in our database, our structural fingerprints nevertheless provide a useful tool for searching for function information in sequence data. The power spectrum fingerprints provide a simple, fast method for comparing a set of functional sequences, in this case transcription factor binding site regions, with the sequences of whole chromosomes. On its own, the power spectrum fingerprint does not find all transcription factor binding sites in a chromosome, but the results presented here show that in combination with other approaches, this technique will improve the chances of identifying functional sequences hidden in genomic data.
An N-terminal Region of Mot-2 Binds to p53 In Vitro

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Sunil C. Kaul

2001-01-01

Full Text Available The mouse mot-2 protein was earlier shown to bind to the tumor suppressor protein, p53. The mot-2 binding site of p53 was mapped to C-terminal amino acid residues 312–352, which includes the cytoplasmic sequestration domain. In the present study, we have found that both mot-1 and mot-2 bind to p53 in vitro. By using His-tagged deletion mutant proteins, the p53-binding domain of mot-2 was mapped to its Nterminal amino acid residues 253–282, which are identical in mot-1 and mot-2 proteins. Some peptides containing the p53-binding region of mot-2 were able to compete with the full-length protein for p53 binding. The data provided rationale for in vitro binding of mot-1 and mot-2 proteins to p53 and supported the conclusion that inability of mot-1 protein to bind p53 in vivo depends on secondary structure or its binding to other cellular factors. Most interestingly, the p53-binding region of mot-2 was common to its MKT-077, a cationic dye that exhibits antitumor activity, binding region. Therefore it is most likely that MKT-077-induced nuclear translocation and restoration of wild-type p53 function in transformed cells takes place by a competitional mechanism.
Monoclonal Antibodies Directed toward the Hepatitis C Virus Glycoprotein E2 Detect Antigenic Differences Modulated by the N-Terminal Hypervariable Region 1 (HVR1), HVR2, and Intergenotypic Variable Region.

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Alhammad, Yousef; Gu, Jun; Boo, Irene; Harrison, David; McCaffrey, Kathleen; Vietheer, Patricia T; Edwards, Stirling; Quinn, Charles; Coulibaly, Fásseli; Poumbourios, Pantelis; Drummer, Heidi E

2015-12-01

Hepatitis C virus (HCV) envelope glycoproteins E1 and E2 form a heterodimer and mediate receptor interactions and viral fusion. Both E1 and E2 are targets of the neutralizing antibody (NAb) response and are candidates for the production of vaccines that generate humoral immunity. Previous studies demonstrated that N-terminal hypervariable region 1 (HVR1) can modulate the neutralization potential of monoclonal antibodies (MAbs), but no information is available on the influence of HVR2 or the intergenotypic variable region (igVR) on antigenicity. In this study, we examined how the variable regions influence the antigenicity of the receptor binding domain of E2 spanning HCV polyprotein residues 384 to 661 (E2661) using a panel of MAbs raised against E2661 and E2661 lacking HVR1, HVR2, and the igVR (Δ123) and well-characterized MAbs isolated from infected humans. We show for a subset of both neutralizing and nonneutralizing MAbs that all three variable regions decrease the ability of MAbs to bind E2661 and reduce the ability of MAbs to inhibit E2-CD81 interactions. In addition, we describe a new MAb directed toward the region spanning residues 411 to 428 of E2 (MAb24) that demonstrates broad neutralization against all 7 genotypes of HCV. The ability of MAb24 to inhibit E2-CD81 interactions is strongly influenced by the three variable regions. Our data suggest that HVR1, HVR2, and the igVR modulate exposure of epitopes on the core domain of E2 and their ability to prevent E2-CD81 interactions. These studies suggest that the function of HVR2 and the igVR is to modulate antibody recognition of glycoprotein E2 and may contribute to immune evasion. This study reveals conformational and antigenic differences between the Δ123 and intact E2661 glycoproteins and provides new structural and functional data about the three variable regions and their role in occluding neutralizing and nonneutralizing epitopes on the E2 core domain. The variable regions may therefore function to
Synthetic localization of a second toxin-binding region within residues α182-198 of Torpedo acetylcholine receptor

International Nuclear Information System (INIS)

Mulac-Jericevic, B.; Atassi, M.Z.

1986-01-01

A peptide, corresponding to the region 182-198 (peptide αT182-198) of the α chain of Torpedo californica acetylcholine (AChR) was synthesized, purified and characterized. The binding activities of this peptide to α-bungarotoxin and to cobratoxin were studied and compared to the activities of the previously reported synthetic peptide αT125-147 of Torpedo α chain. Binding studies were performed by quantitative radiometric titrations by studying the binding of 125 I-labelled peptides to toxin adsorbents and the binding of 125 I labelled toxins to peptide adsorbents. The specificity of the binding was confirmed by appropriate inhibition experiments. The results showed unequivocally that the α chain of AChR contains a second toxin binding region which resides within, but may not comprise all of, the residues 182-198. The binding of toxins to one synthetic region is inhibited by the other. Thus, the α chain of AChR contains at least two toxin binding regions which may either be two faces of a larger single binding site or, alternatively, two binding sites that are spatially very close and thus the binding of one synthetic region to the toxin site could sterically obstruct the binding of the second synthetic region
Climatological variability in regional air pollution

International Nuclear Information System (INIS)

Shannon, J.D.; Trexler, E.C. Jr.

1995-01-01

Although some air pollution modeling studies examine events that have already occurred (e.g., the Chernobyl plume) with relevant meteorological conditions largely known, most pollution modeling studies address expected or potential scenarios for the future. Future meteorological conditions, the major pollutant forcing function other than emissions, are inherently uncertain although much relevant information is contained in past observational data. For convenience in our discussions of regional pollutant variability unrelated to emission changes, we define meteorological variability as short-term (within-season) pollutant variability and climatological variability as year-to-year changes in seasonal averages and accumulations of pollutant variables. In observations and in some of our simulations the effects are confounded because for seasons of two different years both the mean and the within-season character of a pollutant variable may change. Effects of climatological and meteorological variability on means and distributions of air pollution parameters, particularly those related to regional visibility, are illustrated. Over periods of up to a decade climatological variability may mask or overstate improvements resulting from emission controls. The importance of including climatological uncertainties in assessing potential policies, particularly when based partly on calculated source-receptor relationships, is highlighted
N-linked glycosylation of the immunoglobulin variable region

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van de Bovenkamp, Fleur S.; Derksen, Ninotska I. L.; Ooijevaar-de Heer, Pleuni; van Schie, Karin A.; Kruithof, Simone; Berkowska, Magdalena A.; van der Schoot, C. Ellen; Ijspeert, Hanna; van der Burg, Mirjam; Gils, Ann; Hafkenscheid, Lise; Toes, René E. M.; Rombouts, Yoann; Plomp, Rosina; Wuhrer, Manfred; van Ham, S. Marieke; Vidarsson, Gestur; Rispens, Theo

2018-01-01

N-glycosylation sites are introduced at positions in which glycans can affect antigen binding as a result of a specific clustering of progenitor glycosylation sites in the germline sequences of variable domain genes. By analyzing multiple human monoclonal and polyclonal (auto)antibody responses, we
Transforming p21 ras protein: flexibility in the major variable region linking the catalytic and membrane-anchoring domains

DEFF Research Database (Denmark)

Willumsen, B M; Papageorge, A G; Hubbert, N

1985-01-01

or increasing it to 50 amino acids has relatively little effect on the capacity of the gene to induce morphological transformation of NIH 3T3 cells. Assays of GTP binding, GTPase and autophosphorylating activities of such mutant v-rasH-encoded proteins synthesized in bacteria indicated that the sequences...... that is required for post-translational processing, membrane localization and transforming activity of the proteins. We have now used the viral oncogene (v-rasH) of Harvey sarcoma virus to study the major variable region by deleting or duplicating parts of the gene. Reducing this region to five amino acids...... that encode these biochemical activities are located upstream from the major variable region. In the context of transformation, we propose that the region of sequence heterogeneity serves principally to connect the N-terminal catalytic domain with amino acids at the C terminus that are required to anchor...
Binding energy and single-particle energies in the 16O Region

International Nuclear Information System (INIS)

Fiase, J.O.; Sharma, L.K.

2004-01-01

In this paper we present the binding energy of 16 O together with single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Nijmegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.Our calculated binding energy, E B = - 127.8 MeV with r c = 0.241 fm compares well with the experimental binding energy, E B = - 127.6 MeV
Furin proteolytically processes the heparin-binding region of extracellular superoxide dismutase

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Bowler, Russell P; Nicks, Mike; Olsen, Dorte Aa

2002-01-01

Extracellular superoxide dismutase (EC-SOD) is an antioxidant enzyme that attenuates brain and lung injury from oxidative stress. A polybasic region in the carboxyl terminus distinguishes EC-SOD from other superoxide dismutases and determines EC-SOD's tissue half-life and affinity for heparin....... There are two types of EC-SOD that differ based on the presence or absence of this heparin-binding region. It has recently been shown that proteolytic removal of the heparin-binding region is an intracellular event (Enghild, J. J., Thogersen, I. B., Oury, T. D., Valnickova, Z., Hojrup, P., and Crapo, J. D...... of intracellular proteases implicate furin as a processing protease. In vitro experiments using furin and purified EC-SOD suggest that furin proteolytically cleaves EC-SOD in the middle of the polybasic region and then requires an additional carboxypeptidase to remove the remaining lysines and arginines...
Aging-induced changes in brain regional serotonin receptor binding: Effect of Carnosine.

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Banerjee, S; Poddar, M K

2016-04-05

Monoamine neurotransmitter, serotonin (5-HT) has its own specific receptors in both pre- and post-synapse. In the present study the role of carnosine on aging-induced changes of [(3)H]-5-HT receptor binding in different brain regions in a rat model was studied. The results showed that during aging (18 and 24 months) the [(3)H]-5-HT receptor binding was reduced in hippocampus, hypothalamus and pons-medulla with a decrease in their both Bmax and KD but in cerebral cortex the [(3)H]-5-HT binding was increased with the increase of its only Bmax. The aging-induced changes in [(3)H]-5-HT receptor binding with carnosine (2.0 μg/kg/day, intrathecally, for 21 consecutive days) attenuated in (a) 24-month-aged rats irrespective of the brain regions with the attenuation of its Bmax except hypothalamus where both Bmax and KD were significantly attenuated, (b) hippocampus and hypothalamus of 18-month-aged rats with the attenuation of its Bmax, and restored toward the [(3)H]-5-HT receptor binding that observed in 4-month-young rats. The decrease in pons-medullary [(3)H]-5-HT binding including its Bmax of 18-month-aged rats was promoted with carnosine without any significant change in its cerebral cortex. The [(3)H]-5-HT receptor binding with the same dosages of carnosine in 4-month-young rats (a) increased in the cerebral cortex and hippocampus with the increase in their only Bmax whereas (b) decreased in hypothalamus and pons-medulla with a decrease in their both Bmax and KD. These results suggest that carnosine treatment may (a) play a preventive role in aging-induced brain region-specific changes in serotonergic activity (b) not be worthy in 4-month-young rats in relation to the brain regional serotonergic activity. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.
Low 5-HT1B receptor binding in the migraine brain

DEFF Research Database (Denmark)

Deen, Marie; Hansen, Hanne D; Hougaard, Anders

2018-01-01

Background The pathophysiology of migraine may involve dysfunction of serotonergic signaling. In particular, the 5-HT1B receptor is considered a key player due to the efficacy of 5-HT1B receptor agonists for treatment of migraine attacks. Aim To examine the cerebral 5-HT1B receptor binding....... Patients who reported migraine brain regions involved in pain modulation as regions of interest and applied a latent variable model (LVM) to assess the group effect on binding across these regions. Results Our data...... support a model wherein group status predicts the latent variable ( p = 0.038), with migraine patients having lower 5-HT1B receptor binding across regions compared to controls. Further, in a whole-brain voxel-based analysis, time since last migraine attack correlated positively with 5-HT1B receptor...
Definition of IgG- and albumin-binding regions of streptococcal protein G.

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Akerström, B; Nielsen, E; Björck, L

1987-10-05

Protein G, the immunoglobin G-binding surface protein of group C and G streptococci, also binds serum albumin. The albumin-binding site on protein G is distinct from the immunoglobulin G-binding site. By mild acid hydrolysis of the papain-liberated protein G fragment (35 kDa), a 28-kDa fragment was produced which retained full immunoglobulin G-binding activity (determined by Scatchard plotting) but had lost all albumin-binding capacity. A protein G (65 kDa), isolated after cloning and expression of the protein G gene in Escherichia coli, had comparable affinity to immunoglobulin G (5-10 X 10(10)M-1), but much higher affinity to albumin than the 35- and 28-kDa protein G fragments (31, 2.6, and 0 X 10(9)M-1, respectively). The amino-terminal amino acid sequences of the 65-, 35-, and 28-kDa fragments allowed us to exactly locate the three fragments in an overall sequence map of protein G, based on the partial gene sequences published by Guss et al. (Guss, B., Eliasson, M., Olsson, A., Uhlen, M., Frej, A.-K., Jörnvall, H., Flock, J.-I., and Lindberg, M. (1986) EMBO J. 5, 1567-1575) and Fahnestock et al. (Fahnestock, S. R., Alexander, P., Nagle, J., and Filpula, D. (1986) J. Bacteriol. 167, 870-880). In this map could then be deduced the location of three homologous albumin-binding regions and three homologous immunoglobulin G-binding regions.

Adaptive antibody diversification through N-linked glycosylation of the immunoglobulin variable region.

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van de Bovenkamp, Fleur S; Derksen, Ninotska I L; Ooijevaar-de Heer, Pleuni; van Schie, Karin A; Kruithof, Simone; Berkowska, Magdalena A; van der Schoot, C Ellen; IJspeert, Hanna; van der Burg, Mirjam; Gils, Ann; Hafkenscheid, Lise; Toes, René E M; Rombouts, Yoann; Plomp, Rosina; Wuhrer, Manfred; van Ham, S Marieke; Vidarsson, Gestur; Rispens, Theo

2018-02-20

A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N -linked glycans, a process conditional on the introduction of consensus amino acid motifs ( N -glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas. However, the role of these glycans in the humoral immune response remains poorly understood. Interestingly, studies have reported both positive and negative effects on antibody affinity. Our aim was to elucidate the role of variable domain glycans during antigen-specific antibody responses. By analyzing B-cell repertoires by next-generation sequencing, we demonstrate that N -glycosylation sites are introduced at positions in which glycans can affect antigen binding as a result of a specific clustering of progenitor glycosylation sites in the germline sequences of variable domain genes. By analyzing multiple human monoclonal and polyclonal (auto)antibody responses, we subsequently show that this process is subject to selection during antigen-specific antibody responses, skewed toward IgG4, and positively contributes to antigen binding. Together, these results highlight a physiological role for variable domain glycosylation as an additional layer of antibody diversification that modulates antigen binding.
Regional increases in [11C]flumazenil binding after epilepsy surgery

International Nuclear Information System (INIS)

Savic, I.; Blomqvist, G.; Halldin, C.; Litton, J.E.; Gulyas, B.

1998-01-01

Introduction - Animal experiments suggest that epileptic seizures alter the expression of mRNA for neuro-receptors. PET measurements with [ 11 C]flumazenil show that patients with partial seizures have a reduced density of benzodiazepine (BZ) receptors in the epileptogenic regions (ER) and some of the target areas for seizure activity, the so called projection areas. Recent data suggest that the degree of BZ receptor reduction in ER is correlated to seizure frequency. We therefore hypothesized that seizure activity can alter the BZ receptor binding, and that some of these changes could normalize when the seizures disappeared. Methods - In 4 patients whose seizures were generated by mesial temporal lobe structures, BZ receptor density was measured with [ 11 C]flumazenil PET before, and 1 year after the epilepsy surgery and cessation of seizures. By use of a computerized anatomical brain atlas the same regions were analyzed in both PET scans, and the results related to data from 7 healthy controls. Results - Presurgical PET scans showed reductions in BZ receptor density in the epileptogenic regions and some of its primary projection areas. Other cortical regions had normal values. Postsurgically, the calculated BZ receptor density normalized (29±17% increase) in several of the affected projection areas, whereas the values in other cortical regions remained unaltered. Conclusion - Regional reductions in BZ receptor density may be dynamic and related to seizures. The present preliminary observations encourage further studies on seizure-related changes in regional receptor binding in humans. (au)
Effects of short-term variability of meteorological variables on soil temperature in permafrost regions

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Beer, Christian; Porada, Philipp; Ekici, Altug; Brakebusch, Matthias

2018-03-01

Effects of the short-term temporal variability of meteorological variables on soil temperature in northern high-latitude regions have been investigated. For this, a process-oriented land surface model has been driven using an artificially manipulated climate dataset. Short-term climate variability mainly impacts snow depth, and the thermal diffusivity of lichens and bryophytes. These impacts of climate variability on insulating surface layers together substantially alter the heat exchange between atmosphere and soil. As a result, soil temperature is 0.1 to 0.8 °C higher when climate variability is reduced. Earth system models project warming of the Arctic region but also increasing variability of meteorological variables and more often extreme meteorological events. Therefore, our results show that projected future increases in permafrost temperature and active-layer thickness in response to climate change will be lower (i) when taking into account future changes in short-term variability of meteorological variables and (ii) when representing dynamic snow and lichen and bryophyte functions in land surface models.
Serotonin 2A receptor agonist binding in the human brain with [¹¹C]Cimbi-36

DEFF Research Database (Denmark)

Ettrup, Anders; Svarer, Claus; McMahon, Brenda

2016-01-01

INTRODUCTION: [(11)C]Cimbi-36 is a recently developed serotonin 2A (5-HT2A) receptor agonist positron emission tomography (PET) radioligand that has been successfully applied for human neuroimaging. Here, we investigate the test-retest variability of cerebral [(11)C]Cimbi-36 PET and compare [(11)C...... test-retest variability in [(11)C]Cimbi-36 binding measures, and another eight were scanned after a bolus plus constant infusion with [(18)F]altanserin. Regional differences in the brain distribution of [(11)C]Cimbi-36 and [(18)F]altanserin were assessed with a correlation of regional binding measures...... and with voxel-based analysis. RESULTS: Test-retest variability of [(11)C]Cimbi-36 non-displaceable binding potential (BPND) was consistently correlation between regional...
PL/SQL and Bind Variable: the two ways to increase the efficiency of Network Databases

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Hitesh KUMAR SHARMA

2011-12-01

Full Text Available Modern data analysis applications are driven by the Network databases. They are pushing traditional database and data warehousing technologies beyond their limits due to their massively increasing data volumes and demands for low latency. There are three major challenges in working with network databases: interoperability due to heterogeneous data repositories, proactively due to autonomy of data sources and high efficiency to meet the application demand. This paper provides the two ways to meet the third challenge of network databases. This goal can be achieved by network database administrator with the usage of PL/SQL blocks and bind variable. The paper will explain the effect of PL/SQL block and bind variable on Network database efficiency to meet the modern data analysis application demand.
Adrenergic Agonists Bind to Adrenergic-Receptor-Like Regions of the Mu Opioid Receptor, Enhancing Morphine and Methionine-Enkephalin Binding: A New Approach to "Biased Opioids"?

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Root-Bernstein, Robert; Turke, Miah; Subhramanyam, Udaya K Tiruttani; Churchill, Beth; Labahn, Joerg

2018-01-17

Extensive evidence demonstrates functional interactions between the adrenergic and opioid systems in a diversity of tissues and organs. While some effects are due to receptor and second messenger cross-talk, recent research has revealed an extracellular, allosteric opioid binding site on adrenergic receptors that enhances adrenergic activity and its duration. The present research addresses whether opioid receptors may have an equivalent extracellular, allosteric adrenergic binding site that has similar enhancing effects on opioid binding. Comparison of adrenergic and opioid receptor sequences revealed that these receptors share very significant regions of similarity, particularly in some of the extracellular and transmembrane regions associated with adrenergic binding in the adrenergic receptors. Five of these shared regions from the mu opioid receptor (muOPR) were synthesized as peptides and tested for binding to adrenergic, opioid and control compounds using ultraviolet spectroscopy. Adrenergic compounds bound to several of these muOPR peptides with low micromolar affinity while acetylcholine, histamine and various adrenergic antagonists did not. Similar studies were then conducted with purified, intact muOPR with similar results. Combinations of epinephrine with methionine enkephalin or morphine increased the binding of both by about half a log unit. These results suggest that muOPR may be allosterically enhanced by adrenergic agonists.
Regional increases in [{sup 11}C]flumazenil binding after epilepsy surgery

Energy Technology Data Exchange (ETDEWEB)

Savic, I. [Huddinge Hospital, Dept. of Neurology (Sweden); Blomqvist, G. [Karolinska Hospital, Dept. of Clinical Neurophysiology, Stockholm (Sweden); Halldin, C. [Karolinska Hospital, Dept. of Psychiatry, Stockholm (Sweden); Litton, J.E. [Karolinska Hospital, Dept. of Psychology, Stockholm (Sweden); Gulyas, B. [Karolinska Institute, Div. of Human Brain Research (Sweden)

1998-05-01

Introduction - Animal experiments suggest that epileptic seizures alter the expression of mRNA for neuro-receptors. PET measurements with [{sup 11}C]flumazenil show that patients with partial seizures have a reduced density of benzodiazepine (BZ) receptors in the epileptogenic regions (ER) and some of the target areas for seizure activity, the so called projection areas. Recent data suggest that the degree of BZ receptor reduction in ER is correlated to seizure frequency. We therefore hypothesized that seizure activity can alter the BZ receptor binding, and that some of these changes could normalize when the seizures disappeared. Methods - In 4 patients whose seizures were generated by mesial temporal lobe structures, BZ receptor density was measured with [{sup 11}C]flumazenil PET before, and 1 year after the epilepsy surgery and cessation of seizures. By use of a computerized anatomical brain atlas the same regions were analyzed in both PET scans, and the results related to data from 7 healthy controls. Results - Presurgical PET scans showed reductions in BZ receptor density in the epileptogenic regions and some of its primary projection areas. Other cortical regions had normal values. Postsurgically, the calculated BZ receptor density normalized (29{+-}17% increase) in several of the affected projection areas, whereas the values in other cortical regions remained unaltered. Conclusion - Regional reductions in BZ receptor density may be dynamic and related to seizures. The present preliminary observations encourage further studies on seizure-related changes in regional receptor binding in humans. (au) 41 refs.
Genetic variability and natural selection at the ligand domain of the Duffy binding protein in brazilian Plasmodium vivax populations

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Gil Luiz HS

2010-11-01

Full Text Available Abstract Background Plasmodium vivax malaria is a major public health challenge in Latin America, Asia and Oceania, with 130-435 million clinical cases per year worldwide. Invasion of host blood cells by P. vivax mainly depends on a type I membrane protein called Duffy binding protein (PvDBP. The erythrocyte-binding motif of PvDBP is a 170 amino-acid stretch located in its cysteine-rich region II (PvDBPII, which is the most variable segment of the protein. Methods To test whether diversifying natural selection has shaped the nucleotide diversity of PvDBPII in Brazilian populations, this region was sequenced in 122 isolates from six different geographic areas. A Bayesian method was applied to test for the action of natural selection under a population genetic model that incorporates recombination. The analysis was integrated with a structural model of PvDBPII, and T- and B-cell epitopes were localized on the 3-D structure. Results The results suggest that: (i recombination plays an important role in determining the haplotype structure of PvDBPII, and (ii PvDBPII appears to contain neutrally evolving codons as well as codons evolving under natural selection. Diversifying selection preferentially acts on sites identified as epitopes, particularly on amino acid residues 417, 419, and 424, which show strong linkage disequilibrium. Conclusions This study shows that some polymorphisms of PvDBPII are present near the erythrocyte-binding domain and might serve to elude antibodies that inhibit cell invasion. Therefore, these polymorphisms should be taken into account when designing vaccines aimed at eliciting antibodies to inhibit erythrocyte invasion.
Adrenergic Agonists Bind to Adrenergic-Receptor-Like Regions of the Mu Opioid Receptor, Enhancing Morphine and Methionine-Enkephalin Binding: A New Approach to “Biased Opioids”?

Science.gov (United States)

Turke, Miah; Subhramanyam, Udaya K. Tiruttani; Churchill, Beth; Labahn, Joerg

2018-01-01

Extensive evidence demonstrates functional interactions between the adrenergic and opioid systems in a diversity of tissues and organs. While some effects are due to receptor and second messenger cross-talk, recent research has revealed an extracellular, allosteric opioid binding site on adrenergic receptors that enhances adrenergic activity and its duration. The present research addresses whether opioid receptors may have an equivalent extracellular, allosteric adrenergic binding site that has similar enhancing effects on opioid binding. Comparison of adrenergic and opioid receptor sequences revealed that these receptors share very significant regions of similarity, particularly in some of the extracellular and transmembrane regions associated with adrenergic binding in the adrenergic receptors. Five of these shared regions from the mu opioid receptor (muOPR) were synthesized as peptides and tested for binding to adrenergic, opioid and control compounds using ultraviolet spectroscopy. Adrenergic compounds bound to several of these muOPR peptides with low micromolar affinity while acetylcholine, histamine and various adrenergic antagonists did not. Similar studies were then conducted with purified, intact muOPR with similar results. Combinations of epinephrine with methionine enkephalin or morphine increased the binding of both by about half a log unit. These results suggest that muOPR may be allosterically enhanced by adrenergic agonists. PMID:29342106
Adrenergic Agonists Bind to Adrenergic-Receptor-Like Regions of the Mu Opioid Receptor, Enhancing Morphine and Methionine-Enkephalin Binding: A New Approach to “Biased Opioids”?

Directory of Open Access Journals (Sweden)

Robert Root-Bernstein

2018-01-01

Full Text Available Extensive evidence demonstrates functional interactions between the adrenergic and opioid systems in a diversity of tissues and organs. While some effects are due to receptor and second messenger cross-talk, recent research has revealed an extracellular, allosteric opioid binding site on adrenergic receptors that enhances adrenergic activity and its duration. The present research addresses whether opioid receptors may have an equivalent extracellular, allosteric adrenergic binding site that has similar enhancing effects on opioid binding. Comparison of adrenergic and opioid receptor sequences revealed that these receptors share very significant regions of similarity, particularly in some of the extracellular and transmembrane regions associated with adrenergic binding in the adrenergic receptors. Five of these shared regions from the mu opioid receptor (muOPR were synthesized as peptides and tested for binding to adrenergic, opioid and control compounds using ultraviolet spectroscopy. Adrenergic compounds bound to several of these muOPR peptides with low micromolar affinity while acetylcholine, histamine and various adrenergic antagonists did not. Similar studies were then conducted with purified, intact muOPR with similar results. Combinations of epinephrine with methionine enkephalin or morphine increased the binding of both by about half a log unit. These results suggest that muOPR may be allosterically enhanced by adrenergic agonists.
Identification and in silico analysis of helical lipid binding regions in ...

Indian Academy of Sciences (India)

In supplementary table 1, all the results of the lipid binding region analysis for SecA from a number of ..... For those interested, a more detailed description will now be given for this particular analysis. First of ... MCPep Job Status Page Finished.
Regional simulation of interannual variability over South America

Science.gov (United States)

Misra, V.; Dirmeyer, P. A.; Kirtman, B. P.; Juang, H.-M. Henry; Kanamitsu, M.

2002-08-01

Three regional climate simulations covering the austral summer season during three contrasting phases of the El Niño-Southern Oscillation cycle were conducted with the Regional Spectral Model (RSM) developed at the National Centers for Environmental Prediction (NCEP). The simulated interannual variability of precipitation over the Amazon River Basin, the Intertropical Convergence Zone, the Pacific and Atlantic Ocean basins, and extratropical South America compare reasonably well with observations. The RSM optimally filters the peturbations about a time-varying base field, thereby enhancing the information content of the global NCEP reanalysis. The model is better than the reanalysis in reproducing the observed interannual variability of outgoing longwave radiation at both high frequencies (3-30 days) and intraseasonal (30-60 days) scales. The low-level jet shows a peak in its speed in 1998 and a minimum in the 1999 simulations. The lag correlation of the jet index with convection over various areas in continental South America indicates that the jet induces precipitation over the Pampas region downstream. A detailed moisture budget was conducted over various subregions. This budget reveals that moisture flux convergence determines most of the interannual variability of precipitation over the Amazon Basin, the Atlantic Intertropical Convergence Zone, and the Nordeste region of Brazil. However, both surface evaporation and surface moisture flux convergence were found to be critical in determining the interannual variability of precipitation over the southern Pampas, Gran Chaco area, and the South Atlantic Convergence Zone.
Extended hormone binding site of the human thyroid stimulating hormone receptor: distinctive acidic residues in the hinge region are involved in bovine thyroid stimulating hormone binding and receptor activation.

Science.gov (United States)

Mueller, Sandra; Kleinau, Gunnar; Jaeschke, Holger; Paschke, Ralf; Krause, Gerd

2008-06-27

The human thyroid stimulating hormone receptor (hTSHR) belongs to the glycoprotein hormone receptors that bind the hormones at their large extracellular domain. The extracellular hinge region of the TSHR connects the N-terminal leucine-rich repeat domain with the membrane-spanning serpentine domain. From previous studies we reasoned that apart from hormone binding at the leucine-rich repeat domain, additional multiple hormone contacts might exist at the hinge region of the TSHR by complementary charge-charge recognition. Here we investigated highly conserved charged residues in the hinge region of the TSHR by site-directed mutagenesis to identify amino acids interacting with bovine TSH (bTSH). Indeed, the residues Glu-297, Glu-303, and Asp-382 in the TSHR hinge region are essential for bTSH binding and partially for signal transduction. Side chain substitutions showed that the negative charge of Glu-297 and Asp-382 is necessary for recognition of bTSH by the hTSHR. Multiple combinations of alanine mutants of the identified positions revealed an increased negative effect on hormone binding. An assembled model suggests that the deciphered acidic residues form negatively charged patches at the hinge region resulting in an extended binding mode for bTSH on the hTSHR. Our data indicate that certain positively charged residues of bTSH might be involved in interaction with the identified negatively charged amino acids of the hTSHR hinge region. We demonstrate that the hinge region represents an extracellular intermediate connector for both hormone binding and signal transduction of the hTSHR.
Fundamental considerations in ski binding analysis.

Science.gov (United States)

Mote, C D; Hull, M L

1976-01-01

1. The static adjustment of a ski binding by hand or by available machines is only an adjustment and is neither a static nor a dynamic evaluation of the binding design. Bindings of different design with identical static adjustments will perform differently in environments in which the forces are static or dynamic. 2. The concept of binding release force is a useful measure of binding adjustment, but it is inappropriate as a criterion for binding evaluation. First, it does not direct attention toward the injury causing mechanism, strain, or displacement in the leg. Second, it is only part of the evaluation in dynamic problems. 3. The binding release decision in present bindings is displacement controlled. The relative displacement of the boot and ski is the system variable. For any specified relative displacement the binding force can be any of an infinite number of possibilities determined by the loading path. 4. The response of the leg-ski system to external impulses applied to the ski is independent of the boot-ski relative motion as long as the boot recenters quickly in the binding. Response is dependent upon the external impulse plus system inertia, damping and stiffness. 5. When tested under half sinusoidal forces applied to a test ski, all bindings will demonstrate static and impulse loading regions. In the static region the force drives the binding to a relative release displacement. In the impulse region the initial velocity of the ski drives the binding to a release displacement. 6. The transition between the static and impulse loading regions is determined by the binding's capacity to store and dissipate energy along the principal loading path. Increased energy capacity necessitates larger external impulses to produce release. 7. In all bindings examined to date, the transmitted leg displacement or strain at release under static loading exceeds leg strain under dynamic or impact loading. Because static loading is responsible for many injuries, a skier
Competitive Promoter-Associated Matrix Attachment Region Binding of the Arid3a and Cux1 Transcription Factors

Directory of Open Access Journals (Sweden)

Dongkyoon Kim

2017-12-01

Full Text Available Arid3a/Bright/Dril1 is a B cell-specific transactivator that regulates immunoglobulin heavy chain (IgH gene transcription by binding promoter and enhancer-associated matrix attachment regions (MARs within the IgH gene locus. Promoter MAR-mediated Arid3a transactivation is antagonized by direct competition of MAR binding by Cux1/CDP—a ubiquitously expressed repressor originally termed NF-μNR. We report that the NF-μNR complex includes Arid3a in B cells but not in non-B cells through mobility shift assays. The binding activity of NF-μNR and Arid3a in B cells is reciprocally altered during the cell division cycle and by the B cell mitogen lipopolysaccharide LPS. LPS treatment had no effect on Arid3a localization but increased its total abundance within the nucleus and cytoplasm. We show that this increased level of Arid3a is capable of displacing Cux from the MARs to facilitate IgH gene transcription. Finally, we showed that the MARs (termed Bf150 and Tx125 associated with the VH1 rearranged variable region expressed in the S107 murine plasmacytoma, can repress reporter gene transcription in non-B cells and that they can relieve the repression mediated by Eμ enhancer in B cells. These results have significant implications for early human development and demonstrate that MARs in IgH locus, NF-µNR and Arid3a regulate IgH gene expression in a concerted fashion. This paves the way for future studies examining the misregulation of this pathway in pediatric disease.
Effect of the Flexible Regions of the Oncoprotein Mouse Double Minute X on Inhibitor Binding Affinity.

Science.gov (United States)

Qin, Lingyun; Liu, Huili; Chen, Rong; Zhou, Jingjing; Cheng, Xiyao; Chen, Yao; Huang, Yongqi; Su, Zhengding

2017-11-07

The oncoprotein MdmX (mouse double minute X) is highly homologous to Mdm2 (mouse double minute 2) in terms of their amino acid sequences and three-dimensional conformations, but Mdm2 inhibitors exhibit very weak affinity for MdmX, providing an excellent model for exploring how protein conformation distinguishes and alters inhibitor binding. The intrinsic conformation flexibility of proteins plays pivotal roles in determining and predicting the binding properties and the design of inhibitors. Although the molecular dynamics simulation approach enables us to understand protein-ligand interactions, the mechanism underlying how a flexible binding pocket adapts an inhibitor has been less explored experimentally. In this work, we have investigated how the intrinsic flexible regions of the N-terminal domain of MdmX (N-MdmX) affect the affinity of the Mdm2 inhibitor nutlin-3a using protein engineering. Guided by heteronuclear nuclear Overhauser effect measurements, we identified the flexible regions that affect inhibitor binding affinity around the ligand-binding pocket on N-MdmX. A disulfide engineering mutant, N-MdmX C25-C110/C76-C88 , which incorporated two staples to rigidify the ligand-binding pocket, allowed an affinity for nutlin-3a higher than that of wild-type N-MdmX (K d ∼ 0.48 vs K d ∼ 20.3 μM). Therefore, this mutant provides not only an effective protein model for screening and designing of MdmX inhibitors but also a valuable clue for enhancing the intermolecular interactions of the pharmacophores of a ligand with pronounced flexible regions. In addition, our results revealed an allosteric ligand-binding mechanism of N-MdmX in which the ligand initially interacts with a compact core, followed by augmenting intermolecular interactions with intrinsic flexible regions. This strategy should also be applicable to many other protein targets to accelerate drug discovery.
Worldwide genetic variability of the Duffy binding protein: insights into Plasmodium vivax vaccine development.

Science.gov (United States)

Nóbrega de Sousa, Taís; Carvalho, Luzia Helena; Alves de Brito, Cristiana Ferreira

2011-01-01

The dependence of Plasmodium vivax on invasion mediated by Duffy binding protein (DBP) makes this protein a prime candidate for development of a vaccine. However, the development of a DBP-based vaccine might be hampered by the high variability of the protein ligand (DBP(II)), known to bias the immune response toward a specific DBP variant. Here, the hypothesis being investigated is that the analysis of the worldwide DBP(II) sequences will allow us to determine the minimum number of haplotypes (MNH) to be included in a DBP-based vaccine of broad coverage. For that, all DBP(II) sequences available were compiled and MNH was based on the most frequent nonsynonymous single nucleotide polymorphisms, the majority mapped on B and T cell epitopes. A preliminary analysis of DBP(II) genetic diversity from eight malaria-endemic countries estimated that a number between two to six DBP haplotypes (17 in total) would target at least 50% of parasite population circulating in each endemic region. Aiming to avoid region-specific haplotypes, we next analyzed the MNH that broadly cover worldwide parasite population. The results demonstrated that seven haplotypes would be required to cover around 60% of DBP(II) sequences available. Trying to validate these selected haplotypes per country, we found that five out of the eight countries will be covered by the MNH (67% of parasite populations, range 48-84%). In addition, to identify related subgroups of DBP(II) sequences we used a Bayesian clustering algorithm. The algorithm grouped all DBP(II) sequences in six populations that were independent of geographic origin, with ancestral populations present in different proportions in each country. In conclusion, in this first attempt to undertake a global analysis about DBP(II) variability, the results suggest that the development of DBP-based vaccine should consider multi-haplotype strategies; otherwise a putative P. vivax vaccine may not target some parasite populations.
Internal Associations of the Acidic Region of Upstream Binding Factor Control Its Nucleolar Localization.

Science.gov (United States)

Ueshima, Shuhei; Nagata, Kyosuke; Okuwaki, Mitsuru

2017-11-15

Upstream binding factor (UBF) is a member of the high-mobility group (HMG) box protein family, characterized by multiple HMG boxes and a C-terminal acidic region (AR). UBF is an essential transcription factor for rRNA genes and mediates the formation of transcriptionally active chromatin in the nucleolus. However, it remains unknown how UBF is specifically localized to the nucleolus. Here, we examined the molecular mechanisms that localize UBF to the nucleolus. We found that the first HMG box (HMG box 1), the linker region (LR), and the AR cooperatively regulate the nucleolar localization of UBF1. We demonstrated that the AR intramolecularly associates with and attenuates the DNA binding activity of HMG boxes and confers the structured DNA preference to HMG box 1. In contrast, the LR was found to serve as a nuclear localization signal and compete with HMG boxes to bind the AR, permitting nucleolar localization of UBF1. The LR sequence binds DNA and assists the stable chromatin binding of UBF. We also showed that the phosphorylation status of the AR does not clearly affect the localization of UBF1. Our results strongly suggest that associations of the AR with HMG boxes and the LR regulate UBF nucleolar localization. Copyright © 2017 American Society for Microbiology.
Transcription Factors Bind Thousands of Active and InactiveRegions in the Drosophila Blastoderm

Energy Technology Data Exchange (ETDEWEB)

Li, Xiao-Yong; MacArthur, Stewart; Bourgon, Richard; Nix, David; Pollard, Daniel A.; Iyer, Venky N.; Hechmer, Aaron; Simirenko, Lisa; Stapleton, Mark; Luengo Hendriks, Cris L.; Chu, Hou Cheng; Ogawa, Nobuo; Inwood, William; Sementchenko, Victor; Beaton, Amy; Weiszmann, Richard; Celniker, Susan E.; Knowles, David W.; Gingeras, Tom; Speed, Terence P.; Eisen, Michael B.; Biggin, Mark D.

2008-01-10

Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis. Here, we use whole-genome tiling arrays to map sequences bound in Drosophila melanogaster embryos by the six maternal and gap transcription factors that initiate anterior-posterior patterning. We find that these sequence-specific DNA binding proteins bind with quantitatively different specificities to highly overlapping sets of several thousand genomic regions in blastoderm embryos. Specific high- and moderate-affinity in vitro recognition sequences for each factor are enriched in bound regions. This enrichment, however, is not sufficient to explain the pattern of binding in vivo and varies in a context-dependent manner, demonstrating that higher-order rules must govern targeting of transcription factors. The more highly bound regions include all of the over forty well-characterized enhancers known to respond to these factors as well as several hundred putative new cis-regulatory modules clustered near developmental regulators and other genes with patterned expression at this stage of embryogenesis. The new targets include most of the microRNAs (miRNAs) transcribed in the blastoderm, as well as all major zygotically transcribed dorsal-ventral patterning genes, whose expression we show to be quantitatively modulated by anterior-posterior factors. In addition to these highly bound regions, there are several thousand regions that are reproducibly bound at lower levels. However, these poorly bound regions are, collectively, far more distant from genes transcribed in the blastoderm than highly bound regions; are preferentially found in protein-coding sequences; and are less conserved than highly bound regions. Together these observations suggest that many of these poorly-bound regions are not involved in early
The heparin-binding site in tetranectin is located in the N-terminal region and binding does not involve the carbohydrate recognition domain.

Science.gov (United States)

Lorentsen, R H; Graversen, J H; Caterer, N R; Thogersen, H C; Etzerodt, M

2000-04-01

Tetranectin is a homotrimeric plasma and extracellular-matrix protein that binds plasminogen and complex sulphated polysaccharides including heparin. In terms of primary and tertiary structure, tetranectin is related to the collectin family of Ca(2+)-binding C-type lectins. Tetranectin is encoded in three exons. Exon 3 encodes the carbohydrate recognition domain, which binds to kringle 4 in plasminogen at low levels of Ca(2+). Exon 2 encodes an alpha-helix, which is necessary and sufficient to govern the trimerization of tetranectin by assembling into a triple-helical coiled-coil structural element. Here we show that the heparin-binding site in tetranectin resides not in the carbohydrate recognition domain but within the N-terminal region, comprising the 16 amino acid residues encoded by exon 1. In particular, the lysine residues in the decapeptide segment KPKKIVNAKK (tetranectin residues 6-15) are shown to be of primary importance in heparin binding.

Coral bleaching pathways under the control of regional temperature variability

Science.gov (United States)

Langlais, C. E.; Lenton, A.; Heron, S. F.; Evenhuis, C.; Sen Gupta, A.; Brown, J. N.; Kuchinke, M.

2017-11-01

Increasing sea surface temperatures (SSTs) are predicted to adversely impact coral populations worldwide through increasing thermal bleaching events. Future bleaching is unlikely to be spatially uniform. Therefore, understanding what determines regional differences will be critical for adaptation management. Here, using a cumulative heat stress metric, we show that characteristics of regional SST determine the future bleaching risk patterns. Incorporating observed information on SST variability, in assessing future bleaching risk, provides novel options for management strategies. As a consequence, the known biases in climate model variability and the uncertainties in regional warming rate across climate models are less detrimental than previously thought. We also show that the thresholds used to indicate reef viability can strongly influence a decision on what constitutes a potential refugia. Observing and understanding the drivers of regional variability, and the viability limits of coral reefs, is therefore critical for making meaningful projections of coral bleaching risk.
A 31-residue peptide induces aggregation of tau's microtubule-binding region in cells

Science.gov (United States)

Stöhr, Jan; Wu, Haifan; Nick, Mimi; Wu, Yibing; Bhate, Manasi; Condello, Carlo; Johnson, Noah; Rodgers, Jeffrey; Lemmin, Thomas; Acharya, Srabasti; Becker, Julia; Robinson, Kathleen; Kelly, Mark J. S.; Gai, Feng; Stubbs, Gerald; Prusiner, Stanley B.; Degrado, William F.

2017-09-01

The self-propagation of misfolded conformations of tau underlies neurodegenerative diseases, including Alzheimer's. There is considerable interest in discovering the minimal sequence and active conformational nucleus that defines this self-propagating event. The microtubule-binding region, spanning residues 244-372, reproduces much of the aggregation behaviour of tau in cells and animal models. Further dissection of the amyloid-forming region to a hexapeptide from the third microtubule-binding repeat resulted in a peptide that rapidly forms fibrils in vitro. We show that this peptide lacks the ability to seed aggregation of tau244-372 in cells. However, as the hexapeptide is gradually extended to 31 residues, the peptides aggregate more slowly and gain potent activity to induce aggregation of tau244-372 in cells. X-ray fibre diffraction, hydrogen-deuterium exchange and solid-state NMR studies map the beta-forming region to a 25-residue sequence. Thus, the nucleus for self-propagating aggregation of tau244-372 in cells is packaged in a remarkably small peptide.
Direct ATP photolabeling of Escherichia coli recA proteins: identification of regions required for ATP binding

International Nuclear Information System (INIS)

Banks, G.R.; Sedgwick, S.G.

1986-01-01

When the Escherichia coli RecA protein is UV irradiated in the presence of [alpha- 32 P]ATP, a labeled protein--ATP adduct is formed. All the experimental evidence indicates that, in forming such an adduct, the ATP becomes specifically immobilized in the catalytically relevant ATP binding site. The adduct can also be identified after irradiation of E. coli cell lysates in a similar manner. This direct ATP photolabeling of RecA proteins has been used to identify regions of the polypeptide chain involved in the binding of ATP. The photolabeling of a RecA protein that lacks wild-type carboxy-terminal amino acids is not detectable. A RecA protein in which the amino-terminal sequence NH2-Ala-Ile-Asp-Glu-Asn- is replaced by NH2-Thr-Met-Ile-Thr-Asn-Ser-Ser-Ser- is only about 5% as efficiently photolabeled as the wild-type protein. Both of these RecA protein constructions, however, contain all the elements previously implicated, directly or indirectly, in the binding of ATP. ATP-photolabeled RecA protein has also been chemically cleaved at specific amino acids in order to identify regions of the polypeptide chain to which the nucleotide becomes covalently photolinked. The evidence is consistent with a region comprising amino acids 116-170. Thus, this work and that of others suggest that several disparate regions of the unfolded polypeptide chain may combine to form the ATP binding site upon protein folding or may influence binding through long-range effects
Measure of uncertainty in regional grade variability

NARCIS (Netherlands)

Tutmez, B.; Kaymak, U.; Melin, P.; Castillo, O.; Gomez Ramirez, E.; Kacprzyk, J.; Pedrycz, W.

2007-01-01

Because the geological events are neither homogeneous nor isotropic, the geological investigations are characterized by particularly high uncertainties. This paper presents a hybrid methodology for measuring of uncertainty in regional grade variability. In order to evaluate the fuzziness in grade
Study on the binding sites of radiosensitivity associated transcription factor in the promoter region of Ier5 gene

International Nuclear Information System (INIS)

Cui Wei; Yin Lingling; Dong Lingyue

2012-01-01

Objective: To clarify the mechanism of immediate early response gene 5 (Ier5) transcription induced by radiation. Methods: Deletant construction, site-specific mutagenesis,electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) were used to forecast the promoter region, binding sites and transcription factors of Ier5 gene in HeLa cells. Results: The promoter region of Ier5 gene might be in the region of Ier5 -8 deletant (-408 - -238 bp). The Ier5 gene had two transcription factors of GCF and NFI, and GCF had two binding sites located in the region of -388 - -382 bp and -274 - -270 bp of Ier5 promoter. The binding site of NFI was located in -362 - -357 bp of Ier5 promoter. GCF could inhibit the expression of Ier5 gene and this inhibition was diminished when the radiation dose increased. In contrast, NFI increased the expression of Ier5. Conclusions: The most possible region of Ier5 promoter is from -408 to -238 bp which has two binding sites for the radiosensitivity transcription factors of GCF and NFI that could negatively and positively regulate the expression of Ier5 respectively. (authors)
Binding energy and single–particle Energies in the 16 0 region ...

African Journals Online (AJOL)

... single-particle energies in the oxygen region by folding together a Hamiltonian in the rest-frame of the nucleus with two-body correlation functions based on the Njimegen potential. We have found that the binding energies are very sensitive to the core radius rc and that the effects of tensor correlations are non-negligible.
The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

Directory of Open Access Journals (Sweden)

Fabian König

Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.
Independent variable complexity for regional regression of the flow duration curve in ungauged basins

Science.gov (United States)

Fouad, Geoffrey; Skupin, André; Hope, Allen

2016-04-01

The flow duration curve (FDC) is one of the most widely used tools to quantify streamflow. Its percentile flows are often required for water resource applications, but these values must be predicted for ungauged basins with insufficient or no streamflow data. Regional regression is a commonly used approach for predicting percentile flows that involves identifying hydrologic regions and calibrating regression models to each region. The independent variables used to describe the physiographic and climatic setting of the basins are a critical component of regional regression, yet few studies have investigated their effect on resulting predictions. In this study, the complexity of the independent variables needed for regional regression is investigated. Different levels of variable complexity are applied for a regional regression consisting of 918 basins in the US. Both the hydrologic regions and regression models are determined according to the different sets of variables, and the accuracy of resulting predictions is assessed. The different sets of variables include (1) a simple set of three variables strongly tied to the FDC (mean annual precipitation, potential evapotranspiration, and baseflow index), (2) a traditional set of variables describing the average physiographic and climatic conditions of the basins, and (3) a more complex set of variables extending the traditional variables to include statistics describing the distribution of physiographic data and temporal components of climatic data. The latter set of variables is not typically used in regional regression, and is evaluated for its potential to predict percentile flows. The simplest set of only three variables performed similarly to the other more complex sets of variables. Traditional variables used to describe climate, topography, and soil offered little more to the predictions, and the experimental set of variables describing the distribution of basin data in more detail did not improve predictions
Regional impacts of ocean color on tropical Pacific variability

Science.gov (United States)

Anderson, W.; Gnanadesikan, A.; Wittenberg, A.

2009-08-01

The role of the penetration length scale of shortwave radiation into the surface ocean and its impact on tropical Pacific variability is investigated with a fully coupled ocean, atmosphere, land and ice model. Previous work has shown that removal of all ocean color results in a system that tends strongly towards an El Niño state. Results from a suite of surface chlorophyll perturbation experiments show that the mean state and variability of the tropical Pacific is highly sensitive to the concentration and distribution of ocean chlorophyll. Setting the near-oligotrophic regions to contain optically pure water warms the mean state and suppresses variability in the western tropical Pacific. Doing the same above the shadow zones of the tropical Pacific also warms the mean state but enhances the variability. It is shown that increasing penetration can both deepen the pycnocline (which tends to damp El Niño) while shifting the mean circulation so that the wind response to temperature changes is altered. Depending on what region is involved this change in the wind stress can either strengthen or weaken ENSO variability.
Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

Directory of Open Access Journals (Sweden)

Matsutani Sachiko

2004-08-01

Full Text Available Abstract Background In eukaryotes, RNA polymerase III (RNAP III transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs. The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Results Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Conclusion Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and α-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants
Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III.

Science.gov (United States)

Matsutani, Sachiko

2004-08-09

In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFIIIC recognizes a promoter. Although internal promoter sequences are conserved in eukaryotes, no evidence of homology between the B-block binding subunits of vertebrates and yeasts has been reported previously. Here, I reported the results of PSI-BLAST searches using the B-block binding subunits of human and Shizosacchromyces pombe as queries, showing that the same Arabidopsis proteins were hit with low E-values in both searches. Comparison of the convergent iterative alignments obtained by these PSI-BLAST searches revealed that the vertebrate, yeast, and Arabidopsis proteins have similarities in their N-terminal one-third regions. In these regions, there were three domains with conserved sequence similarities, one located in the N-terminal end region. The N-terminal end region of the B-block binding subunit of Saccharomyces cerevisiae is tentatively identified as a HMG box, which is the DNA binding motif. Although I compared the alignment of the N-terminal end regions of the B-block binding subunits, and their homologs, with that of the HMG boxes, it is not clear whether they are related. Molecular phylogenetic analyses using the small subunit rRNA and ubiquitous proteins like actin and alpha-tubulin, show that fungi are more closely related to animals than either is to plants. Interestingly, the results obtained in this study show that, with respect to the B-block binding subunits of TFIIICs, animals appear to be evolutionarily closer to plants than to fungi.
Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors

Science.gov (United States)

2017-01-01

Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression. It is mainly performed by RNA binding proteins and microRNAs, which target RNAs and typically affect their stability. Recent efforts from the scientific community have aimed at understanding post-transcriptional regulation at a global scale by using high-throughput sequencing techniques such as cross-linking and immunoprecipitation (CLIP), which facilitates identification of binding sites of these regulatory factors. However, the diversity in the experimental procedures and bioinformatics analyses has hindered the integration of multiple datasets and thus limited the development of an integrated view of post-transcriptional regulation. In this work, we have performed a comprehensive analysis of 107 CLIP datasets from 49 different RBPs in HEK293 cells to shed light on the complex interactions that govern post-transcriptional regulation. By developing a more stringent CLIP analysis pipeline we have discovered the existence of conserved regulatory AU-rich regions in the 3’UTRs where miRNAs and RBPs that regulate several processes such as polyadenylation or mRNA stability bind. Analogous to promoters, many factors have binding sites overlapping or in close proximity in these hotspots and hence the regulation of the mRNA may depend on their relative concentrations. This hypothesis is supported by RBP knockdown experiments that alter the relative concentration of RBPs in the cell. Upon AGO2 knockdown (KD), transcripts containing “free” target sites show increased expression levels compared to those containing target sites in hotspots, which suggests that target sites within hotspots are less available for miRNAs to bind. Interestingly, these hotspots appear enriched in genes with regulatory functions such as DNA binding and RNA binding. Taken together, our results suggest that hotspots are functional regulatory elements that define an extra layer
Structure-based engineering to restore high affinity binding of an isoform-selective anti-TGFβ1 antibody

Science.gov (United States)

Honey, Denise M.; Best, Annie; Qiu, Huawei

2018-01-01

ABSTRACT Metelimumab (CAT192) is a human IgG4 monoclonal antibody developed as a TGFβ1-specific antagonist. It was tested in clinical trials for the treatment of scleroderma but later terminated due to lack of efficacy. Subsequent characterization of CAT192 indicated that its TGFβ1 binding affinity was reduced by ∼50-fold upon conversion from the parental single-chain variable fragment (scFv) to IgG4. We hypothesized this result was due to decreased conformational flexibility of the IgG that could be altered via engineering. Therefore, we designed insertion mutants in the elbow region and screened for binding and potency. Our results indicated that increasing the elbow region linker length in each chain successfully restored the isoform-specific and high affinity binding of CAT192 to TGFβ1. The crystal structure of the high binding affinity mutant displays large conformational rearrangements of the variable domains compared to the wild-type antigen-binding fragment (Fab) and the low binding affinity mutants. Insertion of two glycines in both the heavy and light chain elbow regions provided sufficient flexibility for the variable domains to extend further apart than the wild-type Fab, and allow the CDR3s to make additional interactions not seen in the wild-type Fab structure. These interactions coupled with the dramatic conformational changes provide a possible explanation of how the scFv and elbow-engineered Fabs bind TGFβ1 with high affinity. This study demonstrates the benefits of re-examining both structure and function when converting scFv to IgG molecules, and highlights the potential of structure-based engineering to produce fully functional antibodies. PMID:29333938
Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

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Barna Dey

2009-05-01

Full Text Available The human immunodeficiency virus type 1 (HIV-1 exterior envelope glycoprotein, gp120, possesses conserved binding sites for interaction with the primary virus receptor, CD4, and also for the co-receptor, generally CCR5. Although gp120 is a major target for virus-specific neutralizing antibodies, the gp120 variable elements and its malleable nature contribute to evasion of effective host-neutralizing antibodies. To understand the conformational character and immunogenicity of the gp120 receptor binding sites as potential vaccine targets, we introduced structure-based modifications to stabilize gp120 core proteins (deleted of the gp120 major variable regions into the conformation recognized by both receptors. Thermodynamic analysis of the re-engineered core with selected ligands revealed significant stabilization of the receptor-binding regions. Stabilization of the co-receptor-binding region was associated with a marked increase in on-rate of ligand binding to this site as determined by surface plasmon resonance. Rabbit immunization studies showed that the conformational stabilization of core proteins, along with increased ligand affinity, was associated with strikingly enhanced humoral immune responses against the co-receptor-binding site. These results demonstrate that structure-based approaches can be exploited to stabilize a conformational site in a large functional protein to enhance immunogenic responses specific for that region.
STATISTICAL INSIGHT INTO THE BINDING REGIONS IN DISORDERED HUMAN PROTEOME

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Uttam Pal

2016-03-01

Full Text Available The human proteome contains a significant number of intrinsically disordered proteins (IDPs. They show unusual structural features that enable them to participate in diverse cellular functions and play significant roles in cell signaling and reorganization processes. In addition, the actions of IDPs, their functional cooperativity, conformational alterations and folding often accompany binding to a target macromolecule. Applying bioinformatics approaches and with the aid of statistical methodologies, we investigated the statistical parameters of binding regions (BRs found in disordered human proteome. In this report, we detailed the bioinformatics analysis of binding regions found in the IDPs. Statistical models for the occurrence of BRs, their length distribution and percent occupancy in the parent proteins are shown. The frequency of BRs followed a Poisson distribution pattern with increasing expectancy with the degree of disorderedness. The length of the individual BRs also followed Poisson distribution with a mean of 6 residues, whereas, percentage of residues in BR showed a normal distribution pattern. We also explored the physicochemical properties such as the grand average of hydropathy (GRAVY and the theoretical isoelectric points (pIs. The theoretical pIs of the BRs followed a bimodal distribution as in the parent proteins. However, the mean acidic/basic pIs were significantly lower/higher than that of the proteins, respectively. We further showed that the amino acid composition of BRs was enriched in hydrophobic residues such as Ala, Val, Ile, Leu and Phe compared to the average sequence content of the proteins. Sequences in a BR showed conformational adaptability mostly towards flexible coil structure and followed by helix, however, the ordered secondary structural conformation was significantly lower in BRs than the proteins. Combining and comparing these statistical information of BRs with other methods may be useful for high
Regional impacts of ocean color on tropical Pacific variability

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W. Anderson

2009-08-01

Full Text Available The role of the penetration length scale of shortwave radiation into the surface ocean and its impact on tropical Pacific variability is investigated with a fully coupled ocean, atmosphere, land and ice model. Previous work has shown that removal of all ocean color results in a system that tends strongly towards an El Niño state. Results from a suite of surface chlorophyll perturbation experiments show that the mean state and variability of the tropical Pacific is highly sensitive to the concentration and distribution of ocean chlorophyll. Setting the near-oligotrophic regions to contain optically pure water warms the mean state and suppresses variability in the western tropical Pacific. Doing the same above the shadow zones of the tropical Pacific also warms the mean state but enhances the variability. It is shown that increasing penetration can both deepen the pycnocline (which tends to damp El Niño while shifting the mean circulation so that the wind response to temperature changes is altered. Depending on what region is involved this change in the wind stress can either strengthen or weaken ENSO variability.
Targets of DNA-binding proteins in bacterial promoter regions present enhanced probabilities for spontaneous thermal openings

International Nuclear Information System (INIS)

Apostolaki, Angeliki; Kalosakas, George

2011-01-01

We mapped promoter regions of double-stranded DNA with respect to the probabilities of appearance of relatively large bubble openings exclusively due to thermal fluctuations at physiological temperatures. We analyzed five well-studied promoter regions of procaryotic type and found a spatial correlation between the binding sites of transcription factors and the position of peaks in the probability pattern of large thermal openings. Other distinct peaks of the calculated patterns correlate with potential binding sites of DNA-binding proteins. These results suggest that a DNA molecule would more frequently expose the bases that participate in contacts with proteins, which would probably enhance the probability of the latter to reach their targets. It also stands for using this method as a means to analyze DNA sequences based on their intrinsic thermal properties
Worldwide genetic variability of the Duffy binding protein: insights into Plasmodium vivax vaccine development.

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Taís Nóbrega de Sousa

Full Text Available The dependence of Plasmodium vivax on invasion mediated by Duffy binding protein (DBP makes this protein a prime candidate for development of a vaccine. However, the development of a DBP-based vaccine might be hampered by the high variability of the protein ligand (DBP(II, known to bias the immune response toward a specific DBP variant. Here, the hypothesis being investigated is that the analysis of the worldwide DBP(II sequences will allow us to determine the minimum number of haplotypes (MNH to be included in a DBP-based vaccine of broad coverage. For that, all DBP(II sequences available were compiled and MNH was based on the most frequent nonsynonymous single nucleotide polymorphisms, the majority mapped on B and T cell epitopes. A preliminary analysis of DBP(II genetic diversity from eight malaria-endemic countries estimated that a number between two to six DBP haplotypes (17 in total would target at least 50% of parasite population circulating in each endemic region. Aiming to avoid region-specific haplotypes, we next analyzed the MNH that broadly cover worldwide parasite population. The results demonstrated that seven haplotypes would be required to cover around 60% of DBP(II sequences available. Trying to validate these selected haplotypes per country, we found that five out of the eight countries will be covered by the MNH (67% of parasite populations, range 48-84%. In addition, to identify related subgroups of DBP(II sequences we used a Bayesian clustering algorithm. The algorithm grouped all DBP(II sequences in six populations that were independent of geographic origin, with ancestral populations present in different proportions in each country. In conclusion, in this first attempt to undertake a global analysis about DBP(II variability, the results suggest that the development of DBP-based vaccine should consider multi-haplotype strategies; otherwise a putative P. vivax vaccine may not target some parasite populations.
Internal variability in a regional climate model over West Africa

Energy Technology Data Exchange (ETDEWEB)

Vanvyve, Emilie; Ypersele, Jean-Pascal van [Universite catholique de Louvain, Institut d' astronomie et de geophysique Georges Lemaitre, Louvain-la-Neuve (Belgium); Hall, Nicholas [Laboratoire d' Etudes en Geophysique et Oceanographie Spatiales/Centre National d' Etudes Spatiales, Toulouse Cedex 9 (France); Messager, Christophe [University of Leeds, Institute for Atmospheric Science, Environment, School of Earth and Environment, Leeds (United Kingdom); Leroux, Stephanie [Universite Joseph Fourier, Laboratoire d' etude des Transferts en Hydrologie et Environnement, BP53, Grenoble Cedex 9 (France)

2008-02-15

Sensitivity studies with regional climate models are often performed on the basis of a few simulations for which the difference is analysed and the statistical significance is often taken for granted. In this study we present some simple measures of the confidence limits for these types of experiments by analysing the internal variability of a regional climate model run over West Africa. Two 1-year long simulations, differing only in their initial conditions, are compared. The difference between the two runs gives a measure of the internal variability of the model and an indication of which timescales are reliable for analysis. The results are analysed for a range of timescales and spatial scales, and quantitative measures of the confidence limits for regional model simulations are diagnosed for a selection of study areas for rainfall, low level temperature and wind. As the averaging period or spatial scale is increased, the signal due to internal variability gets smaller and confidence in the simulations increases. This occurs more rapidly for variations in precipitation, which appear essentially random, than for dynamical variables, which show some organisation on larger scales. (orig.)
Opiate antagonist binding sites in discrete brain regions of spontaneously hypertensive and normotensive Wistar-Kyoto rats

International Nuclear Information System (INIS)

Rahmani, N.H.; Gulati, A.; Bhargava, H.N.

1991-01-01

The binding of 3 H-naltrexone, an opiate receptor antagonist, to membranes of discrete brain regions and spinal cord of 10 week old spontaneously hypertensive (SHR) and normotensive Wistar-Kyoto (WKY) rats was determined. The brain regions examined were hypothalamus, amygdala, hippocampus, corpus striatum, pons and medulla, midbrain and cortex. 3 H-Naltrexone bound to membranes of brain regions and spinal cord at a single high affinity site with an apparent dissociation constant value of 3 nM. The highest density of 3 H-naltrexone binding sites were in hippocampus and lowest in the cerebral cortex. The receptor density (B max value) and apparent dissociation constant (K d value) values of 3 H-naltrexone to bind to opiate receptors on the membranes of amygdala, hippocampus, corpus striatum, pons and medulla, midgrain, cortex and spinal cord of WKY and SHR rates did not differ. The B max value of 3 H-naltrexone binding to membranes of hypothalamus of SHR rates was 518% higher than WKY rats but the K d values in the two strains did not differ. It is concluded that SHR rats have higher density of opiate receptors labeled with 3 H-naltrexone in the hypothalamus only, in comparison with WKY rats, and that such a difference in the density of opiate receptors may be related to the elevated blood pressure in SHR rats

Immunoglobulin Heavy Chain Variable Region and Major Histocompatibility Region Genes Are Linked to Induced Graves' Disease in Females From Two Very Large Families of Recombinant Inbred Mice

Science.gov (United States)

Aliesky, Holly; Banuelos, Bianca; Magana, Jessica; Williams, Robert W.; Rapoport, Basil

2014-01-01

Graves' hyperthyroidism is caused by antibodies to the TSH receptor (TSHR) that mimic thyroid stimulation by TSH. Stimulating TSHR antibodies and hyperthyroidism can be induced by immunizing mice with adenovirus expressing the human TSHR A-subunit. Prior analysis of induced Graves' disease in small families of recombinant inbred (RI) female mice demonstrated strong genetic control but did not resolve trait loci for TSHR antibodies or elevated serum T4. We investigated the genetic basis for induced Graves' disease in female mice of two large RI families and combined data with earlier findings to provide phenotypes for 178 genotypes. TSHR antibodies measured by inhibition of TSH binding to its receptor were highly significantly linked in the BXD set to the major histocompatibility region (chromosome 17), consistent with observations in 3 other RI families. In the LXS family, we detected linkage between T4 levels after TSHR-adenovirus immunization and the Ig heavy chain variable region (Igvh, chromosome 12). This observation is a key finding because components of the antigen binding region of Igs determine antibody specificity and have been previously linked to induced thyroid-stimulating antibodies. Data from the LXS family provide the first evidence in mice of a direct link between induced hyperthyroidism and Igvh genes. A role for major histocompatibility genes has now been established for genetic susceptibility to Graves' disease in both humans and mice. Future studies using arrays incorporating variation in the complex human Ig gene locus will be necessary to determine whether Igvh genes are also linked to Graves' disease in humans. PMID:25051451
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Directory of Open Access Journals (Sweden)

Ashford Paul

2012-03-01

conserved occurrence of surface pockets at the active and regulatory sites; ii a simulated ensemble of unliganded Bcl2 structures reveals extensions of a known ligand-binding pocket not apparent in the apo crystal structure; iii visualisations of interleukin-2 and its homologues highlight conserved pockets at the known receptor interfaces and regions whose conformation is known to change on inhibitor binding. Conclusions Through post-processing of the output of a variety of pocket prediction software, Provar provides a flexible approach to the analysis and visualization of the persistence or variability of pockets in sets of related protein structures.
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

Science.gov (United States)

Ashford, Paul; Moss, David S; Alex, Alexander; Yeap, Siew K; Povia, Alice; Nobeli, Irene; Williams, Mark A

2012-03-14

and regulatory sites; ii) a simulated ensemble of unliganded Bcl2 structures reveals extensions of a known ligand-binding pocket not apparent in the apo crystal structure; iii) visualisations of interleukin-2 and its homologues highlight conserved pockets at the known receptor interfaces and regions whose conformation is known to change on inhibitor binding. Through post-processing of the output of a variety of pocket prediction software, Provar provides a flexible approach to the analysis and visualization of the persistence or variability of pockets in sets of related protein structures.
Strong influence of variable treatment on the performance of numerically defined ecological regions.

Science.gov (United States)

Snelder, Ton; Lehmann, Anthony; Lamouroux, Nicolas; Leathwick, John; Allenbach, Karin

2009-10-01

Numerical clustering has frequently been used to define hierarchically organized ecological regionalizations, but there has been little robust evaluation of their performance (i.e., the degree to which regions discriminate areas with similar ecological character). In this study we investigated the effect of the weighting and treatment of input variables on the performance of regionalizations defined by agglomerative clustering across a range of hierarchical levels. For this purpose, we developed three ecological regionalizations of Switzerland of increasing complexity using agglomerative clustering. Environmental data for our analysis were drawn from a 400 m grid and consisted of estimates of 11 environmental variables for each grid cell describing climate, topography and lithology. Regionalization 1 was defined from the environmental variables which were given equal weights. We used the same variables in Regionalization 2 but weighted and transformed them on the basis of a dissimilarity model that was fitted to land cover composition data derived for a random sample of cells from interpretation of aerial photographs. Regionalization 3 was a further two-stage development of Regionalization 2 where specific classifications, also weighted and transformed using dissimilarity models, were applied to 25 small scale "sub-domains" defined by Regionalization 2. Performance was assessed in terms of the discrimination of land cover composition for an independent set of sites using classification strength (CS), which measured the similarity of land cover composition within classes and the dissimilarity between classes. Regionalization 2 performed significantly better than Regionalization 1, but the largest gains in performance, compared to Regionalization 1, occurred at coarse hierarchical levels (i.e., CS did not increase significantly beyond the 25-region level). Regionalization 3 performed better than Regionalization 2 beyond the 25-region level and CS values continued to
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Energy Technology Data Exchange (ETDEWEB)

MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi; Brown, James B.; Chu, Hou Cheng; Zeng, Lucy; Grondona, Brandi P.; Hechmer, Aaron; Simirenko, Lisa; Keranen, Soile V.E.; Knowles, David W.; Stapleton, Mark; Bickel, Peter; Biggin, Mark D.; Eisen, Michael B.

2009-05-15

BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less conserved non-coding DNA, suggesting that many are likely non-functional. RESULTS: Here we show that an additional 15 transcription factors that regulate other aspects of embryo patterning show a similar quantitative continuum of function and binding to thousands of genomic regions in vivo. Collectively, the 21 regulators show a surprisingly high overlap in the regions they bind given that they belong to 11 DNA binding domain families, specify distinct developmental fates, and can act via different cis-regulatory modules. We demonstrate, however, that quantitative differences in relative levels of binding to shared targets correlate with the known biological and transcriptional regulatory specificities of these factors. CONCLUSIONS: It is likely that the overlap in binding of biochemically and functionally unrelated transcription factors arises from the high concentrations of these proteins in nuclei, which, coupled with their broad DNA binding specificities, directs them to regions of open chromatin. We suggest that most animal transcription factors will be found to show a similar broad overlapping pattern of binding in vivo, with specificity achieved by modulating the amount, rather than the identity, of bound factor.
Opiate antagonist binding sites in discrete brain regions of spontaneously hypertensive and normotensive Wistar-Kyoto rats

Energy Technology Data Exchange (ETDEWEB)

Rahmani, N.H.; Gulati, A.; Bhargava, H.N. (Univ. of Illinois, Chicago (USA))

1991-01-01

The binding of {sup 3}H-naltrexone, an opiate receptor antagonist, to membranes of discrete brain regions and spinal cord of 10 week old spontaneously hypertensive (SHR) and normotensive Wistar-Kyoto (WKY) rats was determined. The brain regions examined were hypothalamus, amygdala, hippocampus, corpus striatum, pons and medulla, midbrain and cortex. {sup 3}H-Naltrexone bound to membranes of brain regions and spinal cord at a single high affinity site with an apparent dissociation constant value of 3 nM. The highest density of {sup 3}H-naltrexone binding sites were in hippocampus and lowest in the cerebral cortex. The receptor density (B{sub max}value) and apparent dissociation constant (K{sub d} value) values of {sup 3}H-naltrexone to bind to opiate receptors on the membranes of amygdala, hippocampus, corpus striatum, pons and medulla, midgrain, cortex and spinal cord of WKY and SHR rates did not differ. The B{sub max} value of {sup 3}H-naltrexone binding to membranes of hypothalamus of SHR rates was 518% higher than WKY rats but the K{sub d} values in the two strains did not differ. It is concluded that SHR rats have higher density of opiate receptors labeled with {sup 3}H-naltrexone in the hypothalamus only, in comparison with WKY rats, and that such a difference in the density of opiate receptors may be related to the elevated blood pressure in SHR rats.
A Single-Domain Llama Antibody Potently Inhibits the Enzymatic Activity of Botulinum Neurotoxin by Binding to the Non-Catalytic [alpha]-Exosite Binding Region

Energy Technology Data Exchange (ETDEWEB)

Dong, Jianbo; Thompson, Aaron A.; Fan, Yongfeng; Lou, Jianlong; Conrad, Fraser; Ho, Mengfei; Pires-Alves, Melissa; Wilson, Brenda A.; Stevens, Raymond C.; Marks, James D. (UIUC); (Scripps); (UCSF)

2010-08-13

Ingestion or inhalation of botulinum neurotoxin (BoNT) results in botulism, a severe and frequently fatal disease. Current treatments rely on antitoxins, which, while effective, cannot reverse symptoms once BoNT has entered the neuron. For treatments that can reverse intoxication, interest has focused on developing inhibitors of the enzymatic BoNT light chain (BoNT Lc). Such inhibitors typically mimic substrate and bind in or around the substrate cleavage pocket. To explore the full range of binding sites for serotype A light chain (BoNT/A Lc) inhibitors, we created a library of non-immune llama single-domain VHH (camelid heavy-chain variable region derived from heavy-chain-only antibody) antibodies displayed on the surface of the yeast Saccharomyces cerevisiae. Library selection on BoNT/A Lc yielded 15 yeast-displayed VHH with equilibrium dissociation constants (K{sub d}) from 230 to 0.03 nM measured by flow cytometry. Eight of 15 VHH inhibited the cleavage of substrate SNAP25 (synaptosome-associated protein of 25,000 Da) by BoNT/A Lc. The most potent VHH (Aa1) had a solution K{sub d} for BoNT/A Lc of 1.47 x 10{sup -10} M and an IC{sub 50} (50% inhibitory concentration) of 4.7 x 10{sup -10} M and was resistant to heat denaturation and reducing conditions. To understand the mechanism by which Aa1 inhibited catalysis, we solved the X-ray crystal structure of the BoNT/A Lc-Aa1 VHH complex at 2.6 {angstrom} resolution. The structure reveals that the Aa1 VHH binds in the {alpha}-exosite of the BoNT/A Lc, far from the active site for catalysis. The study validates the utility of non-immune llama VHH libraries as a source of enzyme inhibitors and identifies the BoNT/A Lc {alpha}-exosite as a target for inhibitor development.
Intraregional and inter-regional variability of herbicide sensitivity in common arable weed populations

DEFF Research Database (Denmark)

de Mol, Friederike; Gerowitt, Bärbel; Kaczmarek, Sylwia

2015-01-01

The question on intraregional versus inter-regional variability in herbicide sensitivity for weed populations is of major importance, both in extrapolation of model parameters and in herbicide zonal approval procedures. We hypothesised that inter-regional variability in herbicide sensitivity for ...
A preferred region for recombinational patch repair in the 5' untranslated region of primer binding site-impaired murine leukemia virus vectors

DEFF Research Database (Denmark)

Mikkelsen, J G; Lund, Anders Henrik; Kristensen, K D

1996-01-01

, suggesting the involvement of a specific endogenous virus-like sequence in patch repair rescue of the primer binding site mutants. The putative recombination partner RNA was found in virions from psi-2 cells as detected by analysis of glutamine tRNA-initiated cDNA and by sequence analysis of regions...... site to allow correct second-strand transfer in reverse transcription. The system thereby selects for a reverse transcriptase-mediated recombination event in the 5' untranslated region. A panel of sequence differences between the recombination partners in this region has allowed mapping of the site...
The discrete and localized nature of the variable emission from active regions

Science.gov (United States)

Arndt, Martina Belz; Habbal, Shadia Rifai; Karovska, Margarita

1994-01-01

Using data from the Extreme Ultraviolet (EUV) Spectroheliometer on Skylab, we study the empirical characteristics of the variable emission in active regions. These simultaneous multi-wavelength observations clearly confirm that active regions consist of a complex of loops at different temperatures. The variable emission from this complex has very well-defined properties that can be quantitatively summarized as follows: (1) It is localized predominantly around the footpoints where it occurs at discrete locations. (2) The strongest variability does not necessarily coincide with the most intense emission. (3) The fraction of the area of the footpoints, (delta n)/N, that exhibits variable emission, varies by +/- 15% as a function of time, at any of the wavelengths measured. It also varies very little from footpoint to footpoint. (4) This fractional variation is temperature dependent with a maximum around 10(exp 5) K. (5) The ratio of the intensity of the variable to the average background emission, (delta I)/(bar-I), also changes with temperature. In addition, we find that these distinctive characteristics persist even when flares occur within the active region.
(+)- and (-)-N-allylnormetazocine binding sites in mouse brain: in vitro and in vivo characterization and regional distribution

International Nuclear Information System (INIS)

Compton, D.R.; Bagley, R.B.; Katzen, J.S.; Martin, B.R.

1987-01-01

In vivo and in vitro binding studies, both in whole brain and in selected areas, indicate that non-identical (+)- and (-)-NANM sites exist in the mouse brain, and each exhibits a different regional distribution. The in vivo binding of (+)- 3 H-NANM was found to be saturable at pharmacologically relevant doses, and represents a relatively small (10 - 22%) portion of total brain (+)- 3 H-NANM concentrations. The in vivo binding of (+)- 3 H-NANM was selectively displaced by (+)-NANM and PCP, and more sensitive to haloperidol and (+)-ketocyclazocine than the (-)- 3 H-NANM site. The in vivo binding of (-)- 3 H-NANM was selectively displaced by (-)-NANM, and more sensitive to naloxone and (-) ketocyclazocine than the (+)- 3 H-NANM site, and insensitive to PCP. This study indicates that the investigation of NANM binding sites is possible using in vivo binding techniques, and that each isomer apparently binds, in the mouse brain, to a single class of distinct sites. 32 references, 4 figures, 2 tables
High-resolution regional climate model evaluation using variable-resolution CESM over California

Science.gov (United States)

Huang, X.; Rhoades, A.; Ullrich, P. A.; Zarzycki, C. M.

2015-12-01

Understanding the effect of climate change at regional scales remains a topic of intensive research. Though computational constraints remain a problem, high horizontal resolution is needed to represent topographic forcing, which is a significant driver of local climate variability. Although regional climate models (RCMs) have traditionally been used at these scales, variable-resolution global climate models (VRGCMs) have recently arisen as an alternative for studying regional weather and climate allowing two-way interaction between these domains without the need for nudging. In this study, the recently developed variable-resolution option within the Community Earth System Model (CESM) is assessed for long-term regional climate modeling over California. Our variable-resolution simulations will focus on relatively high resolutions for climate assessment, namely 28km and 14km regional resolution, which are much more typical for dynamically downscaled studies. For comparison with the more widely used RCM method, the Weather Research and Forecasting (WRF) model will be used for simulations at 27km and 9km. All simulations use the AMIP (Atmospheric Model Intercomparison Project) protocols. The time period is from 1979-01-01 to 2005-12-31 (UTC), and year 1979 was discarded as spin up time. The mean climatology across California's diverse climate zones, including temperature and precipitation, is analyzed and contrasted with the Weather Research and Forcasting (WRF) model (as a traditional RCM), regional reanalysis, gridded observational datasets and uniform high-resolution CESM at 0.25 degree with the finite volume (FV) dynamical core. The results show that variable-resolution CESM is competitive in representing regional climatology on both annual and seasonal time scales. This assessment adds value to the use of VRGCMs for projecting climate change over the coming century and improve our understanding of both past and future regional climate related to fine
The association of heavy and light chain variable domains in antibodies: implications for antigen specificity.

KAUST Repository

Chailyan, Anna

2011-06-28

The antigen-binding site of immunoglobulins is formed by six regions, three from the light and three from the heavy chain variable domains, which, on association of the two chains, form the conventional antigen-binding site of the antibody. The mode of interaction between the heavy and light chain variable domains affects the relative position of the antigen-binding loops and therefore has an effect on the overall conformation of the binding site. In this article, we analyze the structure of the interface between the heavy and light chain variable domains and show that there are essentially two different modes for their interaction that can be identified by the presence of key amino acids in specific positions of the antibody sequences. We also show that the different packing modes are related to the type of recognized antigen.
DNA clasping by mycobacterial HU: the C-terminal region of HupB mediates increased specificity of DNA binding.

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Sandeep Kumar

Full Text Available BACKGROUND: HU a small, basic, histone like protein is a major component of the bacterial nucleoid. E. coli has two subunits of HU coded by hupA and hupB genes whereas Mycobacterium tuberculosis (Mtb has only one subunit of HU coded by ORF Rv2986c (hupB gene. One noticeable feature regarding Mtb HupB, based on sequence alignment of HU orthologs from different bacteria, was that HupB(Mtb bears at its C-terminal end, a highly basic extension and this prompted an examination of its role in Mtb HupB function. METHODOLOGY/PRINCIPAL FINDINGS: With this objective two clones of Mtb HupB were generated; one expressing full length HupB protein (HupB(Mtb and another which expresses only the N terminal region (first 95 amino acid of hupB (HupB(MtbN. Gel retardation assays revealed that HupB(MtbN is almost like E. coli HU (heat stable nucleoid protein in terms of its DNA binding, with a binding constant (K(d for linear dsDNA greater than 1000 nM, a value comparable to that obtained for the HUalphaalpha and HUalphabeta forms. However CTR (C-terminal Region of HupB(Mtb imparts greater specificity in DNA binding. HupB(Mtb protein binds more strongly to supercoiled plasmid DNA than to linear DNA, also this binding is very stable as it provides DNase I protection even up to 5 minutes. Similar results were obtained when the abilities of both proteins to mediate protection against DNA strand cleavage by hydroxyl radicals generated by the Fenton's reaction, were compared. It was also observed that both the proteins have DNA binding preference for A:T rich DNA which may occur at the regulatory regions of ORFs and the oriC region of Mtb. CONCLUSIONS/SIGNIFICANCE: These data thus point that HupB(Mtb may participate in chromosome organization in-vivo, it may also play a passive, possibly an architectural role.
Impact of region contouring variability on image-based focal therapy evaluation

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Gibson, Eli; Donaldson, Ian A.; Shah, Taimur T.; Hu, Yipeng; Ahmed, Hashim U.; Barratt, Dean C.

2016-03-01

Motivation: Focal therapy is an emerging low-morbidity treatment option for low-intermediate risk prostate cancer; however, challenges remain in accurately delivering treatment to specified targets and determining treatment success. Registered multi-parametric magnetic resonance imaging (MPMRI) acquired before and after treatment can support focal therapy evaluation and optimization; however, contouring variability, when defining the prostate, the clinical target volume (CTV) and the ablation region in images, reduces the precision of quantitative image-based focal therapy evaluation metrics. To inform the interpretation and clarify the limitations of such metrics, we investigated inter-observer contouring variability and its impact on four metrics. Methods: Pre-therapy and 2-week-post-therapy standard-of-care MPMRI were acquired from 5 focal cryotherapy patients. Two clinicians independently contoured, on each slice, the prostate (pre- and post-treatment) and the dominant index lesion CTV (pre-treatment) in the T2-weighted MRI, and the ablated region (post-treatment) in the dynamic-contrast- enhanced MRI. For each combination of clinician contours, post-treatment images were registered to pre-treatment images using a 3D biomechanical-model-based registration of prostate surfaces, and four metrics were computed: the proportion of the target tissue region that was ablated and the target:ablated region volume ratio for each of two targets (the CTV and an expanded planning target volume). Variance components analysis was used to measure the contribution of each type of contour to the variance in the therapy evaluation metrics. Conclusions: 14-23% of evaluation metric variance was attributable to contouring variability (including 6-12% from ablation region contouring); reducing this variability could improve the precision of focal therapy evaluation metrics.
HuR binding to AU-rich elements present in the 3' untranslated region of Classical swine fever virus

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Huang Chin-Cheng

2011-07-01

Full Text Available Abstract Background Classical swine fever virus (CSFV is the member of the genus Pestivirus under the family Flaviviridae. The 5' untranslated region (UTR of CSFV contains the IRES, which is a highly structured element that recruits the translation machinery. The 3' UTR is usually the recognition site of the viral replicase to initiate minus-strand RNA synthesis. Adenosine-uridine rich elements (ARE are instability determinants present in the 3' UTR of short-lived mRNAs. However, the presence of AREs in the 3' UTR of CSFV conserved in all known strains has never been reported. This study inspects a possible role of the ARE in the 3' UTR of CSFV. Results Using RNA pull-down and LC/MS/MS assays, this study identified at least 32 possible host factors derived from the cytoplasmic extracts of PK-15 cells that bind to the CSFV 3' UTR, one of which is HuR. HuR is known to bind the AREs and protect the mRNA from degradation. Using recombinant GST-HuR, this study demonstrates that HuR binds to the ARE present in the 3' UTR of CSFV in vitro and that the binding ability is conserved in strains irrespective of virulence. Conclusions This study identified one of the CSFV 3' UTR binding proteins HuR is specifically binding to in the ARE region.
Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci

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Salvatore Loguercio

2018-03-01

Full Text Available CCCTC-binding factor (CTCF is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells and developmental stage-specificity (pre-B vs. pro-B in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for
A photoaffinity scan maps regions of the p85 SH2 domain involved in phosphoprotein binding.

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Williams, K P; Shoelson, S E

1993-03-15

Src homology 2 (SH2) domains are modular phosphotyrosine binding pockets found within a wide variety of cytoplasmic signaling molecules. Here we develop a new approach to analyzing protein-protein interfaces termed photoaffinity scanning, and apply the method to map regions of the phosphatidylinositol 3-kinase p85 SH2 domain that participate in phospho-protein binding. Each residue except phosphotyrosine (pY) within a tightly binding, IRS-1-derived phosphopeptide (GNGDpYMPMSPKS) was substituted with the photoactive amino acid, benzoylphenylalanine (Bpa). Whereas most substitutions had little effect on binding affinity, Bpa substitution of either Met (+1 and +3 with respect to pY) reduced affinity 50-100-fold to confirm their importance in the pYMXM recognition motif. In three cases photolysis of SH2 domain/Bpa phosphopeptide complexes led to cross-linking of > 50% of the SH2 domain; cross-link positions were identified by microsequence, amino acid composition, and electrospray mass spectrometric analyses. Bpa-1 cross-links within alpha-helix I, whereas Bpa+1 and Bpa+4 cross-link the SH2 domain within the flexible loop C-terminal to alpha-helix II. Moreover, cross-linking at any position prevents SH2 domain cleavage at a trypsin-sensitive site within the flexible loop between beta-strands 1 and 2. Therefore, at least three distinct SH2 regions in addition to the beta-sheet participate in phosphoprotein binding; the loop cross-linked by phosphopeptide residues C-terminal to pY appears to confer specificity to the phosphoprotein/SH2 domain interaction.
A Salmonella typhimurium-translocated Glycerophospholipid:Cholesterol Acyltransferase Promotes Virulence by Binding to the RhoA Protein Switch Regions

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LaRock, Doris L.; Brzovic, Peter S.; Levin, Itay; Blanc, Marie-Pierre; Miller, Samuel I.

2012-08-24

Salmonella enterica serovar typhimurium translocates a glycerophospholipid: cholesterol acyltransferase (SseJ) into the host cytosol after its entry into mammalian cells. SseJ is recruited to the cytoplasmic face of the host cell phagosome membrane where it is activated upon binding the small GTPase, RhoA. SseJ is regulated similarly to cognate eukaryotic effectors, as only the GTP-bound form of RhoA family members stimulates enzymatic activity. Using NMR and biochemistry, this work demonstrates that SseJ competes effectively with Rhotekin, ROCK, and PKN1 in binding to a similar RhoA surface. The RhoA surface that binds SseJ includes the regulatory switch regions that control activation of mammalian effectors. These data were used to create RhoA mutants with altered SseJ binding and activation. This structure-function analysis supports a model in which SseJ activation occurs predominantly through binding to residues within switch region II. We further defined the nature of the interaction between SseJ and RhoA by constructing SseJ mutants in the RhoA binding surface. These data indicate that SseJ binding to RhoA is required for recruitment of SseJ to the endosomal network and for full Salmonella virulence for inbred susceptible mice, indicating that regulation of SseJ by small GTPases is an important virulence strategy of this bacterial pathogen. The dependence of a bacterial effector on regulation by a mammalian GTPase defines further how intimately host pathogen interactions have coevolved through similar and divergent evolutionary strategies.
Development of a localized probabilistic sensitivity method to determine random variable regional importance

International Nuclear Information System (INIS)

Millwater, Harry; Singh, Gulshan; Cortina, Miguel

2012-01-01

There are many methods to identify the important variable out of a set of random variables, i.e., “inter-variable” importance; however, to date there are no comparable methods to identify the “region” of importance within a random variable, i.e., “intra-variable” importance. Knowledge of the critical region of an input random variable (tail, near-tail, and central region) can provide valuable information towards characterizing, understanding, and improving a model through additional modeling or testing. As a result, an intra-variable probabilistic sensitivity method was developed and demonstrated for independent random variables that computes the partial derivative of a probabilistic response with respect to a localized perturbation in the CDF values of each random variable. These sensitivities are then normalized in absolute value with respect to the largest sensitivity within a distribution to indicate the region of importance. The methodology is implemented using the Score Function kernel-based method such that existing samples can be used to compute sensitivities for negligible cost. Numerical examples demonstrate the accuracy of the method through comparisons with finite difference and numerical integration quadrature estimates. - Highlights: ► Probabilistic sensitivity methodology. ► Determines the “region” of importance within random variables such as left tail, near tail, center, right tail, etc. ► Uses the Score Function approach to reuse the samples, hence, negligible cost. ► No restrictions on the random variable types or limit states.

Integrated Variable Speed Limits Control and Ramp Metering for Bottleneck Regions on Freeway

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Ming-hui Ma

2015-01-01

Full Text Available To enhance the efficiency of the existing freeway system and therefore to mitigate traffic congestion and related problems on the freeway mainline lane-drop bottleneck region, the advanced strategy for bottleneck control is essential. This paper proposes a method that integrates variable speed limits and ramp metering for freeway bottleneck region control to relieve the chaos in bottleneck region. To this end, based on the analyses of spatial-temporal patterns of traffic flow, a macroscopic traffic flow model is extended to describe the traffic flow operating characteristic by considering the impacts of variable speed limits in mainstream bottleneck region. In addition, to achieve the goal of balancing the priority of the vehicles on mainline and on-ramp, increasing capacity, and reducing travel delay on bottleneck region, an improved control model, as well as an advanced control strategy that integrates variable speed limits and ramp metering, is developed. The proposed method is tested in simulation for a real freeway infrastructure feed and calibrates real traffic variables. The results demonstrate that the proposed method can substantially improve the traffic flow efficiency of mainline and on-ramp and enhance the quality of traffic flow at the investigated freeway mainline bottleneck.
Development and characterization of polyclonal antibodies against the linker region of the telomere-binding protein TRF2

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Nadya V. Ilicheva

2018-03-01

Full Text Available Background: TRF2 (telomeric repeat binding factor 2 is an essential component of the telomere-binding protein complex shelterin. TRF2 induces the formation of a special structure of telomeric DNA and counteracts activation of DNA damage-response pathways telomeres. TRF2 has a poorly characterized linker region (udTRF2 between its homodimerization and DNA-binding domains. Some lines of evidence have shown that this region could be involved in TRF2 interaction with nuclear lamina. Results: In this study, the fragment of the TERF2 gene encoding udTRF2 domain of telomere-binding protein TRF2 was produced by PCR and cloned into the pET32a vector. The resulting plasmid pET32a-udTRF2 was used for the expression of the recombinant udTRF2 in E. coli RosettaBlue (DE3. The protein was isolated and purified using ammonium sulfate precipitation followed by ion-exchange chromatography. The purified recombinant protein udTRF2 was injected into guinea pigs to generate polyclonal antibodies. The ability of anti-udTRF2 antibodies to bind endogenous TRF2 in human skin fibroblasts was tested by western blotting and immunofluorescent staining. Conclusions: In this study, the recombinant protein udTRF2 and antibodies to it were generated. Both protein and antibodies will provide a useful tool for investigation of the functions of the udTRF2 domain and its role in the interaction between TRF2 and nuclear lamina. Keywords: Chromosomes, Molecular cloning, Nuclear lamina, Nucleoprotein complexes, Polyclonal antibodies, Recombinant polypeptide, Shelterin, Telomere-binding protein TRF2, Telomeres, Telomeric DNA, TTAGGG repeats
Amino Terminal Region of Dengue Virus NS4A Cytosolic Domain Binds to Highly Curved Liposomes

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Yu-Fu Hung

2015-07-01

Full Text Available Dengue virus (DENV is an important human pathogen causing millions of disease cases and thousands of deaths worldwide. Non-structural protein 4A (NS4A is a vital component of the viral replication complex (RC and plays a major role in the formation of host cell membrane-derived structures that provide a scaffold for replication. The N-terminal cytoplasmic region of NS4A(1–48 is known to preferentially interact with highly curved membranes. Here, we provide experimental evidence for the stable binding of NS4A(1–48 to small liposomes using a liposome floatation assay and identify the lipid binding sequence by NMR spectroscopy. Mutations L6E;M10E were previously shown to inhibit DENV replication and to interfere with the binding of NS4A(1–48 to small liposomes. Our results provide new details on the interaction of the N-terminal region of NS4A with membranes and will prompt studies of the functional relevance of the curvature sensitive membrane anchor at the N-terminus of NS4A.
Test-retest reproducibility of [{sup 11}C]PBR28 binding to TSPO in healthy control subjects

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Collste, K.; Forsberg, A.; Varrone, A.; Amini, N.; Halldin, C.; Farde, L.; Cervenka, S. [Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatry Research, Stockholm (Sweden); Aeinehband, S. [Karolinska Institutet, Department of Clinical Neuroscience, Neuroimmunology Unit, Stockholm (Sweden); Yakushev, I. [Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatry Research, Stockholm (Sweden); Technische Universitaet Muenchen, Department of Nuclear Medicine and TUM Neuroimaging Center (TUM-NIC), Munich (Germany)

2016-01-15

The PET radioligand [{sup 11}C]PBR28 binds to the translocator protein (TSPO), a marker of brain immune activation. We examined the reproducibility of [{sup 11}C]PBR28 binding in healthy subjects with quantification on a regional and voxel-by-voxel basis. In addition, we performed a preliminary analysis of diurnal changes in TSPO availability. Twelve subjects were examined using a high-resolution research tomograph and [{sup 11}C]PBR28, six in the morning and afternoon of the same day, and six in the morning on two separate days. Regional volumes of distribution (V{sub T}) were derived using a region-of-interest based two-tissue compartmental analysis (2TCM), as well as a parametric approach. Metabolite-corrected arterial plasma was used as input function. For the whole sample, the mean absolute variability in V{sub T} in the grey matter (GM) was 18.3 ± 12.7 %. Intraclass correlation coefficients in GM regions ranged from 0.90 to 0.94. Reducing the time of analysis from 91 to 63 min yielded a variability of 16.9 ± 14.9 %. There was a strong correlation between the parametric and 2TCM-derived GM values (r = 0.99). A significant increase in GM V{sub T} was observed between the morning and afternoon examinations when using secondary methods of quantification (p = 0.028). In the subjects examined at the same time of the day, the absolute variability was 15.9 ± 12.2 % for the 91-min 2TCM data. V{sub T} of [{sup 11}C]PBR28 binding showed medium reproducibility and high reliability in GM regions. Our findings support the use of parametric approaches for determining [{sup 11}C]PBR28 V{sub T} values, and indicate that the acquisition time could be shortened. Diurnal changes in TSPO binding in the brain may be a potential confounder in clinical studies and should be investigated further. (orig.)
Selective interaction of heparin with the variable region 3 within surface glycoprotein of laboratory-adapted feline immunodeficiency virus.

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Qiong-Ying Hu

Full Text Available Heparan sulfate proteoglycans (HSPG can act as binding receptors for certain laboratory-adapted (TCA strains of feline immunodeficiency virus (FIV and human immunodeficiency virus (HIV. Heparin, a soluble heparin sulfate (HS, can inhibit TCA HIV and FIV entry mediated by HSPG interaction in vitro. In the present study, we further determined the selective interaction of heparin with the V3 loop of TCA of FIV. Our current results indicate that heparin selectively inhibits infection by TCA strains, but not for field isolates (FS. Heparin also specifically interferes with TCA surface glycoprotein (SU binding to CXCR4, by interactions with HSPG binding sites on the V3 loop of the FIV envelope protein. Peptides representing either the N- or C-terminal side of the V3 loop and containing HSPG binding sites were able to compete away the heparin block of TCA SU binding to CXCR4. Heparin does not interfere with the interaction of SU with anti-V3 antibodies that target the CXCR4 binding region or with the interaction between FS FIV and anti-V3 antibodies since FS SU has no HSPG binding sites within the HSPG binding region. Our data show that heparin blocks TCA FIV infection or entry not only through its competition of HSPG on the cell surface interaction with SU, but also by its interference with CXCR4 binding to SU. These studies aid in the design and development of heparin derivatives or analogues that can inhibit steps in virus infection and are informative regarding the HSPG/SU interaction.
Airborne black carbon concentrations over an urban region in western India-temporal variability, effects of meteorology, and source regions.

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Bapna, Mukund; Sunder Raman, Ramya; Ramachandran, S; Rajesh, T A

2013-03-01

This study characterizes over 5 years of high time resolution (5 min), airborne black carbon (BC) concentrations (July 2003 to December 2008) measured over Ahmedabad, an urban region in western India. The data were used to obtain different time averages of BC concentrations, and these averages were then used to assess the diurnal, seasonal, and annual variability of BC over the study region. Assessment of diurnal variations revealed a strong association between BC concentrations and vehicular traffic. Peaks in BC concentration were co-incident with the morning (0730 to 0830, LST) and late evening (1930 to 2030, LST) rush hour traffic. Additionally, diurnal variability in BC concentrations during major festivals (Diwali and Dushera during the months of October/November) revealed an increase in BC concentrations due to fireworks displays. Maximum half hourly BC concentrations during the festival days were as high as 79.8 μg m(-3). However, the high concentrations rapidly decayed suggesting that local meteorology during the festive season was favorable for aerosol dispersion. A multiple linear regression (MLR) model with BC as the dependent variable and meteorological parameters as independent variables was fitted. The variability in temperature, humidity, wind speed, and wind direction accounted for about 49% of the variability in measured BC concentrations. Conditional probability function (CPF) analysis was used to identify the geographical location of local source regions contributing to the effective BC measured (at 880 nm) at the receptor site. The east north-east (ENE) direction to the receptor was identified as a major source region. National highway (NH8) and two coal-fired thermal power stations (at Gandhinagar and Sabarmati) were located in the identified direction, suggesting that local traffic and power plant emissions were likely contributors to the measured BC.
Binding kinetics of 11C-N-methyl piperidyl benzilate (11C-NMPB) in a rhesus monkey brain using the cerebellum as a reference region

International Nuclear Information System (INIS)

Itoh, Takashi; Tanaka, Masayasu; Suzuki, Kasutoshi; Kobayashi, Kaoru; Inoue, Osamu

2005-01-01

The binding kinetics of' 11 C-N-methyl piperidyl benzilate ( 11 C-NMPB) in rhesus monkey brain were studied using animal positron emission tomography (PET) (SHR2000). This study is intended to assess the validity of the method using the cerebellum as a reference region, and to evaluate the effects of anesthesia on 11 C -NMPB binding. Two monkeys, anesthetized with ketamine, received intravenous 11 C-NMPB alone (370-760 MBq, 11 C-NMPB accumulated densely in the striatum and cerebral cortex with time. In contrast, the tracer accumulation significantly decreased with increased doses of nonradioactive NMPB. In the cerebellum, on the other hand, the accumulation of 11 C-NMPB remained low and the tracer was slowly eliminated from the brain following the injection. 11 C-NMPB binding in the cerebellum was barely affected by the increased dose of nonradioactive NMPB. We thus concluded that the specific 11 C-NMPB binding was negligible in the cerebellum, and performed simplified evaluation of 11 C-NMPB binding in each brain region by a graphical method using the cerebellum as a reference region. PET was conducted 26 times, in total both in ketamine-anesthetized and awake monkeys (n=3 each). Measurements of 11 C-NMPB binding showed good run-to-run reproducibility within individual animals. When 11 C-NMPB binding was compared between ketamine-treated and awake animals, a significant increase in 11 C-NMPB binding was observed in the striatum but not in other brain regions of ketamine-treated animals. (author)
Regional frameworks applied to hydrology: can landscape-based frameworks capture the hydrologic variability?

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R. McManamay; D. Orth; C. Dolloff; E. Frimpong

2011-01-01

Regional frameworks have been used extensively in recent years to aid in broad-scale management. Widely used landscape-based regional frameworks, such as hydrologic landscape regions (HLRs) and physiographic provinces, may provide predictive tools of hydrologic variability. However, hydrologic-based regional frameworks, created using only streamflow data, are also...
Assessment of regional air pollution variability in Istanbul

International Nuclear Information System (INIS)

Sen, Z.; Oztopal, A.

2001-01-01

Air pollution concentrations have temporal and spatial variations depending on the prevailing weather conditions, topographic features, city building heights and locations. When the measurements of air pollutants are available at set measurement sites, the regional variability degree of air pollutants is quantified using the point cumulative semi-variogram (PCSV). This technique provides a systematic method for calculating the changes in the concentrations of air pollutants with distance from a specific site. Regional variations of sulphur dioxide (SO 2 ) and total suspended particulate (TSP) matter concentrations in Istanbul city were evaluated using the PCSV concept. The data were available from 16 different air pollution measurement stations scattered all over the city for a period from 1988 to 1994. Monthly regional variation maps were drawn in and around the city at different radii of influence. These maps provide a reference for measuring future changes of air pollution in the city. (author)
Global MYCN transcription factor binding analysis in neuroblastoma reveals association with distinct E-box motifs and regions of DNA hypermethylation.

LENUS (Irish Health Repository)

Murphy, Derek M

2009-01-01

BACKGROUND: Neuroblastoma, a cancer derived from precursor cells of the sympathetic nervous system, is a major cause of childhood cancer related deaths. The single most important prognostic indicator of poor clinical outcome in this disease is genomic amplification of MYCN, a member of a family of oncogenic transcription factors. METHODOLOGY: We applied MYCN chromatin immunoprecipitation to microarrays (ChIP-chip) using MYCN amplified\\/non-amplified cell lines as well as a conditional knockdown cell line to determine the distribution of MYCN binding sites within all annotated promoter regions. CONCLUSION: Assessment of E-box usage within consistently positive MYCN binding sites revealed a predominance for the CATGTG motif (p<0.0016), with significant enrichment of additional motifs CATTTG, CATCTG, CAACTG in the MYCN amplified state. For cell lines over-expressing MYCN, gene ontology analysis revealed enrichment for the binding of MYCN at promoter regions of numerous molecular functional groups including DNA helicases and mRNA transcriptional regulation. In order to evaluate MYCN binding with respect to other genomic features, we determined the methylation status of all annotated CpG islands and promoter sequences using methylated DNA immunoprecipitation (MeDIP). The integration of MYCN ChIP-chip and MeDIP data revealed a highly significant positive correlation between MYCN binding and DNA hypermethylation. This association was also detected in regions of hemizygous loss, indicating that the observed association occurs on the same homologue. In summary, these findings suggest that MYCN binding occurs more commonly at CATGTG as opposed to the classic CACGTG E-box motif, and that disease associated over expression of MYCN leads to aberrant binding to additional weaker affinity E-box motifs in neuroblastoma. The co-localization of MYCN binding and DNA hypermethylation further supports the dual role of MYCN, namely that of a classical transcription factor affecting the
The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif

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Grishin Nick V

2009-01-01

Full Text Available Abstract Background Argonaute (Ago proteins interact with small regulatory RNAs to mediate gene regulatory pathways. A recent report by Kiriakidou et al. 1 describes an MC sequence region identified in Ago2 that displays similarity to the cap-binding motif in translation initiation factor 4E (eIF4E. In a cap-bound eIF4E structure, two important aromatic residues of the motif stack on either side of a 7-methylguanosine 5'-triphosphate (m7Gppp base. The corresponding Ago2 aromatic residues (F450 and F505 were hypothesized to perform the same cap-binding function. However, the detected similarity between the MC sequence and the eIF4E cap-binding motif was questionable. Results A number of sequence-based and structure-based bioinformatics methods reveal the reported similarity between the Ago2 MC sequence region and the eIF4E cap-binding motif to be spurious. Alternatively, the MC sequence region is confidently assigned to the N-terminus of the Ago piwi module, within the mid domain of experimentally determined prokaryotic Ago structures. Confident mapping of the Ago2 MC sequence region to the piwi mid domain results in a homology-based structure model that positions the identified aromatic residues over 20 Å apart, with one of the aromatic side chains (F450 contributing instead to the hydrophobic core of the domain. Conclusion Correct functional prediction based on weak sequence similarity requires substantial evolutionary and structural support. The evolutionary context of the Ago mid domain suggested by multiple sequence alignment is limited to a conserved hydrophobicity profile required for the fold and a motif following the MC region that binds guide RNA. Mapping of the MC sequence to the mid domain structure reveals Ago2 aromatics that are incompatible with eIF4E-like mRNA cap-binding, yet display some limited local structure similarities that cause the chance sequence match to eIF4E. Reviewers This article was reviewed by Arcady Mushegian
Characterizing CDOM Spectral Variability Across Diverse Regions and Spectral Ranges

Science.gov (United States)

Grunert, Brice K.; Mouw, Colleen B.; Ciochetto, Audrey B.

2018-01-01

Satellite remote sensing of colored dissolved organic matter (CDOM) has focused on CDOM absorption (aCDOM) at a reference wavelength, as its magnitude provides insight into the underwater light field and large-scale biogeochemical processes. CDOM spectral slope, SCDOM, has been treated as a constant or semiconstant parameter in satellite retrievals of aCDOM despite significant regional and temporal variabilities. SCDOM and other optical metrics provide insights into CDOM composition, processing, food web dynamics, and carbon cycling. To date, much of this work relies on fluorescence techniques or aCDOM in spectral ranges unavailable to current and planned satellite sensors (e.g., global variability in SCDOM and fit deviations in the aCDOM spectra using the recently proposed Gaussian decomposition method. From this, we investigate if global variability in retrieved SCDOM and Gaussian components is significant and regionally distinct. We iteratively decreased the spectral range considered and analyzed the number, location, and magnitude of fitted Gaussian components to understand if a reduced spectral range impacts information obtained within a common spectral window. We compared the fitted slope from the Gaussian decomposition method to absorption-based indices that indicate CDOM composition to determine the ability of satellite-derived slope to inform the analysis and modeling of large-scale biogeochemical processes. Finally, we present implications of the observed variability for remote sensing of CDOM characteristics via SCDOM.
The hydroxyapatite-binding regions of a rat salivary glycoprotein.

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Embery, G; Green, D R

1989-09-01

The regions of a salivary sulphated glycoprotein which are involved in its attachment to hydroxyapatite (Biogel HTP) have been characterised. The sulphated glycoprotein, a 35S-labelled preparation from mixed palatal and buccal minor gland secretions of the rat was bound onto hydroxyapatite and the resultant glycoprotein-hydroxyapatite complex was sequentially digested with pronase E and alpha-L-fucosidase, a treatment which released 86.8% +/- 1.7% of the radioactivity of the initially bound glycoprotein. The fragments which remained attached to the hydroxyapatite after enzymic digestion were fractionated on Sephadex G-25 and analysed for carbohydrate and amino acid components. A range of amino acids were detected which could reflect both glycosylated and non-glycosylated-binding regions. Sialic acid, although considered to be involved in the attachment process was not detected in any of the fragments remaining after enzymic digestion, a finding which provides indirect evidence that the enzymically liberated products do not subsequently re-attach to the hydroxyapatite surface. The notable feature of the fractions with average Mr estimated at 1000 or less is the high proportion of N-acetylhexosamine and N-acetylgalactosamine. It is apparent that the hexosamine residues, which normally bear the ester sulphate moieties of sulphated glycoproteins, play an important role in the attachment of sulphated glycoproteins to hydroxyapatite.
RBPmap: a web server for mapping binding sites of RNA-binding proteins.

Science.gov (United States)

Paz, Inbal; Kosti, Idit; Ares, Manuel; Cline, Melissa; Mandel-Gutfreund, Yael

2014-07-01

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Impact of Variable-Resolution Meshes on Regional Climate Simulations

Science.gov (United States)

Fowler, L. D.; Skamarock, W. C.; Bruyere, C. L.

2014-12-01

The Model for Prediction Across Scales (MPAS) is currently being used for seasonal-scale simulations on globally-uniform and regionally-refined meshes. Our ongoing research aims at analyzing simulations of tropical convective activity and tropical cyclone development during one hurricane season over the North Atlantic Ocean, contrasting statistics obtained with a variable-resolution mesh against those obtained with a quasi-uniform mesh. Analyses focus on the spatial distribution, frequency, and intensity of convective and grid-scale precipitations, and their relative contributions to the total precipitation as a function of the horizontal scale. Multi-month simulations initialized on May 1st 2005 using ERA-Interim re-analyses indicate that MPAS performs satisfactorily as a regional climate model for different combinations of horizontal resolutions and transitions between the coarse and refined meshes. Results highlight seamless transitions for convection, cloud microphysics, radiation, and land-surface processes between the quasi-uniform and locally- refined meshes, despite the fact that the physics parameterizations were not developed for variable resolution meshes. Our goal of analyzing the performance of MPAS is twofold. First, we want to establish that MPAS can be successfully used as a regional climate model, bypassing the need for nesting and nudging techniques at the edges of the computational domain as done in traditional regional climate modeling. Second, we want to assess the performance of our convective and cloud microphysics parameterizations as the horizontal resolution varies between the lower-resolution quasi-uniform and higher-resolution locally-refined areas of the global domain.
The Receptor-Binding Domain in the VP1u Region of Parvovirus B19.

Science.gov (United States)

Leisi, Remo; Di Tommaso, Chiarina; Kempf, Christoph; Ros, Carlos

2016-02-24

Parvovirus B19 (B19V) is known as the human pathogen causing the mild childhood disease erythema infectiosum. B19V shows an extraordinary narrow tissue tropism for erythroid progenitor cells in the bone marrow, which is determined by a highly restricted uptake. We have previously shown that the specific internalization is mediated by the interaction of the viral protein 1 unique region (VP1u) with a yet unknown cellular receptor. To locate the receptor-binding domain (RBD) within the VP1u, we analyzed the effect of truncations and mutations on the internalization capacity of the recombinant protein into UT7/Epo cells. Here we report that the N-terminal amino acids 5-80 of the VP1u are necessary and sufficient for cellular binding and internalization; thus, this N-terminal region represents the RBD required for B19V uptake. Using site-directed mutagenesis, we further identified a cluster of important amino acids playing a critical role in VP1u internalization. In silico predictions and experimental results suggest that the RBD is structured as a rigid fold of three α-helices. Finally, we found that dimerization of the VP1u leads to a considerably enhanced cellular binding and internalization. Taken together, we identified the RBD that mediates B19V uptake and mapped functional and structural motifs within this sequence. The findings reveal insights into the uptake process of B19V, which contribute to understand the pathogenesis of the infection and the neutralization of the virus by the immune system.
In vivo positron emission tomography imaging with [{sup 11}C]ABP688: binding variability and specificity for the metabotropic glutamate receptor subtype 5 in baboons

Energy Technology Data Exchange (ETDEWEB)

DeLorenzo, Christine; Brennan, Kathleen G. [Columbia University College of Physicians and Surgeons, Division of Molecular Imaging and Neuropathology, Department of Psychiatry, NYSPI Mail Unit 42, New York, NY (United States); Milak, Matthew S.; Parsey, Ramin V. [Columbia University College of Physicians and Surgeons, Division of Molecular Imaging and Neuropathology, Department of Psychiatry, NYSPI Mail Unit 42, New York, NY (United States); New York State Psychiatric Institute, New York, NY (United States); Kumar, J.S.D.; Mann, J.J. [Columbia University College of Physicians and Surgeons, Division of Molecular Imaging and Neuropathology, Department of Psychiatry, NYSPI Mail Unit 42, New York, NY (United States); New York State Psychiatric Institute, New York, NY (United States); Columbia University College of Physicians and Surgeons, Department of Radiology, New York, NY (United States)

2011-06-15

Metabotropic glutamate receptor subtype 5 (mGluR5) dysfunction has been implicated in several disorders. [{sup 11}C]ABP688, a positron emission tomography (PET) ligand targeting mGluR5, could be a valuable tool in the development of novel therapeutics for these disorders by establishing in vivo drug occupancy. Due to safety concerns in humans, these studies may be performed in nonhuman primates. Therefore, in vivo characterization of [{sup 11}C]ABP688 in nonhuman primates is essential. Test-retest studies were performed in baboons (Papio anubis) to compare modeling approaches and determine the optimal reference region. The mGluR5-specific antagonist 3-((2-methyl-1,3-thiazol-4-yl)ethynyl)pyridine (MTEP) was then used in test-block studies, in which ligand binding was measured before and after MTEP administration. Test/block data were analyzed both by calculating changes in binding and using a graphical approach, which allowed estimation of both MTEP occupancy and nonspecific binding. Test-retest results, which have not been previously reported for [{sup 11}C]ABP688, indicated that [{sup 11}C]ABP688 variability is low using an unconstrained two-tissue compartment model. The most appropriate, though not ideal, reference region was found to be the gray matter of the cerebellum. Using these optimal modeling techniques on the test/block data, about 90% occupancy was estimated by the graphical approach. These studies are the first to demonstrate the specificity of [{sup 11}C]ABP688 for mGluR5 with in vivo PET in nonhuman primates. The results indicate that, in baboons, occupancy of mGluR5 is detectable by in vivo PET, a useful finding for proceeding to human studies, or performing further baboon studies, quantifying the in vivo occupancy of novel therapeutics targeting mGluR5. (orig.)
Morphometric variability of Arctodiaptomus salinus (Copepoda) in the Mediterranean-Black Sea region

OpenAIRE

ANUFRIIEVA, Elena V.; SHADRIN, Nickolai V.

2015-01-01

Inter-species variability in morphological traits creates a need to know the range of variability of characteristics in the species for taxonomic and ecological tasks. Copepoda Arctodiaptomus salinus, which inhabits water bodies across Eurasia and North Africa, plays a dominant role in plankton of different water bodies-from fresh to hypersaline. This work assesses the intra- and inter-population morphometric variability of A. salinus in the Mediterranean-Black Sea region and discusses some o...
An observational and modeling study of the regional impacts of climate variability

Science.gov (United States)

Horton, Radley M.

Climate variability has large impacts on humans and their agricultural systems. Farmers are at the center of this agricultural network, but it is often agricultural planners---regional planners, extension agents, commodity groups and cooperatives---that translate climate information for users. Global climate models (GCMs) are a leading tool for understanding and predicting climate and climate change. Armed with climate projections and forecasts, agricultural planners adapt their decision-making to optimize outcomes. This thesis explores what GCMs can, and cannot, tell us about climate variability and change at regional scales. The question is important, since high-quality regional climate projections could assist farmers and regional planners in key management decisions, contributing to better agricultural outcomes. To answer these questions, climate variability and its regional impacts are explored in observations and models for the current and future climate. The goals are to identify impacts of observed variability, assess model simulation of variability, and explore how climate variability and its impacts may change under enhanced greenhouse warming. Chapter One explores how well Goddard Institute for Space Studies (GISS) atmospheric models, forced by historical sea surface temperatures (SST), simulate climatology and large-scale features during the exceptionally strong 1997--1999 El Nino Southern Oscillation (ENSO) cycle. Reasonable performance in this 'proof of concept' test is considered a minimum requirement for further study of variability in models. All model versions produce appropriate local changes with ENSO, indicating that with correct ocean temperatures these versions are capable of simulating the large-scale effects of ENSO around the globe. A high vertical resolution model (VHR) provides the best simulation. Evidence is also presented that SST anomalies outside the tropical Pacific may play a key role in generating remote teleconnections even
Life-history strategies associated with local population variability confer regional stability.

Science.gov (United States)

Pribil, Stanislav; Houlahan, Jeff E

2003-07-07

A widely held ecological tenet is that, at the local scale, populations of K-selected species (i.e. low fecundity, long lifespan and large body size) will be less variable than populations of r-selected species (i.e. high fecundity, short lifespan and small body size). We examined the relationship between long-term population trends and life-history attributes for 185 bird species in the Czech Republic and found that, at regional spatial scales and over moderate temporal scales (100-120 years), K-selected bird species were more likely to show both large increases and decreases in population size than r-selected species. We conclude that life-history attributes commonly associated with variable populations at the local scale, confer stability at the regional scale.

Factor H Binds to the Hypervariable Region of Many Streptococcus pyogenes M Proteins but Does Not Promote Phagocytosis Resistance or Acute Virulence

Science.gov (United States)

Kristensen, Bodil M.; Olsen, John E.; Harris, Claire L.; Ufret-Vincenty, Rafael L.; Stålhammar-Carlemalm, Margaretha; Lindahl, Gunnar

2013-01-01

Many pathogens express a surface protein that binds the human complement regulator factor H (FH), as first described for Streptococcus pyogenes and the antiphagocytic M6 protein. It is commonly assumed that FH recruited to an M protein enhances virulence by protecting the bacteria against complement deposition and phagocytosis, but the role of FH-binding in S. pyogenes pathogenesis has remained unclear and controversial. Here, we studied seven purified M proteins for ability to bind FH and found that FH binds to the M5, M6 and M18 proteins but not the M1, M3, M4 and M22 proteins. Extensive immunochemical analysis indicated that FH binds solely to the hypervariable region (HVR) of an M protein, suggesting that selection has favored the ability of certain HVRs to bind FH. These FH-binding HVRs could be studied as isolated polypeptides that retain ability to bind FH, implying that an FH-binding HVR represents a distinct ligand-binding domain. The isolated HVRs specifically interacted with FH among all human serum proteins, interacted with the same region in FH and showed species specificity, but exhibited little or no antigenic cross-reactivity. Although these findings suggested that FH recruited to an M protein promotes virulence, studies in transgenic mice did not demonstrate a role for bound FH during acute infection. Moreover, phagocytosis tests indicated that ability to bind FH is neither sufficient nor necessary for S. pyogenes to resist killing in whole human blood. While these data shed new light on the HVR of M proteins, they suggest that FH-binding may affect S. pyogenes virulence by mechanisms not assessed in currently used model systems. PMID:23637608
Factor H binds to the hypervariable region of many Streptococcus pyogenes M proteins but does not promote phagocytosis resistance or acute virulence.

Directory of Open Access Journals (Sweden)

Mattias C U Gustafsson

Full Text Available Many pathogens express a surface protein that binds the human complement regulator factor H (FH, as first described for Streptococcus pyogenes and the antiphagocytic M6 protein. It is commonly assumed that FH recruited to an M protein enhances virulence by protecting the bacteria against complement deposition and phagocytosis, but the role of FH-binding in S. pyogenes pathogenesis has remained unclear and controversial. Here, we studied seven purified M proteins for ability to bind FH and found that FH binds to the M5, M6 and M18 proteins but not the M1, M3, M4 and M22 proteins. Extensive immunochemical analysis indicated that FH binds solely to the hypervariable region (HVR of an M protein, suggesting that selection has favored the ability of certain HVRs to bind FH. These FH-binding HVRs could be studied as isolated polypeptides that retain ability to bind FH, implying that an FH-binding HVR represents a distinct ligand-binding domain. The isolated HVRs specifically interacted with FH among all human serum proteins, interacted with the same region in FH and showed species specificity, but exhibited little or no antigenic cross-reactivity. Although these findings suggested that FH recruited to an M protein promotes virulence, studies in transgenic mice did not demonstrate a role for bound FH during acute infection. Moreover, phagocytosis tests indicated that ability to bind FH is neither sufficient nor necessary for S. pyogenes to resist killing in whole human blood. While these data shed new light on the HVR of M proteins, they suggest that FH-binding may affect S. pyogenes virulence by mechanisms not assessed in currently used model systems.
Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

DEFF Research Database (Denmark)

Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

2004-01-01

CD163 is the macrophage receptor for endocytosis of haptoglobin.hemoglobin complexes. The extracellular region consisting of nine scavenger receptor cysteine rich (SRCR) domains also circulates in plasma as a soluble protein. By ligand binding analysis of a broad spectrum of soluble CD163...... truncation variants, the amino-terminal third of the SRCR region was shown to be crucial for the binding of haptoglobin.hemoglobin complexes. By Western blotting of the CD163 variants, a panel of ten monoclonal antibodies was mapped to SRCR domains 1, 3, 4, 6, 7, and 9, respectively. Only the two antibodies...... to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant...
Reduction in camera-specific variability in [{sup 123}I]FP-CIT SPECT outcome measures by image reconstruction optimized for multisite settings: impact on age-dependence of the specific binding ratio in the ENC-DAT database of healthy controls

Energy Technology Data Exchange (ETDEWEB)

Buchert, Ralph; Lange, Catharina [Charite - Universitaetsmedizin Berlin, Department of Nuclear Medicine, Berlin (Germany); Kluge, Andreas; Bronzel, Marcus [ABX-CRO advanced pharmaceutical services Forschungsgesellschaft m.b.H., Dresden (Germany); Tossici-Bolt, Livia [University Hospital Southampton NHS Foundation Trust, Department of Medical Physics, Southampton (United Kingdom); Dickson, John [University College London Hospital NHS Foundation Trust, Institute of Nuclear Medicine, London (United Kingdom); Asenbaum, Susanne [Medical University of Vienna, Department of Nuclear Medicine, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, L. Oezlem Atay [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Svarer, Claus [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Koulibaly, Pierre-Malick [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Department of Neuroscience (DINOGMI), Clinical Neurology Unit, Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Sabri, Osama [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Tatsch, Klaus [Municipal Hospital of Karlsruhe Inc, Department of Nuclear Medicine, Karlsruhe (Germany); Borght, Thierry vander [CHU Namur, IREC, Nuclear Medicine Division, Universite catholique de Louvain, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Varrone, Andrea [Karolinska University Hospital, Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm (Sweden); Iida, Hidehiro [National Cerebral and Cardiovascular Center - Research Institute, Osaka (Japan)

2016-07-15

Quantitative estimates of dopamine transporter availability, determined with [{sup 123}I]FP-CIT SPECT, depend on the SPECT equipment, including both hardware and (reconstruction) software, which limits their use in multicentre research and clinical routine. This study tested a dedicated reconstruction algorithm for its ability to reduce camera-specific intersubject variability in [{sup 123}I]FP-CIT SPECT. The secondary aim was to evaluate binding in whole brain (excluding striatum) as a reference for quantitative analysis. Of 73 healthy subjects from the European Normal Control Database of [{sup 123}I]FP-CIT recruited at six centres, 70 aged between 20 and 82 years were included. SPECT images were reconstructed using the QSPECT software package which provides fully automated detection of the outer contour of the head, camera-specific correction for scatter and septal penetration by transmission-dependent convolution subtraction, iterative OSEM reconstruction including attenuation correction, and camera-specific ''to kBq/ml'' calibration. LINK and HERMES reconstruction were used for head-to-head comparison. The specific striatal [{sup 123}I]FP-CIT binding ratio (SBR) was computed using the Southampton method with binding in the whole brain, occipital cortex or cerebellum as the reference. The correlation between SBR and age was used as the primary quality measure. The fraction of SBR variability explained by age was highest (1) with QSPECT, independently of the reference region, and (2) with whole brain as the reference, independently of the reconstruction algorithm. QSPECT reconstruction appears to be useful for reduction of camera-specific intersubject variability of [{sup 123}I]FP-CIT SPECT in multisite and single-site multicamera settings. Whole brain excluding striatal binding as the reference provides more stable quantitative estimates than occipital or cerebellar binding. (orig.)
Maturation of Shark Single-Domain (IgNAR) Antibodies: Evidence for Induced-Fit Binding

Energy Technology Data Exchange (ETDEWEB)

Stanfield, R.L.; Dooley, H.; Verdino, P.; Flajnik, M.F.; Wilson, I.A.; /Scripps Res. Inst. /Maryland U.

2007-07-13

Sharks express an unusual heavy-chain isotype called IgNAR, whose variable regions bind antigen as independent soluble domains. To further probe affinity maturation of the IgNAR response, we structurally characterized the germline and somatically matured versions of a type II variable (V) region, both in the presence and absence of its antigen, hen egg-white lysozyme. Despite a disulfide bond linking complementarity determining regions (CDRs) 1 and 3, both germline and somatically matured V regions displayed significant structural changes in these CDRs upon complex formation with antigen. Somatic mutations in the IgNAR V region serve to increase the number of contacts with antigen, as reflected by a tenfold increase in affinity, and one of these mutations appears to stabilize the CDR3 region. In addition, a residue in the HV4 loop plays an important role in antibody-antigen interaction, consistent with the high rate of somatic mutations in this non-CDR loop.
Moment-to-Moment BOLD Signal Variability Reflects Regional Changes in Neural Flexibility across the Lifespan.

Science.gov (United States)

Nomi, Jason S; Bolt, Taylor S; Ezie, C E Chiemeka; Uddin, Lucina Q; Heller, Aaron S

2017-05-31

Variability of neuronal responses is thought to underlie flexible and optimal brain function. Because previous work investigating BOLD signal variability has been conducted within task-based fMRI contexts on adults and older individuals, very little is currently known regarding regional changes in spontaneous BOLD signal variability in the human brain across the lifespan. The current study used resting-state fMRI data from a large sample of male and female human participants covering a wide age range (6-85 years) across two different fMRI acquisition parameters (TR = 0.645 and 1.4 s). Variability in brain regions including a key node of the salience network (anterior insula) increased linearly across the lifespan across datasets. In contrast, variability in most other large-scale networks decreased linearly over the lifespan. These results demonstrate unique lifespan trajectories of BOLD variability related to specific regions of the brain and add to a growing literature demonstrating the importance of identifying normative trajectories of functional brain maturation. SIGNIFICANCE STATEMENT Although brain signal variability has traditionally been considered a source of unwanted noise, recent work demonstrates that variability in brain signals during task performance is related to brain maturation in old age as well as individual differences in behavioral performance. The current results demonstrate that intrinsic fluctuations in resting-state variability exhibit unique maturation trajectories in specific brain regions and systems, particularly those supporting salience detection. These results have implications for investigations of brain development and aging, as well as interpretations of brain function underlying behavioral changes across the lifespan. Copyright © 2017 the authors 0270-6474/17/375539-10$15.00/0.
Morphometric variability of Arctodiaptomus salinus (Copepoda) in the Mediterranean-Black Sea region.

Science.gov (United States)

Anufriieva, Elena V; Shadrin, Nickolai V

2015-11-18

Inter-species variability in morphological traits creates a need to know the range of variability of characteristics in the species for taxonomic and ecological tasks. Copepoda Arctodiaptomus salinus, which inhabits water bodies across Eurasia and North Africa, plays a dominant role in plankton of different water bodies-from fresh to hypersaline. This work assesses the intra- and inter-population morphometric variability of A. salinus in the Mediterranean-Black Sea region and discusses some observed regularities. The variability of linear body parameters and proportions was studied. The impacts of salinity, temperature, and population density on morphological characteristics and their variability can manifest themselves in different ways at the intra- and inter-population levels. A significant effect of salinity, pH and temperature on the body proportions was not found. Their intra-population variability is dependent on temperature and salinity. Sexual dimorphism of A. salinus manifests in different linear parameters, proportions, and their variability. There were no effects of temperature, pH and salinity on the female/male parameter ratio. There were significant differences in the body proportions of males and females in different populations. The influence of temperature, salinity, and population density can be attributed to 80%-90% of intra-population variability of A. salinus. However, these factors can explain less than 40% of inter-population differences. Significant differences in the body proportions of males and females from different populations may suggest that some local populations of A. salinus in the Mediterranean-Black Sea region are in the initial stages of differentiation.
Regional blockade by neuroleptic drugs of in vivo 3H-spiperone binding in the rat brain. Relation to blockade of apomorphine induced hyperactivity and stereotypies

International Nuclear Information System (INIS)

Koehler, C.; Haglund, L.; Oegren, S.-O.; Aengeby, T.

1981-01-01

The regional prevention by neuroleptic drugs of specific in vivo 3 H-spiperone binding was studied in the rat brain. L-sulpiride, thioridazine and clozapine were found to reduce the 3 H-spiperone bindings selectively in the olfactory tubercle, septum, substantia nigra and frontal cortex but not the striatum at dose levels which preferentially block apomorphine (APO) induced hyperactivity. The maximal prevention of specific 3 H-spiperone binding by l-sulpiride and clozapine reached 60-80% in the former structures while the displacement of striatal 3 H-spiperone binding did not exceed 40%. In contrast to l-sulpiride, thioridazine and clozapine both chlorpromazine and haloperidol reduced the 3 H-spiperone binding to the same extent in all regions studied. Chlorpromazine and haloperidol were potent in prevention of striatal 3 H-spiperone binding in vivo which reached 60-80% in this structure. (Author)
Structures of the Streptococcus sanguinis SrpA Binding Region with Human Sialoglycans Suggest Features of the Physiological Ligand.

Science.gov (United States)

Loukachevitch, Lioudmila V; Bensing, Barbara A; Yu, Hai; Zeng, Jie; Chen, Xi; Sullam, Paul M; Iverson, T M

2016-10-11

Streptococcus sanguinis is a leading cause of bacterial infective endocarditis, a life-threatening infection of heart valves. S. sanguinis binds to human platelets with high avidity, and this adherence is likely to enhance virulence. Previous studies suggest that a serine-rich repeat adhesin termed SrpA mediates the binding of S. sanguinis to human platelets via its interaction with sialoglycans on the receptor GPIbα. However, in vitro binding assays with SrpA and defined sialoglycans failed to identify specific high-affinity ligands. To improve our understanding of the interaction between SrpA and human platelets, we determined cocrystal structures of the SrpA sialoglycan binding region (SrpA BR ) with five low-affinity ligands: three sialylated trisaccharides (sialyl-T antigen, 3'-sialyllactose, and 3'-sialyl-N-acetyllactosamine), a sialylated tetrasaccharide (sialyl-Lewis X ), and a sialyl galactose disaccharide component common to these sialoglyans. We then combined structural analysis with mutagenesis to further determine whether our observed interactions between SrpA BR and glycans are important for binding to platelets and to better map the binding site for the physiological receptor. We found that the sialoglycan binding site of SrpA BR is significantly larger than the sialoglycans cocrystallized in this study, which suggests that binding of SrpA to platelets either is multivalent or occurs via a larger, disialylated glycan.
Extreme Variables in Star Forming Regions

Science.gov (United States)

Contreras Peña, Carlos Eduardo

2015-01-01

in two multi-epoch infrared surveys: the UKIDSS Galactic Plane Survey (GPS) and the Vista Variables in the Via Lactea (VVV). In order to further investigate the nature of the selected variable stars, we use photometric information arising from public surveys at near- to far-infrared wavelengths. In addition we have performed spectroscopic and photometric follow-up for a large subset of the samples arising from GPS and VVV. We analyse the widely separated two-epoch K-band photometry in the 5th, 7th and 8th data releases of the UKIDSS Galactic Plane Survey. We find 71 stars with ΔK > 1 mag, including 2 previously known OH/IR stars and a Nova. Even though the mid-plane is mostly excluded from the dataset, we find the majority (66%) of our sample to be within known star forming regions (SFRs), with two large concentrations in the Serpens OB2 association (11 stars) and the Cygnus-X complex (27 stars). The analysis of the multi-epoch K-band photometry of 2010-2012 data from VVV covering the Galactic disc at |b| explained as arising from shock-excited emission caused by molecular outflows. Whether these molecular outflows are related to outbursts events cannot be confirmed from our data. Adding the GPS and VVV spectroscopic results, we find that between 6 and 14 objects are new additions to the FUor class from their close resemblance to the near-infrared spectra of FUors, and at least 23 more objects are new additions to the eruptive variable class. For most of these we are unable to classify them into any of the original definitions for this variable class. In any case, we are adding up to 37 new stars to the eruptive variable class which would double the current number of known objects. We note that most objects are found to be deeply embedded optically invisible stars, thus increasing the number of objects belonging to this subclass by a much larger factor. In general, objects in our samples which are found to be likely eruptive variable stars show a mixture of
Mesopause region temperature variability and its trend in southern Brazil

Science.gov (United States)

Venturini, Mateus S.; Bageston, José V.; Caetano, Nattan R.; Peres, Lucas V.; Bencherif, Hassan; Schuch, Nelson J.

2018-03-01

Nowadays, the study of the upper atmosphere is increasing, mostly because of the need to understand the patterns of Earth's atmosphere. Since studies on global warming have become very important for the development of new technologies, understanding all regions of the atmosphere becomes an unavoidable task. In this paper, we aim to analyze the temperature variability and its trend in the mesosphere and lower thermosphere (MLT) region during a period of 12 years (from 2003 to 2014). For this purpose, three different heights, i.e., 85, 90 and 95 km, were focused on in order to investigate the upper atmosphere, and a geographic region different to other studies was chosen, in the southern region of Brazil, centered in the city of Santa Maria, RS (29°41'02'' S; 53°48'25'' W). In order to reach the objectives of this work, temperature data from the SABER instrument (Sounding of the Atmosphere using Broadband Emission Radiometry), aboard NASA's Thermosphere Ionosphere Mesosphere Energetics Dynamics (TIMED) satellite, were used. Finally, two cases were studied related to distinct grids of latitude/longitude used to obtain the mean temperature profiles. The first case considered a grid of 20° × 20° lat/long, centered in Santa Maria, RS, Brazil. In the second case, the region was reduced to a size of 15° × 15° in order to compare the results and discuss the two cases in terms of differences or similarities in temperature trends. Observations show that the size of the geographical area used for the average temperature profiles can influence the results of variability and trend of the temperature. In addition, reducing the time duration of analyses from 24 to 12 h a day also influences the trend significantly. For the smaller geographical region (15° × 15°) and the 12 h daily time window (09:00-21:00 UT) it was found that the main contributions for the temperature variability at the three heights were the annual and semi-annual cycles and the solar flux influence
Identification and verification of hybridoma-derived monoclonal antibody variable region sequences using recombinant DNA technology and mass spectrometry.

Science.gov (United States)

Babrak, Lmar; McGarvey, Jeffery A; Stanker, Larry H; Hnasko, Robert

2017-10-01

Antibody engineering requires the identification of antigen binding domains or variable regions (VR) unique to each antibody. It is the VR that define the unique antigen binding properties and proper sequence identification is essential for functional evaluation and performance of recombinant antibodies (rAb). This determination can be achieved by sequence analysis of immunoglobulin (Ig) transcripts obtained from a monoclonal antibody (MAb) producing hybridoma and subsequent expression of a rAb. However the polyploidy nature of a hybridoma cell often results in the added expression of aberrant immunoglobulin-like transcripts or even production of anomalous antibodies which can confound production of rAb. An incorrect VR sequence will result in a non-functional rAb and de novo assembly of Ig primary structure without a sequence map is challenging. To address these problems, we have developed a methodology which combines: 1) selective PCR amplification of VR from both the heavy and light chain IgG from hybridoma, 2) molecular cloning and DNA sequence analysis and 3) tandem mass spectrometry (MS/MS) on enzyme digests obtained from the purified IgG. Peptide analysis proceeds by evaluating coverage of the predicted primary protein sequence provided by the initial DNA maps for the VR. This methodology serves to both identify and verify the primary structure of the MAb VR for production as rAb. Published by Elsevier Ltd.
Quantitative analyses of regional [{sup 11}C]PE2I binding to the dopamine transporter in the human brain: a PET study

Energy Technology Data Exchange (ETDEWEB)

Jucaite, Aurelija [Karolinska Institutet, Department of Woman and Child Health, Stockholm (Sweden); Odano, Ikuo [Niigata University, Department of Sensory and Integrative Medicine, Asahimachi-dori Niigata (Japan); Olsson, Hans; Pauli, Stefan; Halldin, Christer; Farde, Lars [Karolinska Institutet, Psychiatry Section, Department of Clinical Neuroscience, Stockholm (Sweden)

2006-06-15

The dopamine transporter (DAT) is a plasma membrane protein of central interest in the pathophysiology of neuropsychiatric disorders and is known to be a target for psychostimulant drugs. [{sup 11}C]PE2I is a new radioligand which binds selectively and with moderate affinity to central DAT, as has been demonstrated in vitro by autoradiography and in vivo by positron emission tomography (PET). The aims of the present PET study were to quantify regional [{sup 11}C]PE2I binding to DAT in the human brain and to compare quantitative methods with regard to suitability for applied clinical studies. One PET measurement was performed in each of eight healthy male subjects. The binding potential (BP) values were obtained by applying kinetic compartment analysis, which uses the metabolite-corrected arterial plasma curve as an input function. They were compared with the BP values quantified by two reference tissue approaches, using cerebellum as a reference region representing free and non-specific radioligand binding. The radioactivity concentration was highest in the striatum, lower in the midbrain and very low in the cerebellum. The regional [{sup 11}C]PE2I binding could be interpreted by kinetic compartment models. However, the BP values in the striatum obtained by the compartment analyses were about 30% higher than the BP values obtained using reference tissue methods. We suggest that the difference may be explained by the inaccurate metabolite correction, small amounts of radioactive metabolites that could account for the presence of non-specific binding in the cerebellum and insufficient data acquisition time. (orig.)
Regionalizing Africa: Patterns of Precipitation Variability in Observations and Global Climate Models

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Badr, Hamada S.; Dezfuli, Amin K.; Zaitchik, Benjamin F.; Peters-Lidard, Christa D.

2016-01-01

Many studies have documented dramatic climatic and environmental changes that have affected Africa over different time scales. These studies often raise questions regarding the spatial extent and regional connectivity of changes inferred from observations and proxies and/or derived from climate models. Objective regionalization offers a tool for addressing these questions. To demonstrate this potential, applications of hierarchical climate regionalizations of Africa using observations and GCM historical simulations and future projections are presented. First, Africa is regionalized based on interannual precipitation variability using Climate Hazards Group Infrared Precipitation with Stations (CHIRPS) data for the period 19812014. A number of data processing techniques and clustering algorithms are tested to ensure a robust definition of climate regions. These regionalization results highlight the seasonal and even month-to-month specificity of regional climate associations across the continent, emphasizing the need to consider time of year as well as research question when defining a coherent region for climate analysis. CHIRPS regions are then compared to those of five GCMs for the historic period, with a focus on boreal summer. Results show that some GCMs capture the climatic coherence of the Sahel and associated teleconnections in a manner that is similar to observations, while other models break the Sahel into uncorrelated subregions or produce a Sahel-like region of variability that is spatially displaced from observations. Finally, shifts in climate regions under projected twenty-first-century climate change for different GCMs and emissions pathways are examined. A projected change is found in the coherence of the Sahel, in which the western and eastern Sahel become distinct regions with different teleconnections. This pattern is most pronounced in high-emissions scenarios.
Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig) proteins.

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Raman, Rajeev; Rajanikanth, V; Palaniappan, Raghavan U M; Lin, Yi-Pin; He, Hongxuan; McDonough, Sean P; Sharma, Yogendra; Chang, Yung-Fu

2010-12-29

Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig) proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big) domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th) (Lig A9) and 10(th) repeats (Lig A10); and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon). All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm), probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.
Constancy despite variability: Local and regional macrofaunal diversity in intertidal seagrass beds

Science.gov (United States)

Boyé, Aurélien; Legendre, Pierre; Grall, Jacques; Gauthier, Olivier

2017-12-01

The importance of seagrass habitat for the diversity of benthic fauna has been extensively studied worldwide. Most of the information available is, however, about α diversity while little consideration has been given to β diversity. To fill the knowledge gaps regarding the variability of epifaunal and infaunal seagrass assemblages at large spatial and temporal scales, we scrutinized an extensive dataset covering five years of monitoring of eight intertidal Zostera marina meadows around Brittany (France). High species richness arose at the regional scale from the combination of high local diversity of the meadows and substantial among-meadows β diversity. Epifauna and infauna appeared as distinct self-communities as they displayed different spatial and temporal patterns and varied in their responses to local hydrological conditions. Infauna had higher total β diversity than epifauna due to a tighter link to the great variability of local environmental conditions in the region. Both exhibited substantial variations in species composition and community structure with variations of dominant species that were accompanied by extensive change in numerous rare species. The dominant epifaunal species were all grazers. Changes in species composition were induced mostly by species replacement and rarely by richness differences between meadows. Indeed, species richness remained within a narrow range for all seagrass beds, suggesting a potential carrying capacity for species richness of the meadows. Overall, all meadows contributed equally to the regional turnover of seagrass macrofauna, emphasizing high variability and complementarity among beds at the regional scale. The implications of this substantial within-seagrass variability for the functioning of benthic ecosystems at broad scale and for conservation purposes in habitat mosaics warrant further investigations but our results clearly advocate taking into account within-habitat variation when evaluating the diversity
Long-term Variability of H2CO Masers in Star-forming Regions

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Andreev, N.; Araya, E. D.; Hoffman, I. M.; Hofner, P.; Kurtz, S.; Linz, H.; Olmi, L.; Lorran-Costa, I.

2017-10-01

We present results of a multi-epoch monitoring program on variability of 6 cm formaldehyde (H2CO) masers in the massive star-forming region NGC 7538 IRS 1 from 2008 to 2015, conducted with the Green Bank Telescope, the Westerbork Radio Telescope , and the Very Large Array. We found that the similar variability behaviors of the two formaldehyde maser velocity components in NGC 7538 IRS 1 (which was pointed out by Araya and collaborators in 2007) have continued. The possibility that the variability is caused by changes in the maser amplification path in regions with similar morphology and kinematics is discussed. We also observed 12.2 GHz methanol and 22.2 GHz water masers toward NGC 7538 IRS 1. The brightest maser components of CH3OH and H2O species show a decrease in flux density as a function of time. The brightest H2CO maser component also shows a decrease in flux density and has a similar LSR velocity to the brightest H2O and 12.2 GHz CH3OH masers. The line parameters of radio recombination lines and the 20.17 and 20.97 GHz CH3OH transitions in NGC 7538 IRS 1 are also reported. In addition, we observed five other 6 cm formaldehyde maser regions. We found no evidence of significant variability of the 6 cm masers in these regions with respect to previous observations, the only possible exception being the maser in G29.96-0.02. All six sources were also observed in the {{{H}}}213{CO} isotopologue transition of the 6 cm H2CO line; {{{H}}}213{CO} absorption was detected in five of the sources. Estimated column density ratios [{{{H}}}212{CO}]/[{{{H}}}213{CO}] are reported.
Grasping the nettle: A bacterial invasin that targets immunoglobulin variable domains.

Science.gov (United States)

Barlow, Paul

2018-06-01

In a new paper, the protein InvD from Yersinia pseudotuberculosis , a zoonotic pathogen, is shown to assist late-stage invasion of intestinal epithelia. Remarkably, InvD acts by binding the Fab region of IgG or IgA. It straddles adjacent light-chain and heavy-chain variable domains, but its binding is different from that of antigens in that complementarity-determining regions do not participate. Structure determination revealed that its Fab-interacting domain adopts an immunoglobulin-like fold, fused to the preceding immunoglobulin-like domain and carried on a long stalk anchored to the bacterial outer membrane. Possible roles of this unusual host-pathogen interaction include avoidance of clearance from the intestine by secretory IgA. © 2018 Barlow.
Binding of mouse immunoglobulin G to polylysine-coated glass substrate for immunodiagnosis

Science.gov (United States)

Vashist, Sandeep Kumar; Tewari, Rupinder; Bajpai, Ram Prakash; Bharadwaj, Lalit Mohan; Raiteri, Roberto

2006-12-01

We report a method for immobilizing mouse immunoglobulin G (IgG) on polylysine-coated glass substrate for immunodiagnostic applications. Mouse IgG molecules were immobilized on polylysine-coated glass substrate employing 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and protein A. The amino groups of the polylysine-coated glass slide were cross linked to the carboxyl groups of protein A employing EDC crosslinker. Protein A was employed as it binds to the constant Fc region of antibodies keeping their antigen binding sites on the variable F ab region free to bind to antigens. The qualitative analysis of surface immobilized mouse IgG was done by fluorescent microscopy employing fluorescein isothiocyanate (FITC) labeled mouse IgG molecules. The immobilization densities of protein A and mouse IgG were determined by 3, 3', 4, 4'-tetramethyl benzidine (TMB) substrate assay employing horse radish peroxidise labelled molecules and were found to be 130 +/- 17 ng/cm2 and 596 +/- 31 ng/cm2 respectively. The biomolecular coatings analyzed by atomic force microscopy (AFM) were found to be uniform.
[3]tetrahydrotrazodone binding. Association with serotonin binding sites

International Nuclear Information System (INIS)

Kendall, D.A.; Taylor, D.P.; Enna, S.J.

1983-01-01

High (17 nM) and low (603 nM) affinity binding sites for [ 3 ]tetrahydrotrazodone ([ 3 ] THT), a biologically active analogue of trazodone, have been identified in rat brain membranes. The substrate specificity, concentration, and subcellular and regional distributions of these sites suggest that they may represent a component of the serotonin transmitter system. Pharmacological analysis of [ 3 ]THT binding, coupled with brain lesion and drug treatment experiments, revealed that, unlike other antidepressants, [ 3 ] THT does not attach to either a biogenic amine transporter or serotonin binding sites. Rather, it would appear that [ 3 ]THT may be an antagonist ligand for the serotonin binding site. This probe may prove of value in defining the mechanism of action of trazodone and in further characterizing serotonin receptors

OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.

Directory of Open Access Journals (Sweden)

Tong Li

Full Text Available Antibody-based therapeutics provides novel and efficacious treatments for a number of diseases. Traditional experimental approaches for designing therapeutic antibodies rely on raising antibodies against a target antigen in an immunized animal or directed evolution of antibodies with low affinity for the desired antigen. However, these methods remain time consuming, cannot target a specific epitope and do not lead to broad design principles informing other studies. Computational design methods can overcome some of these limitations by using biophysics models to rationally select antibody parts that maximize affinity for a target antigen epitope. This has been addressed to some extend by OptCDR for the design of complementary determining regions. Here, we extend this earlier contribution by addressing the de novo design of a model of the entire antibody variable region against a given antigen epitope while safeguarding for immunogenicity (Optimal Method for Antibody Variable region Engineering, OptMAVEn. OptMAVEn simulates in silico the in vivo steps of antibody generation and evolution, and is capable of capturing the critical structural features responsible for affinity maturation of antibodies. In addition, a humanization procedure was developed and incorporated into OptMAVEn to minimize the potential immunogenicity of the designed antibody models. As case studies, OptMAVEn was applied to design models of neutralizing antibodies targeting influenza hemagglutinin and HIV gp120. For both HA and gp120, novel computational antibody models with numerous interactions with their target epitopes were generated. The observed rates of mutations and types of amino acid changes during in silico affinity maturation are consistent with what has been observed during in vivo affinity maturation. The results demonstrate that OptMAVEn can efficiently generate diverse computational antibody models with both optimized binding affinity to antigens and reduced
TAF(II)170 interacts with the concave surface of TATA-binding protein to inhibit its DNA binding activity.

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Pereira, L A; van der Knaap, J A; van den Boom, V; van den Heuvel, F A; Timmers, H T

2001-11-01

The human RNA polymerase II transcription factor B-TFIID consists of TATA-binding protein (TBP) and the TBP-associated factor (TAF) TAF(II)170 and can rapidly redistribute over promoter DNA. Here we report the identification of human TBP-binding regions in human TAF(II)170. We have defined the TBP interaction domain of TAF(II)170 within three amino-terminal regions: residues 2 to 137, 290 to 381, and 380 to 460. Each region contains a pair of Huntington-elongation-A subunit-Tor repeats and exhibits species-specific interactions with TBP family members. Remarkably, the altered-specificity TBP mutant (TBP(AS)) containing a triple mutation in the concave surface is defective for binding the TAF(II)170 amino-terminal region of residues 1 to 504. Furthermore, within this region the TAF(II)170 residues 290 to 381 can inhibit the interaction between Drosophila TAF(II)230 (residues 2 to 81) and TBP through competition for the concave surface of TBP. Biochemical analyses of TBP binding to the TATA box indicated that TAF(II)170 region 290-381 inhibits TBP-DNA complex formation. Importantly, the TBP(AS) mutant is less sensitive to TAF(II)170 inhibition. Collectively, our results support a mechanism in which TAF(II)170 induces high-mobility DNA binding by TBP through reversible interactions with its concave DNA binding surface.
Highly potent antimicrobial peptides from N-terminal membrane-binding region of E. coli MreB.

Science.gov (United States)

Saikia, Karabi; Sravani, Yalavarthi Durga; Ramakrishnan, Vibin; Chaudhary, Nitin

2017-02-23

Microbial pathogenesis is a serious health concern. The threat escalates as the existing conventional antimicrobials are losing their efficacy against the evolving pathogens. Peptides hold promise to be developed into next-generation antibiotics. Antimicrobial peptides adopt amphipathic structures that could selectively bind to and disrupt the microbial membranes. Interaction of proteins with membranes is central to all living systems and we reasoned that the membrane-binding domains in microbial proteins could be developed into efficient antimicrobials. This is an interesting approach as self-like sequences could elude the microbial strategies of degrading the antimicrobial peptides, one of the mechanisms of showing resistance to antimicrobials. We selected the 9-residue-long membrane-binding region of E. coli MreB protein. The 9-residue peptide (C-terminal amide) and its N-terminal acetylated analog displayed broad-spectrum activity, killing Gram-negative bacteria, Gram-positive bacteria, and fungi. Extension with a tryptophan residue at the N-terminus drastically improved the activity of the peptides with lethal concentrations ≤10 μM against all the organisms tested. The tryptophan-extended peptides caused complete killing of C. albicans as well as gentamicin and methicillin resistant S. aureus at 5 μM concentration. Lipid-binding studies and electron microscopic analyses of the peptide-treated microbes suggest membrane disruption as the mechanism of killing.
GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site*

Science.gov (United States)

Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

2015-01-01

K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4BWT-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4BWT-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. PMID:26453300
Mitochondrial DNA control region variability in wild boars from west Balkans

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Đan Mihajla

2013-01-01

Full Text Available The wild boar (Sus scrofa is one of most abundant game species in hunting areas of Balkan region. The large fraction of pre-glacial genetic diversity in wild boar populations from the Balkans was addressed due to high proportion of unique mtDNA haplotypes found in Greece, indicating Balkan as main refugial area for wild boars. The aim of the present study is to characterize mitochondrial DNA control region variability in wild boars from different areas in the West Balkan region, in order to evaluate level of genetic variability, to detect unique haplotypes and to infer possible structuring. The total number of 163 individuals from different sampling localities were included in the study. A fragment of the mtDNA control region was amplified and sequenced by standard procedures. Population genetic analyses were performed using several computer packages: BioEdit, ARLEQUIN 3.5.1.2., Network 4.6.0.0 and MEGA5. Eleven different haplotypes were identified and haplotype diversity was 0.676, nucleotide diversity 0.0026, and the average number of nucleotide differences (k 1.169. The mismatch distribution and neutrality tests indicated the expansion of the all populations. It is shown that high level of genetic diversity is present in the wild boars from the West Balkan region and we have managed to detect regional unique haplotypes in high frequency. Genetic diversity differences have been found in regional wild boar groups, clustering them in two main clusters, but further speculations on the reasons for the observed clustering are prevented due to restricted informativness of the single locus marker. Obtained knowledge of genetic variation in the wild boar may be relevant for improving knowledge of the phylogeny and phylogeography of the wild boars, but as well as for hunting societies and responsible authorities for the effective control of wild boar populations.
Regional blockade by neuroleptic drugs of in vivo /sup 3/H-spiperone binding in the rat brain. Relation to blockade of apomorphine induced hyperactivity and stereotypies

Energy Technology Data Exchange (ETDEWEB)

Koehler, C; Haglund, L; Oegren, S O; Aengeby, T [Astra Lackemedel AB, Soedertaelje (Sweden). Dept. of Pharmacology

1981-01-01

The regional prevention by neuroleptic drugs of specific in vivo /sup 3/H-spiperone binding was studied in the rat brain. L-sulpiride, thioridazine and clozapine were found to reduce the /sup 3/H-spiperone bindings selectively in the olfactory tubercle, septum, substantia nigra and frontal cortex but not the striatum at dose levels which preferentially block apomorphine (APO) induced hyperactivity. The maximal prevention of specific /sup 3/H-spiperone binding by l-sulpiride and clozapine reached 60-80% in the former structures while the displacement of striatal /sup 3/H-spiperone binding did not exceed 40%. In contrast to l-sulpiride, thioridazine and clozapine both chlorpromazine and haloperidol reduced the /sup 3/H-spiperone binding to the same extent in all regions studied. Chlorpromazine and haloperidol were potent in prevention of striatal /sup 3/H-spiperone binding in vivo which reached 60-80% in this structure.
Sequence variability is correlated with weak immunogenicity in Streptococcus pyogenes M protein

Science.gov (United States)

Lannergård, Jonas; Kristensen, Bodil M; Gustafsson, Mattias C U; Persson, Jenny J; Norrby-Teglund, Anna; Stålhammar-Carlemalm, Margaretha; Lindahl, Gunnar

2015-01-01

The M protein of Streptococcus pyogenes, a major bacterial virulence factor, has an amino-terminal hypervariable region (HVR) that is a target for type-specific protective antibodies. Intriguingly, the HVR elicits a weak antibody response, indicating that it escapes host immunity by two mechanisms, sequence variability and weak immunogenicity. However, the properties influencing the immunogenicity of regions in an M protein remain poorly understood. Here, we studied the antibody response to different regions of the classical M1 and M5 proteins, in which not only the HVR but also the adjacent fibrinogen-binding B repeat region exhibits extensive sequence divergence. Analysis of antisera from S. pyogenes-infected patients, infected mice, and immunized mice showed that both the HVR and the B repeat region elicited weak antibody responses, while the conserved carboxy-terminal part was immunodominant. Thus, we identified a correlation between sequence variability and weak immunogenicity for M protein regions. A potential explanation for the weak immunogenicity was provided by the demonstration that protease digestion selectively eliminated the HVR-B part from whole M protein-expressing bacteria. These data support a coherent model, in which the entire variable HVR-B part evades antibody attack, not only by sequence variability but also by weak immunogenicity resulting from protease attack. PMID:26175306
Effects of mutants in bHLH region on structure stability and protein-DNA binding energy in DECs.

Science.gov (United States)

Kong, Yi; Wang, Zhen; Jia, Yanfei; Li, Ping; Hao, Shuhua; Wang, Yunshan

2017-07-01

The human DEC subfamily contains two highly conserved members belonging to basic helix-loop-helix (bHLH) transcription factors. This conserved family is spread widely among various species with the function of regulating various crucial molecular signaling pathways. Due to the significance of DECs for important biological processes, their relationship with diseases and the lack of experimentally proven structures, we have implemented a comparative modeling for the bHLH region of DECs as homodimers with themselves and heterodimers with HES-1. Three mutants with predicted roles in reducing intramolecular binding (H57A, R65A, and LL7879AA in DEC1 and LL7071AA in DEC2) were investigated on DEC monomers. Molecular dynamics (MD) simulations were also employed to evaluate the behavior of the mutant molecules in aqueous solution. The monomer was divided into subregions for accurate investigation. The fluctuation in the basic region of mutants was higher than that of wild-type molecules. The binding energy value between protein and DNA obviously increased in the homodimer harboring R65A mutants, which led to more unstable status between protein and DNA. Thus, the mutant R65A interfered DNA-binding affinity. A study on the spatial structures of wild-type and mutant DECs may facilitate functional prediction for mutation effects and dynamic behavior under various conditions and may ultimately help in targeted drug design.
Brain serotonin 4 receptor binding is inversely associated with verbal memory recall

DEFF Research Database (Denmark)

Stenbæk, Dea S; Fisher, Patrick M; Ozenne, Brice

2017-01-01

the association between cerebral 5-HT 4R binding and affective verbal memory recall. METHODS: Twenty-four healthy volunteers were scanned with the 5-HT 4R radioligand [11C]SB207145 and positron emission tomography, and were tested with the Verbal Affective Memory Test-24. The association between 5-HT 4R binding...... and affective verbal memory was evaluated using a linear latent variable structural equation model. RESULTS: We observed a significant inverse association across all regions between 5-HT 4R binding and affective verbal memory performances for positive (p = 5.5 × 10-4) and neutral (p = .004) word recall......BACKGROUND: We have previously identified an inverse relationship between cerebral serotonin 4 receptor (5-HT 4R) binding and nonaffective episodic memory in healthy individuals. Here, we investigate in a novel sample if the association is related to affective components of memory, by examining...
Binding affinities of cationic dyes in the presence of activated charcoal and anionic surfactant in the premicellar region

Science.gov (United States)

Ali, Farman; Ibrahim, Muhammad; Khan, Fawad; Bibi, Iram; Shah, Syed W. H.

2018-03-01

Binding preferences of cationic dyes malachite green and methylene blue in a mixed charcoal-sodium dodecyl sulfate system have been investigated using UV-visible absorption spectroscopy. The dye adsorption shows surfactant-dependent patterns, indicating diverse modes of interactions. At low surfactant concentration, a direct binding to charcoal is preferred. Comparatively greater quantities of surfactant lead to attachment of dye-surfactant complex to charcoal through hydrophobic interactions. A simple model was employed for determination of equilibrium constant K eq and concentration of dye-surfactant ion pair N DS for both dyes. The values of binding parameters revealed that malachite green was directly adsorbed onto charcoal, whereas methylene blue was bound through surfactant monomers. The model is valid for low surfactant concentrations in the premicellar region. These findings have significance for material and environmental sciences.
Proteomics shows Hsp70 does not bind peptide sequences indiscriminately in vivo

International Nuclear Information System (INIS)

Grossmann, Michael E.; Madden, Benjamin J.; Gao, Fan; Pang, Yuan-Ping; Carpenter, John E.; McCormick, Daniel; Young, Charles Y.F.

2004-01-01

Heat shock protein 70 (Hsp70) binds peptide and has several functions that include protein folding, protein trafficking, and involvement with immune function. However, endogenous Hsp70-binding peptides had not previously been identified. Therefore, we eluted and identified several hundred endogenously bound peptides from Hsp70 using liquid chromatography ion trap mass spectrophotometry (LC-ITMS). Our work shows that the peptides are capable of binding Hsp70 as previously described. They are generally 8-26 amino acids in length and correspond to specific regions of many proteins. Through computationally assisted analysis of peptides eluted from Hsp70 we determined variable amino acid sequences, including a 5 amino acid core sequence that Hsp70 favorably binds. We also developed a computer algorithm that predicts Hsp70 binding within proteins. This work helps to define what peptides are bound by Hsp70 in vivo and suggests that Hsp70 facilitates peptide selection by aiding a funneling mechanism that is flexible but allows only a limited number of peptides to be processed
Crystal structures of the ligand-binding region of uPARAP

DEFF Research Database (Denmark)

Yuan, Cai; Jürgensen, Henrik J; Engelholm, Lars H

2016-01-01

The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix...... remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain....... These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other...
Regional in vivo binding of (/sup 3/H)N-propylnorapomorphine in the mouse brain. Evidence for labelling of central dopamine receptors

Energy Technology Data Exchange (ETDEWEB)

Koehler, C; Fuxe, K; Ross, S B [Astra Pharmaceuticals AB, Soedertaelje (Sweden)

1981-07-10

Tail vein injections of (/sup 3/H)N-propylnorapomorphine ((/sup 3/H)NPA) in male mice resulted in a dose-related accumulation of radioactivity in the following brain regions: striatum (max), olfactory tubercle and cerebellum (min). The specific binding was saturable with increasing concentrations of the drug and stereospecifically displaced by (+)butaclamol. Dopamine agonists (apomorphine, NPA and bromocriptine) and antagonists (spiperone, haloperidol, (+)butaclamol and l-sulpiride) all caused dose-dependent prevention of (/sup 3/H)NPA binding. Mianserin, phenoxybenzamine and propranolol did not prevent the in vivo (/sup 3/H)NPA binding suggesting that (/sup 3/H)NPA binds specifically to dopamine receptors in the striatum and the olfactory tubercle of the mouse.
Capturing subregional variability in regional-scale climate change vulnerability assessments of natural resources

Science.gov (United States)

Polly C. Buotte; David L. Peterson; Kevin S. McKelvey; Jeffrey A. Hicke

2016-01-01

Natural resource vulnerability to climate change can depend on the climatology and ecological conditions at a particular site. Here we present a conceptual framework for incorporating spatial variability in natural resource vulnerability to climate change in a regional-scale assessment. The framework was implemented in the first regional-scale vulnerability...
Characterization of Staphylococcus aureus Primosomal DnaD Protein: Highly Conserved C-Terminal Region Is Crucial for ssDNA and PriA Helicase Binding but Not for DnaA Protein-Binding and Self-Tetramerization.

Directory of Open Access Journals (Sweden)

Yen-Hua Huang

Full Text Available The role of DnaD in the recruitment of replicative helicase has been identified. However, knowledge of the DNA, PriA, and DnaA binding mechanism of this protein for the DnaA- and PriA-directed replication primosome assemblies is limited. We characterized the DNA-binding properties of DnaD from Staphylococcus aureus (SaDnaD and analyzed its interactions with SaPriA and SaDnaA. The gel filtration chromatography analysis of purified SaDnaD and its deletion mutant proteins (SaDnaD1-195, SaDnaD1-200 and SaDnaD1-204 showed a stable tetramer in solution. This finding indicates that the C-terminal region aa 196-228 is not crucial for SaDnaD oligomerization. SaDnaD forms distinct complexes with ssDNA of different lengths. In fluorescence titrations, SaDnaD bound to ssDNA with a binding-site size of approximately 32 nt. A stable complex of SaDnaD1-195, SaDnaD1-200, and SaDnaD1-204 with ssDNA dT40 was undetectable, indicating that the C-terminal region of SaDnaD (particularly aa 205-228 is crucial for ssDNA binding. The SPR results revealed that SaDnaD1-195 can interact with SaDnaA but not with SaPriA, which may indicate that DnaD has different binding sites for PriA and DnaA. Both SaDnaD and SaDnaDY176A mutant proteins, but not SaDnaD1-195, can significantly stimulate the ATPase activity of SaPriA. Hence, the stimulation effect mainly resulted from direct contact within the protein-protein interaction, not via the DNA-protein interaction. Kinetic studies revealed that the SaDnaD-SaPriA interaction increases the Vmax of the SaPriA ATPase fivefold without significantly affecting the Km. These results indicate that the conserved C-terminal region is crucial for ssDNA and PriA helicase binding, but not for DnaA protein-binding and self-tetramerization.
Characterization of the dextran-binding domain in the glucan-binding protein C of Streptococcus mutans.

Science.gov (United States)

Takashima, Y; Fujita, K; Ardin, A C; Nagayama, K; Nomura, R; Nakano, K; Matsumoto-Nakano, M

2015-10-01

Streptococcus mutans produces multiple glucan-binding proteins (Gbps), among which GbpC encoded by the gbpC gene is known to be a cell-surface-associated protein involved in dextran-induced aggregation. The purpose of the present study was to characterize the dextran-binding domain of GbpC using bioinformatics analysis and molecular techniques. Bioinformatics analysis specified five possible regions containing molecular binding sites termed GB1 through GB5. Next, truncated recombinant GbpC (rGbpC) encoding each region was produced using a protein expression vector and five deletion mutant strains were generated, termed CDGB1 through CDGB5 respectively. The dextran-binding rates of truncated rGbpC that included the GB1, GB3, GB4 and GB5 regions in the upstream sequences were higher than that of the construct containing GB2 in the downstream region. In addition, the rates of dextran-binding for strains CDGB4 and CD1, which was entire gbpC deletion mutant, were significantly lower than for the other strains, while those of all other deletion mutants were quite similar to that of the parental strain MT8148. Biofilm structures formed by CDGB4 and CD1 were not as pronounced as that of MT8148, while those formed by other strains had greater density as compared to that of CD1. Our results suggest that the dextran-binding domain may be located in the GB4 region in the interior of the gbpC gene. Bioinformatics analysis is useful for determination of functional domains in many bacterial species. © 2015 The Society for Applied Microbiology.
Systemic injection of kainic acid: Gliosis in olfactory and limbic brain regions quantified with [3H]PK 11195 binding autoradiography

International Nuclear Information System (INIS)

Altar, C.A.; Baudry, M.

1990-01-01

Neurodegenerative diseases may result from excessive stimulation of excitatory amino acid receptors by endogenous ligands. Because neuronal degeneration is associated with glial proliferation and hypertrophy, the degenerative changes throughout rat brain following the systemic administration of kainic acid (12 mg/kg) were mapped with quantitative autoradiography of [3H]PK 11195. This radioligand binds to a mitochondrial benzodiazepine binding site (MBBS) on microglia and astrocytes. Analysis of eight horizontal and four coronal brain levels revealed up to 16-fold increases in [3H]PK 11195 binding from 1 to 5 weeks but not 1 day after kainate injection. Increases in [3H]PK 11195 binding were predominantly in ventral limbic brain regions and olfactory projections to neocortical areas, with the olfactory cortex greater than subiculum/CA1 greater than anterior olfactory nucleus, medial thalamic nucleus, and piriform cortex greater than cingulate cortex and rostral hippocampus greater than dentate gyrus, septum, and amygdala greater than entorhinal cortex and temporal cortex. Little or no enhancement of [3H]PK 11195 binding was observed in numerous regions including the caudate-putamen, substantia nigra, nucleus accumbens, olfactory tubercle, cerebellum, thalamic nuclei, choroid plexus, medulla, parietal or occipital cortex, or pons. A 2-fold greater extent of neurodegeneration was obtained in ventral portions of the olfactory bulb, entorhinal cortex, temporal cortex, and dentate gyrus compared with the dorsal portions of these structures. The pattern of increase in [3H]PK 11195 binding closely matched the patterns of neuronal degeneration reported following parenteral kainate injection. These findings strengthen the notion that quantitative autoradiography of [3H]PK 11195 is a valuable tool to quantify the extent of neuronal degeneration
Climate Drivers of Spatiotemporal Variability of Precipitation in the Source Region of Yangtze River

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Du, Y.; Berndtsson, R.; An, D.; Yuan, F.

2017-12-01

Variability of precipitation regime has significant influence on the environment sustainability in the source region of Yangtze River, especially when the vegetation degradation and biodiversity reduction have already occurred. Understanding the linkage between variability of local precipitation and global teleconnection patterns is essential for water resources management. Based on physical reasoning, indices of the climate drivers can provide a practical way of predicting precipitation. Due to high seasonal variability of precipitation, climate drivers of the seasonal precipitation also varies. However, few reports have gone through the teleconnections between large scale patterns with seasonal precipitation in the source region of Yangtze River. The objectives of this study are therefore (1) assessment of temporal trend and spatial variability of precipitation in the source region of Yangtze River; (2) identification of climate indices with strong influence on seasonal precipitation anomalies; (3) prediction of seasonal precipitation based on revealed climate indices. Principal component analysis and Spearman rank correlation were used to detect significant relationships. A feed-forward artificial neural network(ANN) was developed to predict seasonal precipitation using significant correlated climate indices. Different influencing climate indices were revealed for precipitation in each season, with significant level and lag times. Significant influencing factors were selected to be the predictors for ANN model. With correlation coefficients between observed and simulated precipitation over 0.5, the results were eligible to predict the precipitation of spring, summer and winter using teleconnections, which can improve integrated water resources management in the source region of Yangtze River.
Improving preparedness of farmers to Climate Variability: A case study of Vidarbha region of Maharashtra, India

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Swami, D.; Parthasarathy, D.; Dave, P.

2016-12-01

A key objective of the ongoing research is to understand the risk and vulnerability of agriculture and farming communities with respect to multiple climate change attributes, particularly monsoon variability and hydrology such as ground water availability. Climate Variability has always been a feature affecting Indian agriculture but the nature and characteristics of this variability is not well understood. Indian monsoon patterns are highly variable and most of the studies focus on larger domain such as Central India or Western coast (Ghosh et al., 2009) but district level analysis is missing i.e. the linkage between agriculture and climate variables at finer scale has not been investigated comprehensively. For example, Eastern Vidarbha region in Maharashtra is considered as one of the most agriculturally sensitive region in India, where every year a large number of farmers commit suicide. The main reasons for large number of suicides are climate related stressors such as droughts, hail storms, and monsoon variability aggravated with poor socio-economic conditions. Present study has tried to explore the areas in Vidarbha region of Maharashtra where famers and crop productivity, specifically cotton, sorghum, is highly vulnerable to monsoon variability, hydrological and socio-economic variables which are further modelled to determine the maximal contributing factor towards crops and farmers' vulnerability. After analysis using primary and secondary data, it will aid in decision making regarding field operations such as time of sowing, harvesting and irrigation requirements by optimizing the cropping pattern with climatic, hydrological and socio-economic variables. It also suggests the adaptation strategies to farmers regarding different types of cropping and water harvesting practices, optimized dates and timings for harvesting, sowing, water and nutrient requirements of particular crops according to the specific region. Primarily along with secondary analysis
The hydrophobic core of twin-arginine signal sequences orchestrates specific binding to Tat-pathway related chaperones.

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Anitha Shanmugham

Full Text Available Redox enzyme maturation proteins (REMPs bind pre-proteins destined for translocation across the bacterial cytoplasmic membrane via the twin-arginine translocation system and enable the enzymatic incorporation of complex cofactors. Most REMPs recognize one specific pre-protein. The recognition site usually resides in the N-terminal signal sequence. REMP binding protects signal peptides against degradation by proteases. REMPs are also believed to prevent binding of immature pre-proteins to the translocon. The main aim of this work was to better understand the interaction between REMPs and substrate signal sequences. Two REMPs were investigated: DmsD (specific for dimethylsulfoxide reductase, DmsA and TorD (specific for trimethylamine N-oxide reductase, TorA. Green fluorescent protein (GFP was genetically fused behind the signal sequences of TorA and DmsA. This ensures native behavior of the respective signal sequence and excludes any effects mediated by the mature domain of the pre-protein. Surface plasmon resonance analysis revealed that these chimeric pre-proteins specifically bind to the cognate REMP. Furthermore, the region of the signal sequence that is responsible for specific binding to the corresponding REMP was identified by creating region-swapped chimeric signal sequences, containing parts of both the TorA and DmsA signal sequences. Surprisingly, specificity is not encoded in the highly variable positively charged N-terminal region of the signal sequence, but in the more similar hydrophobic C-terminal parts. Interestingly, binding of DmsD to its model substrate reduced membrane binding of the pre-protein. This property could link REMP-signal peptide binding to its reported proofreading function.

Analysis of the relation between socioeconomic variables and truck trips in the metropolitan region of Rio de Janeiro

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Beatriz Lagnier Gil Ferreira

2016-04-01

Full Text Available The goal of this paper is to analyze the relation between socioeconomic variables and freight trip generation, regarding the Metropolitan Region of Rio de Janeiro, through the use of linear regression models. A systematic literature review is conducted in order to identify which independent variables could be used in the models. The variables found are mostly related to the establishment, such as number of employees, floor area, number of stores among others; and socioeconomic variables, such as population, households and jobs in the region. The relation between the latter and number of truck trips is verified with linear regression models, and the results show that the models are valid and the variables are able to explain the freight flow in the region studied, contributing to the region’s transport planning and to the strategic planning of companies that operate in the region.
INTRINSIC REGULATION OF HEMOGLOBIN EXPRESSION BY VARIABLE SUBUNIT INTERFACE STRENGTHS

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Manning, James M.; Popowicz, Anthony M.; Padovan, Julio C.; Chait, Brian T.; Manning, Lois R.

2012-01-01

SUMMARY The expression of the six types of human hemoglobin subunits over time is currently considered to be regulated mainly by transcription factors that bind to upstream control regions of the gene (the “extrinsic” component of regulation). Here we describe how subunit pairing and further assembly to tetramers in the liganded state is influenced by the affinity of subunits for one another (the “intrinsic” component of regulation). The adult hemoglobin dimers have the strongest subunit interfaces and the embryonic hemoglobins are the weakest with fetal hemoglobins of intermediate strength, corresponding to the temporal order of their expression. These variable subunit binding strengths and the attenuating effects of acetylation contribute to the differences with which these hemoglobin types form functional O2-binding tetramers consistent with gene switching. PMID:22129306
Two centuries of observed atmospheric variability and change over the North Sea region

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Stendel, Martin; van den Besselaar, Else; Hannachi, Abdel; Kent, Elizabeth; Lefebvre, Christiana; Rosenhagen, Gudrun; Schenk, Frederik; van der Schrier, Gerard; Woollings, Tim

2016-04-01

In the upcoming North Sea Region Climate Change Assessment (NOSCCA), we present a synthesis of current knowledge about past, present and possible future climate change in the North Sea region. A climate change assessment from published scientific work has been conducted as a kind of regional IPCC report, and a book has been produced that will be published by Springer in 2016. In the framework of the NOSCCA project, we examine past and present studies of variability and changes in atmospheric variables within the North Sea region over the instrumental period, roughly the past 200 years, based on observations and reanalyses. The variables addressed in this presentation are large-scale circulation, pressure and wind, surface air temperature, precipitation and radiative properties (clouds, solar radiation, and sunshine duration). While air temperature over land, not unexpectedly, has increased everywhere in the North Sea region, with strongest trends in spring and in the north of the region, a precipitation increase has been observed in the north and a decrease in the south of the region. This pattern goes along with a north-eastward shift of storm tracks and is in agreement with climate model projections under enhanced greenhouse gas concentrations. For other variables, it is not obvious which part of the observed changes may be due to anthropogenic activities and which is internally forced. It remains also unclear to what extent atmospheric circulation over the North Sea region is influenced by distant factors, in particular Arctic sea-ice decline in recent decades. There are indications of an increase in the number of deep cyclones (but not in the total number of cyclones), while storminess since the late 19th century shows no robust trends. The persistence of circulation types appears to have increased over the last century, and consequently, there is an indication for 'more extreme' extreme events. However, changes in extreme weather events are difficult to assess
Reduction in camera-specific variability in [(123)I]FP-CIT SPECT outcome measures by image reconstruction optimized for multisite settings

DEFF Research Database (Denmark)

Buchert, Ralph; Kluge, Andreas; Tossici-Bolt, Livia

2016-01-01

the Southampton method with binding in the whole brain, occipital cortex or cerebellum as the reference. The correlation between SBR and age was used as the primary quality measure. RESULTS: The fraction of SBR variability explained by age was highest (1) with QSPECT, independently of the reference region, and (2...... as the reference provides more stable quantitative estimates than occipital or cerebellar binding....
GTP Binding and Oncogenic Mutations May Attenuate Hypervariable Region (HVR)-Catalytic Domain Interactions in Small GTPase K-Ras4B, Exposing the Effector Binding Site.

Science.gov (United States)

Lu, Shaoyong; Banerjee, Avik; Jang, Hyunbum; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth

2015-11-27

K-Ras4B, a frequently mutated oncogene in cancer, plays an essential role in cell growth, differentiation, and survival. Its C-terminal membrane-associated hypervariable region (HVR) is required for full biological activity. In the active GTP-bound state, the HVR interacts with acidic plasma membrane (PM) headgroups, whereas the farnesyl anchors in the membrane; in the inactive GDP-bound state, the HVR may interact with both the PM and the catalytic domain at the effector binding region, obstructing signaling and nucleotide exchange. Here, using molecular dynamics simulations and NMR, we aim to figure out the effects of nucleotides (GTP and GDP) and frequent (G12C, G12D, G12V, G13D, and Q61H) and infrequent (E37K and R164Q) oncogenic mutations on full-length K-Ras4B. The mutations are away from or directly at the HVR switch I/effector binding site. Our results suggest that full-length wild-type GDP-bound K-Ras4B (K-Ras4B(WT)-GDP) is in an intrinsically autoinhibited state via tight HVR-catalytic domain interactions. The looser association in K-Ras4B(WT)-GTP may release the HVR. Some of the oncogenic mutations weaken the HVR-catalytic domain association in the K-Ras4B-GDP/-GTP bound states, which may facilitate the HVR disassociation in a nucleotide-independent manner, thereby up-regulating oncogenic Ras signaling. Thus, our results suggest that mutations can exert their effects in more than one way, abolishing GTP hydrolysis and facilitating effector binding. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Fine definition of the CXCR4-binding region on the V3 loop of feline immunodeficiency virus surface glycoprotein.

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Qiong-Ying Hu

2010-05-01

Full Text Available The chemokine receptor CXCR4 is shared by primary and laboratory-adapted strains of feline immunodeficiency virus (FIV for viral entry. Our previous studies implicated a contiguous nine-amino-acid region of the V3 loop of the FIV envelope surface as important in CXCR4 binding and virus entry. The binding is specific for CXCR4 since it can be inhibited by AMD3100, a selective CXCR4 inhibitor. Additional site-directed mutagenesis was used to further reveal the key residues. Binding studies indicated that basic residues R395, K397, R399 as well as N398 are critical for CXCR4 binding. The effect of other amino acid residues on receptor binding depends on the type of amino acid residue substituted. The binding study results were confirmed on human CXCR4-expressing SupT1 cells and correlated with entry efficiency using a virus entry assay. Amino acid residues critical for CXCR4 are not critical for interactions with the primary binding receptor CD134, which has an equivalent role as CD4 for HIV-1 binding. The ELISA results show that W394 and W400 are crucial for the recognition by neutralizing anti-V3 antibodies. Since certain strains of HIV-1 also use CXCR4 as the entry receptor, the findings make the feline model attractive for development of broad-based entry antagonists and for study of the molecular mechanism of receptor/virus interactions.
Five of Five VHHs Neutralizing Poliovirus Bind the Receptor-Binding Site.

Science.gov (United States)

Strauss, Mike; Schotte, Lise; Thys, Bert; Filman, David J; Hogle, James M

2016-01-13

Nanobodies, or VHHs, that recognize poliovirus type 1 have previously been selected and characterized as candidates for antiviral agents or reagents for standardization of vaccine quality control. In this study, we present high-resolution cryo-electron microscopy reconstructions of poliovirus with five neutralizing VHHs. All VHHs bind the capsid in the canyon at sites that extensively overlap the poliovirus receptor-binding site. In contrast, the interaction involves a unique (and surprisingly extensive) surface for each of the five VHHs. Five regions of the capsid were found to participate in binding with all five VHHs. Four of these five regions are known to alter during the expansion of the capsid associated with viral entry. Interestingly, binding of one of the VHHs, PVSS21E, resulted in significant changes of the capsid structure and thus seems to trap the virus in an early stage of expansion. We describe the cryo-electron microscopy structures of complexes of five neutralizing VHHs with the Mahoney strain of type 1 poliovirus at resolutions ranging from 3.8 to 6.3Å. All five VHHs bind deep in the virus canyon at similar sites that overlap extensively with the binding site for the receptor (CD155). The binding surfaces on the VHHs are surprisingly extensive, but despite the use of similar binding surfaces on the virus, the binding surface on the VHHs is unique for each VHH. In four of the five complexes, the virus remains essentially unchanged, but for the fifth there are significant changes reminiscent of but smaller in magnitude than the changes associated with cell entry, suggesting that this VHH traps the virus in a previously undescribed early intermediate state. The neutralizing mechanisms of the VHHs and their potential use as quality control agents for the end game of poliovirus eradication are discussed. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Effects of Recent Regional Soil Moisture Variability on Global Net Ecosystem CO2 Exchange

Science.gov (United States)

Jones, L. A.; Madani, N.; Kimball, J. S.; Reichle, R. H.; Colliander, A.

2017-12-01

Soil moisture exerts a major regional control on the inter-annual variability of the global land sink for atmospheric CO2. In semi-arid regions, annual biomass production is closely coupled to variability in soil moisture availability, while in cold-season-affected regions, summer drought offsets the effects of advancing spring phenology. Availability of satellite solar-induced fluorescence (SIF) observations and improvements in atmospheric inversions has led to unprecedented ability to monitor atmospheric sink strength. However, discrepancies still exist between such top-down estimates as atmospheric inversion and bottom-up process and satellite driven models, indicating that relative strength, mechanisms, and interaction of driving factors remain poorly understood. We use soil moisture fields informed by Soil Moisture Active Passive Mission (SMAP) observations to compare recent (2015-2017) and historic (2000-2014) variability in net ecosystem land-atmosphere CO2 exchange (NEE). The operational SMAP Level 4 Carbon (L4C) product relates ground-based flux tower measurements to other bottom-up and global top-down estimates to underlying soil moisture and other driving conditions using data-assimilation-based SMAP Level 4 Soil Moisture (L4SM). Droughts in coastal Brazil, South Africa, Eastern Africa, and an anomalous wet period in Eastern Australia were observed by L4C. A seasonal seesaw pattern of below-normal sink strength at high latitudes relative to slightly above-normal sink strength for mid-latitudes was also observed. Whereas SMAP-based soil moisture is relatively informative for short-term temporal variability, soil moisture biases that vary in space and with season constrain the ability of the L4C estimates to accurately resolve NEE. Such biases might be caused by irrigation and plant-accessible ground-water. Nevertheless, SMAP L4C daily NEE estimates connect top-down estimates to variability of effective driving factors for accurate estimates of regional
Anti-HIV double variable domain immunoglobulins binding both gp41 and gp120 for targeted delivery of immunoconjugates.

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Ryan B Craig

Full Text Available BACKGROUND: Anti-HIV immunoconjugates targeted to the HIV envelope protein may be used to eradicate the latent reservoir of HIV infection using activate-and-purge protocols. Previous studies have identified the two target epitopes most effective for the delivery of cytotoxic immunoconjugates the CD4-binding site of gp120, and the hairpin loop of gp41. Here we construct and test tetravalent double variable domain immunoglobulin molecules (DVD-Igs that bind to both epitopes. METHODS: Synthetic genes that encode DVD-Igs utilizing V-domains derived from human anti-gp120 and anti-gp41 Abs were designed and expressed in 293F cells. A series of constructs tested different inter-V-linker domains and orientations of the two V domains. Antibodies were tested for binding to recombinant Ag and native Env expressed on infected cells, for neutralization of infectious HIV, and for their ability to deliver cytotoxic immunoconjugates to infected cells. FINDINGS: The outer V-domain was the major determinant of binding and functional activity of the DVD-Ig. Function of the inner V-domain and bifunctional binding required at least 15 AA in the inter-V-domain linker. A molecular model showing the spatial orientation of the two epitopes is consistent with this observation. Linkers that incorporated helical domains (A[EAAAK](nA resulted in more effective DVD-Igs than those based solely on flexible domains ([GGGGS](n. In general, the DVD-Igs outperformed the less effective parental antibody and equaled the activity of the more effective. The ability of the DVD-Igs to deliver cytotoxic immunoconjugates in the absence of soluble CD4 was improved over that of either parent. CONCLUSIONS: DVD-Igs can be designed that bind to both gp120 and gp41 on the HIV envelope. DVD-Igs are effective in delivering cytotoxic immunoconjugates. The optimal design of these DVD-Igs, in which both domains are fully functional, has not yet been achieved.
Homologous regions of Fen1 and p21Cip1 compete for binding to the same site on PCNA: a potential mechanism to co-ordinate DNA replication and repair.

Science.gov (United States)

Warbrick, E; Lane, D P; Glover, D M; Cox, L S

1997-05-15

Following genomic damage, the cessation of DNA replication is co-ordinated with onset of DNA repair; this co-ordination is essential to avoid mutation and genomic instability. To investigate these phenomena, we have analysed proteins that interact with PCNA, which is required for both DNA replication and repair. One such protein is p21Cip1, which inhibits DNA replication through its interaction with PCNA, while allowing repair to continue. We have identified an interaction between PCNA and the structure specific nuclease, Fen1, which is involved in DNA replication. Deletion analysis suggests that p21Cip1 and Fen1 bind to the same region of PCNA. Within Fen1 and its homologues a small region (10 amino acids) is sufficient for PCNA binding, which contains an 8 amino acid conserved PCNA-binding motif. This motif shares critical residues with the PCNA-binding region of p21Cip1. A PCNA binding peptide from p21Cip1 competes with Fen1 peptides for binding to PCNA, disrupts the Fen1-PCNA complex in replicating cell extracts, and concomitantly inhibits DNA synthesis. Competition between homologous regions of Fen1 and p21Cip1 for binding to the same site on PCNA may provide a mechanism to co-ordinate the functions of PCNA in DNA replication and repair.
Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region*

Science.gov (United States)

Jang, Hyunbum; Abraham, Sherwin J.; Chavan, Tanmay S.; Hitchinson, Ben; Khavrutskii, Lyuba; Tarasova, Nadya I.; Nussinov, Ruth; Gaponenko, Vadim

2015-01-01

K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling. PMID:25713064
NEAR-INFRARED VARIABILITY AMONG YOUNG STELLAR OBJECTS IN THE STAR FORMATION REGION CYGNUS OB7

Energy Technology Data Exchange (ETDEWEB)

Wolk, Scott J.; Rice, Thomas S. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Aspin, Colin [Institute for Astronomy, University of Hawaii at Manoa, 640 North Aohoku Place, Hilo, HI 96720 (United States)

2013-08-20

We present an analysis of near-infrared time-series photometry in J, H, and K bands for about 100 epochs of a 1 Degree-Sign Multiplication-Sign 1 Degree-Sign region of the Lynds 1003/1004 dark cloud in the Cygnus OB7 region. Augmented by data from the Wide-field Infrared Survey Explorer, we identify 96 candidate disk bearing young stellar objects (YSOs) in the region. Of these, 30 are clearly Class I or earlier. Using the Wide-Field Imaging Camera on the United Kingdom Infrared Telescope, we were able to obtain photometry over three observing seasons, with photometric uncertainty better than 0.05 mag down to J Almost-Equal-To 17. We study detailed light curves and color trajectories of {approx}50 of the YSOs in the monitored field. We investigate the variability and periodicity of the YSOs and find the data are consistent with all YSOs being variable in these wavelengths on timescales of a few years. We divide the variability into four observational classes: (1) stars with periodic variability stable over long timescales, (2) variables which exhibit short-lived cyclic behavior, (3) long-duration variables, and (4) stochastic variables. Some YSO variability defies simple classification. We can explain much of the observed variability as being due to dynamic and rotational changes in the disk, including an asymmetric or changing blocking fraction, changes to the inner disk hole size, as well as changes to the accretion rate. Overall, we find that the Class I:Class II ratio of the cluster is consistent with an age of <1 Myr, with at least one individual, wildly varying source {approx}100, 000 yr old. We have also discovered a Class II eclipsing binary system with a period of 17.87 days.
Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig proteins.

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Rajeev Raman

Full Text Available BACKGROUND: Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. PRINCIPAL FINDINGS: We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th (Lig A9 and 10(th repeats (Lig A10; and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon. All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm, probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. CONCLUSIONS: We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.
YSOVAR: Mid-infrared variability in the star-forming region Lynds 1688

Energy Technology Data Exchange (ETDEWEB)

Günther, H. M.; Poppenhaeger, K.; Wolk, S. J.; Hora, J. L. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Cody, A. M. [Spitzer Science Center, California Institute of Technology, Pasadena, CA 91125 (United States); Covey, K. R. [Lowell Observatory, 1400 West Mars Hill Road, Flagstaff, AZ 86001 (United States); Hillenbrand, L. A. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Plavchan, P. [NASA Exoplanet Science Institute, California Institute of Technology, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Rebull, L. M.; Stauffer, J. R. [Spitzer Science Center/Caltech, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Allen, L. [National Optical Astronomy Observatories, Tucson, AZ 85719 (United States); Bayo, A. [Max Planck Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg (Germany); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Meng, H. Y. A. [Infrared Processing and Analysis Center, California Institute of Technology, MC 100-22, 770 South Wilson Avenue, Pasadena, CA 91125 (United States); Morales-Calderón, M. [Centro de Astrobiología (INTA-CSIC), ESAC Campus, P.O. Box 78, E-28691 Villanueva de la Canada (Spain); Parks, J. R. [Department of Physics and Astronomy, Georgia State University, 25 Park Place South, Atlanta, GA 30303 (United States); Song, Inseok, E-mail: hguenther@cfa.harvard.edu [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States)

2014-12-01

The emission from young stellar objects (YSOs) in the mid-infrared (mid-IR) is dominated by the inner rim of their circumstellar disks. We present IR data from the Young Stellar Object VARiability (YSOVAR) survey of ∼800 objects in the direction of the Lynds 1688 (L1688) star-forming region over four visibility windows spanning 1.6 yr using the Spitzer Space Telescope in its warm mission phase. Among all light curves, 57 sources are cluster members identified based on their spectral energy distribution and X-ray emission. Almost all cluster members show significant variability. The amplitude of the variability is larger in more embedded YSOs. Ten out of 57 cluster members have periodic variations in the light curves with periods typically between three and seven days, but even for those sources, significant variability in addition to the periodic signal can be seen. No period is stable over 1.6 yr. Nonperiodic light curves often still show a preferred timescale of variability that is longer for more embedded sources. About half of all sources exhibit redder colors in a fainter state. This is compatible with time-variable absorption toward the YSO. The other half becomes bluer when fainter. These colors can only be explained with significant changes in the structure of the inner disk. No relation between mid-IR variability and stellar effective temperature or X-ray spectrum is found.
Hydroclimatic variability in the Lake Mondsee region and its relationships with large-scale climate anomaly patterns

Science.gov (United States)

Rimbu, Norel; Ionita, Monica; Swierczynski, Tina; Brauer, Achim; Kämpf, Lucas; Czymzik, Markus

2017-04-01

Flood triggered detrital layers in varved sediments of Lake Mondsee, located at the northern fringe of the European Alps (47°48'N,13°23'E), provide an important archive of regional hydroclimatic variability during the mid- to late Holocene. To improve the interpretation of the flood layer record in terms of large-scale climate variability, we investigate the relationships between observational hydrological records from the region, like the Mondsee lake level, the runoff of the lake's main inflow Griesler Ache, with observed precipitation and global climate patterns. The lake level shows a strong positive linear trend during the observational period in all seasons. Additionally, lake level presents important interannual to multidecadal variations. These variations are associated with distinct seasonal atmospheric circulation patterns. A pronounced anomalous anticyclonic center over the Iberian Peninsula is associated with high lake levels values during winter. This center moves southwestward during spring, summer and autumn. In the same time, a cyclonic anomaly center is recorded over central and western Europe. This anomalous circulation extends southwestward from winter to autumn. Similar atmospheric circulation patterns are associated with river runoff and precipitation variability from the region. High lake levels are associated with positive local precipitation anomalies in all seasons as well as with negative local temperature anomalies during spring, summer and autumn. A correlation analysis reveals that lake level, runoff and precipitation variability is related to large-scale sea surface temperature anomaly patterns in all seasons suggesting a possible impact of large-scale climatic modes, like the North Atlantic Oscillation and Atlantic Multidecadal Oscillation on hydroclimatic variability in the Lake Mondsee region. The results presented in this study can be used for a more robust interpretation of the long flood layer record from Lake Mondsee sediments
AHM1, a Novel Type of Nuclear Matrix–Localized, MAR Binding Protein with a Single AT Hook and a J Domain–Homologous Region

Science.gov (United States)

Morisawa, Gaku; Han-yama, Atsushi; Moda, Ichiro; Tamai, Atsushi; Iwabuchi, Masaki; Meshi, Tetsuo

2000-01-01

Interactions between the nuclear matrix and special regions of chromosomal DNA called matrix attachment regions (MARs) have been implicated in various nuclear functions. We have identified a novel protein from wheat, AT hook–containing MAR binding protein1 (AHM1), that binds preferentially to MARs. A multidomain protein, AHM1 has the special combination of a J domain–homologous region and a Zn finger–like motif (a J-Z array) and an AT hook. For MAR binding, the AT hook at the C terminus was essential, and an internal portion containing the Zn finger–like motif was additionally required in vivo. AHM1 was found in the nuclear matrix fraction and was localized in the nucleoplasm. AHM1 fused to green fluorescent protein had a speckled distribution pattern inside the nucleus. AHM1 is most likely a nuclear matrix component that functions between intranuclear framework and MARs. J-Z arrays can be found in a group of (hypothetical) proteins in plants, which may share some functions, presumably to recruit specific Hsp70 partners as co-chaperones. PMID:11041885
Sequence variability is correlated with weak immunogenicity in Streptococcus pyogenes M protein.

Science.gov (United States)

Lannergård, Jonas; Kristensen, Bodil M; Gustafsson, Mattias C U; Persson, Jenny J; Norrby-Teglund, Anna; Stålhammar-Carlemalm, Margaretha; Lindahl, Gunnar

2015-10-01

The M protein of Streptococcus pyogenes, a major bacterial virulence factor, has an amino-terminal hypervariable region (HVR) that is a target for type-specific protective antibodies. Intriguingly, the HVR elicits a weak antibody response, indicating that it escapes host immunity by two mechanisms, sequence variability and weak immunogenicity. However, the properties influencing the immunogenicity of regions in an M protein remain poorly understood. Here, we studied the antibody response to different regions of the classical M1 and M5 proteins, in which not only the HVR but also the adjacent fibrinogen-binding B repeat region exhibits extensive sequence divergence. Analysis of antisera from S. pyogenes-infected patients, infected mice, and immunized mice showed that both the HVR and the B repeat region elicited weak antibody responses, while the conserved carboxy-terminal part was immunodominant. Thus, we identified a correlation between sequence variability and weak immunogenicity for M protein regions. A potential explanation for the weak immunogenicity was provided by the demonstration that protease digestion selectively eliminated the HVR-B part from whole M protein-expressing bacteria. These data support a coherent model, in which the entire variable HVR-B part evades antibody attack, not only by sequence variability but also by weak immunogenicity resulting from protease attack. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
The Tokar Gap Jet: Regional Circulation, Diurnal Variability, and Moisture Transport Based on Numerical Simulations

KAUST Repository

Davis, Shannon R.; Pratt, Lawrence J.; Jiang, Houshuo

2015-01-01

The structure, variability, and regional connectivity of the Tokar Gap jet (TGJ) are described using WRF Model analyses and supporting atmospheric datasets from the East African–Red Sea–Arabian Peninsula (EARSAP) region during summer 2008. Sources
Characterization of the Deep Water Surface Wave Variability in the California Current Region

Science.gov (United States)

Villas Bôas, Ana B.; Gille, Sarah T.; Mazloff, Matthew R.; Cornuelle, Bruce D.

2017-11-01

Surface waves are crucial for the dynamics of the upper ocean not only because they mediate exchanges of momentum, heat, energy, and gases between the ocean and the atmosphere, but also because they determine the sea state. The surface wave field in a given region is set by the combination of local and remote forcing. The present work characterizes the seasonal variability of the deep water surface wave field in the California Current region, as retrieved from over two decades of satellite altimetry data combined with wave buoys and wave model hindcast (WaveWatch III). In particular, the extent to which the local wind modulates the variability of the significant wave height, peak period, and peak direction is assessed. During spring/summer, regional-scale wind events of up to 10 m/s are the dominant forcing for waves off the California coast, leading to relatively short-period waves (8-10 s) that come predominantly from the north-northwest. The wave climatology throughout the California Current region shows average significant wave heights exceeding 2 m during most of the year, which may have implications for the planning and retrieval methods of the Surface Water and Ocean Topography (SWOT) satellite mission.
Variability and change of sea level and its components in the Indo-Pacific region during the altimetry era

Science.gov (United States)

Wu, Quran; Zhang, Xuebin; Church, John A.; Hu, Jianyu

2017-03-01

Previous studies have shown that regional sea level exhibits interannual and decadal variations associated with the modes of climate variability. A better understanding of those low-frequency sea level variations benefits the detection and attribution of climate change signals. Nonetheless, the contributions of thermosteric, halosteric, and mass sea level components to sea level variability and trend patterns remain unclear. By focusing on signals associated with dominant climate modes in the Indo-Pacific region, we estimate the interannual and decadal fingerprints and trend of each sea level component utilizing a multivariate linear regression of two adjoint-based ocean reanalyses. Sea level interannual, decadal, and trend patterns primarily come from thermosteric sea level (TSSL). Halosteric sea level (HSSL) is of regional importance in the Pacific Ocean on decadal time scale and dominates sea level trends in the northeast subtropical Pacific. The compensation between TSSL and HSSL is identified in their decadal variability and trends. The interannual and decadal variability of temperature generally peak at subsurface around 100 m but that of salinity tend to be surface-intensified. Decadal temperature and salinity signals extend deeper into the ocean in some regions than their interannual equivalents. Mass sea level (MassSL) is critical for the interannual and decadal variability of sea level over shelf seas. Inconsistencies exist in MassSL trend patterns among various estimates. This study highlights regions where multiple processes work together to control sea level variability and change. Further work is required to better understand the interaction of different processes in those regions.

Optical photometric variable stars towards the Galactic H II region NGC 2282

Science.gov (United States)

Dutta, Somnath; Mondal, Soumen; Joshi, Santosh; Jose, Jessy; Das, Ramkrishna; Ghosh, Supriyo

2018-05-01

We report here CCD I-band time series photometry of a young (2-5 Myr) cluster NGC 2282, in order to identify and understand the variability of pre-main-sequence (PMS) stars. The I-band photometry, down to ˜20.5 mag, enables us to probe the variability towards the lower mass end (˜0.1 M⊙) of PMS stars. From the light curves of 1627 stars, we identified 62 new photometric variable candidates. Their association with the region was established from H α emission and infrared (IR) excess. Among 62 variables, 30 young variables exhibit H α emission, near-IR (NIR)/mid-IR (MIR) excess or both and are candidate members of the cluster. Out of 62 variables, 41 are periodic variables, with a rotation rate ranging from 0.2-7 d. The period distribution exhibits a median period at ˜1 d, as in many young clusters (e.g. NGC 2264, ONC, etc.), but it follows a unimodal distribution, unlike others that have bimodality, with slow rotators peaking at ˜6-8 d. To investigate the rotation-disc and variability-disc connection, we derived the NIR excess from Δ(I - K) and the MIR excess from Spitzer [3.6]-[4.5] μm data. No conclusive evidence of slow rotation with the presence of discs around stars and fast rotation for discless stars is obtained from our periodic variables. A clear increasing trend of the variability amplitude with IR excess is found for all variables.
Regions of variability for a class of analytic and locally univalent ...

Indian Academy of Sciences (India)

f ′′(0) whenever f varies over the class C(A,B). Keywords. Janowski class; univalent functions; variability regions. 2000 Mathematics Subject Classification. 30C45. 1. Introduction and preliminary results. Let C be the complex plane. We use the following notations for open and closed discs with center c and radius r in the ...
Interannual variability in the extent of wetland-stream connectivity within the Prairie Pothole Region

Science.gov (United States)

Melanie Vanderhoof; Laurie Alexander

2016-01-01

The degree of hydrological connectivity between wetland systems and downstreamÂ receiving waters can be expected to influence the volume and variability of stream discharge.Â The Prairie Pothole Region contains a high density of depressional wetland features, aÂ consequence of glacial retreat. Spatial variability in wetland density, drainage evolution,Â and precipitation...
Conserved Binding Regions Provide the Clue for Peptide-Based Vaccine Development: A Chemical Perspective

Directory of Open Access Journals (Sweden)

Hernando Curtidor

2017-12-01

Full Text Available Synthetic peptides have become invaluable biomedical research and medicinal chemistry tools for studying functional roles, i.e., binding or proteolytic activity, naturally-occurring regions’ immunogenicity in proteins and developing therapeutic agents and vaccines. Synthetic peptides can mimic protein sites; their structure and function can be easily modulated by specific amino acid replacement. They have major advantages, i.e., they are cheap, easily-produced and chemically stable, lack infectious and secondary adverse reactions and can induce immune responses via T- and B-cell epitopes. Our group has previously shown that using synthetic peptides and adopting a functional approach has led to identifying Plasmodium falciparum conserved regions binding to host cells. Conserved high activity binding peptides’ (cHABPs physicochemical, structural and immunological characteristics have been taken into account for properly modifying and converting them into highly immunogenic, protection-inducing peptides (mHABPs in the experimental Aotus monkey model. This article describes stereo–electron and topochemical characteristics regarding major histocompatibility complex (MHC-mHABP-T-cell receptor (TCR complex formation. Some mHABPs in this complex inducing long-lasting, protective immunity have been named immune protection-inducing protein structures (IMPIPS, forming the subunit components in chemically synthesized vaccines. This manuscript summarizes this particular field and adds our recent findings concerning intramolecular interactions (H-bonds or π-interactions enabling proper IMPIPS structure as well as the peripheral flanking residues (PFR to stabilize the MHCII-IMPIPS-TCR interaction, aimed at inducing long-lasting, protective immunological memory.
Mechanisms of membrane binding of small GTPase K-Ras4B farnesylated hypervariable region.

Science.gov (United States)

Jang, Hyunbum; Abraham, Sherwin J; Chavan, Tanmay S; Hitchinson, Ben; Khavrutskii, Lyuba; Tarasova, Nadya I; Nussinov, Ruth; Gaponenko, Vadim

2015-04-10

K-Ras4B belongs to a family of small GTPases that regulates cell growth, differentiation and survival. K-ras is frequently mutated in cancer. K-Ras4B association with the plasma membrane through its farnesylated and positively charged C-terminal hypervariable region (HVR) is critical to its oncogenic function. However, the structural mechanisms of membrane association are not fully understood. Here, using confocal microscopy, surface plasmon resonance, and molecular dynamics simulations, we observed that K-Ras4B can be distributed in rigid and loosely packed membrane domains. Its membrane binding domain interaction with phospholipids is driven by membrane fluidity. The farnesyl group spontaneously inserts into the disordered lipid microdomains, whereas the rigid microdomains restrict the farnesyl group penetration. We speculate that the resulting farnesyl protrusion toward the cell interior allows oligomerization of the K-Ras4B membrane binding domain in rigid microdomains. Unlike other Ras isoforms, K-Ras4B HVR contains a single farnesyl modification and positively charged polylysine sequence. The high positive charge not only modulates specific HVR binding to anionic phospholipids but farnesyl membrane orientation. Phosphorylation of Ser-181 prohibits spontaneous farnesyl membrane insertion. The mechanism illuminates the roles of HVR modifications in K-Ras4B targeting microdomains of the plasma membrane and suggests an additional function for HVR in regulation of Ras signaling. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Receptor type I and type II binding regions and the peptidyl-prolyl isomerase site of cyclophilin B are required for enhancement of T-lymphocyte adhesion to fibronectin.

Science.gov (United States)

Carpentier, Mathieu; Allain, Fabrice; Slomianny, Marie-Christine; Durieux, Sandrine; Vanpouille, Christophe; Haendler, Bernard; Spik, Geneviève

2002-04-23

Cyclophilin B (CyPB), a cyclosporin A (CsA) binding protein, interacts with two types of binding sites at the surface of T-lymphocytes. The type I sites correspond to functional receptors involved in endocytosis and the type II sites to sulfated glycosaminoglycans (GAGs). Mutational analysis of CyPB has revealed that W128, which is part of the CsA-binding pocket, is implicated in the binding to the functional type I receptors and that two amino acid clusters located in the N-terminus ensure the binding to GAGs. The peptidyl-prolyl isomerase activity of CyPB is not required for receptor binding. We have recently demonstrated that CyPB enhances adhesion of peripheral blood T-lymphocytes to fibronectin, a component of the extracellular matrix. We intended to identify additional amino acids involved in the binding of CyPB to its functional type I receptor and to determine regions responsible for the stimulation of peripheral blood T-lymphocyte adhesion. We determined that residues R76, G77, K132, D155, and D158 of the calcineurin (CN) interacting region were implicated in the recognition of type I receptor but not of GAGs. We also found that two different changes in the N-terminal extension that abated binding to GAGs prevented adhesion of peripheral blood T-lymphocytes to coated CyPB, whereas abbrogation of the PPIase activity had no effect. On the other hand, the adhesion of peripheral blood T-lymphocytes to coated fibronectin was not stimulated by CyPB mutants devoid of either type I receptor or GAGs binding activity or by mutants of the PPIase site. Altogether, the results demonstrate that different regions of CyPB are involved in peripheral blood T-lymphocyte activation and imply a novel important physiological function for peptidyl-prolyl isomerase activity.
Regional variability of farmer decision making and irrigation water use: insights from a data-scarce region of North India

Science.gov (United States)

O'Keeffe, Jimmy; Buytaert, Wouter; Brozović, Nick; Mijic, Ana

2014-05-01

Over the last fifty years, changes in agriculture brought about by the Green Revolution have transformed India from a famine-prone, drought-susceptible country into the worlds' third largest grain producer and one of the most intensively irrigated parts of the globe. Regionally, cheap energy, subsidised seeds and fertilisers, and in some areas Government purchase guarantees for grain promote the intensification of farming. While this allows farmers to survive, it also aggravates the drain agriculture is having on resources, particularly energy and water. Analysis at a regional scale, however, masks the considerable spatial variability that exists on a more localised level and must be taken into consideration to understand correctly aggregate system response to policy, hydrologic, and climatic change. In this study we present and analyse the results from over 100 farmer interviews conducted in the data-scarce districts of Jalaun and Sitapur on the Gangetic Plains of Uttar Pradesh during the post monsoon period of 2013. Variables such as the volumes and timing of irrigation water applied, sources of water, methods of abstraction and irrigation, and costs incurred are mapped, using qualitative data analysis and GIS. Large differences between the districts emerge, for instance in the region of Jalaun where cheaper canal water is available in addition to groundwater. This has enabled farmers to afford more water efficient technologies such as sprinklers, a practice not found in Sitapur which depends almost exclusively on more expensive diesel pumps. Results are used to delineate the spatial variability in water use practices, along with farmer behaviour and decision making. The primary data are compared with socio-economic information taken from regionally produced statistical abstracts. The combined data are used to identify the main drivers that influence farmer decision-making, which is in turn leading to groundwater overdraught in many parts of North India. Finally
Regulation of CYP3A4 by pregnane X receptor: The role of nuclear receptors competing for response element binding

Energy Technology Data Exchange (ETDEWEB)

Istrate, Monica A., E-mail: monicai@scripps.edu [Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Auerbachstr. 112, D-70376 Stuttgart (Germany); Nussler, Andreas K., E-mail: nuessler@uchir.me.tum.de [Department of Traumatology, Technical University Munich, Ismaningerstr. 22, 81675 Munich (Germany); Eichelbaum, Michel, E-mail: michel.eichelbaum@ikp-stuttgart.de [Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Auerbachstr. 112, D-70376 Stuttgart (Germany); Burk, Oliver, E-mail: oliver.burk@ikp-stuttgart.de [Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany, and University of Tuebingen, Auerbachstr. 112, D-70376 Stuttgart (Germany)

2010-03-19

Induction of the major drug metabolizing enzyme CYP3A4 by xenobiotics contributes to the pronounced interindividual variability of its expression and often results in clinically relevant drug-drug interactions. It is mainly mediated by PXR, which regulates CYP3A4 expression by binding to several specific elements in the 5' upstream regulatory region of the gene. Induction itself shows a marked interindividual variability, whose underlying determinants are only partly understood. In this study, we investigated the role of nuclear receptor binding to PXR response elements in CYP3A4, as a potential non-genetic mechanism contributing to interindividual variability of induction. By in vitro DNA binding experiments, we showed that several nuclear receptors bind efficiently to the proximal promoter ER6 and distal xenobiotic-responsive enhancer module DR3 motifs. TR{alpha}1, TR{beta}1, COUP-TFI, and COUP-TFII further demonstrated dose-dependent repression of PXR-mediated CYP3A4 enhancer/promoter reporter activity in transient transfection in the presence and absence of the PXR inducer rifampin, while VDR showed this effect only in the absence of treatment. By combining functional in vitro characterization with hepatic expression analysis, we predict that TR{alpha}1, TR{beta}1, COUP-TFI, and COUP-TFII show a strong potential for the repression of PXR-mediated activation of CYP3A4 in vivo. In summary, our results demonstrate that nuclear receptor binding to PXR response elements interferes with PXR-mediated expression and induction of CYP3A4 and thereby contributes to the interindividual variability of induction.
Binding-site analysis of opioid receptors using monoclonal anti-idiotypic antibodies

International Nuclear Information System (INIS)

Conroy, W.G.

1988-01-01

Structural relatedness between the variable region of anti-ligand antibodies and opioid binding sites allowed the generation of anti-idiotypic antibodies which recognized opioid receptors. The IgG 3 k antibodies which bound to opioid receptors were obtained when an anti-morphine antiserum was the idiotype. Both antibodies bound to opioid receptors, but only one of these blocked the binding of [ 3 H]naloxone. The antibody which did not inhibit the binding of [ 3 H]naloxone was itself displaced from the receptor by opioid ligands. The unique binding properties displayed by this antibody indicated that anti-idiotypic antibodies are not always a perfect image of the original ligand, and therefore may be more useful than typical ligands as probes for the receptor. An auto-anti-idiotypic technique was successfully used to obtain anti-opioid receptor antibodies. Another IgG 3 k antibody that blocked the binding of [ 3 H]naloxone to rat brain opioid receptors was obtained when a mouse was immunized with naloxone conjugated to bovine serum albumin. These data confirmed that an idiotype-anti-idiotype network which can generate an anti-receptor antibody normally functions when an opioid ligand is introduced into an animal in an immunogenic form
Crystal structure of the botulinum neurotoxin type G binding domain: insight into cell surface binding.

Science.gov (United States)

Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R; Stevens, Raymond C

2010-04-16

Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-A X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent. Copyright (c) 2010. Published by Elsevier Ltd.
Cellular homeoproteins, SATB1 and CDP, bind to the unique region between the human cytomegalovirus UL127 and major immediate-early genes

International Nuclear Information System (INIS)

Lee Jialing; Klase, Zachary; Gao Xiaoqi; Caldwell, Jeremy S.; Stinski, Mark F.; Kashanchi, Fatah; Chao, S.-H.

2007-01-01

An AT-rich region of the human cytomegalovirus (CMV) genome between the UL127 open reading frame and the major immediate-early (MIE) enhancer is referred to as the unique region (UR). It has been shown that the UR represses activation of transcription from the UL127 promoter and functions as a boundary between the divergent UL127 and MIE genes during human CMV infection [Angulo, A., Kerry, D., Huang, H., Borst, E.M., Razinsky, A., Wu, J., Hobom, U., Messerle, M., Ghazal, P., 2000. Identification of a boundary domain adjacent to the potent human cytomegalovirus enhancer that represses transcription of the divergent UL127 promoter. J. Virol. 74 (6), 2826-2839; Lundquist, C.A., Meier, J.L., Stinski, M.F., 1999. A strong negative transcriptional regulatory region between the human cytomegalovirus UL127 gene and the major immediate-early enhancer. J. Virol. 73 (11), 9039-9052]. A putative forkhead box-like (FOX-like) site, AAATCAATATT, was identified in the UR and found to play a key role in repression of the UL127 promoter in recombinant virus-infected cells [Lashmit, P.E., Lundquist, C.A., Meier, J.L., Stinski, M.F., 2004. Cellular repressor inhibits human cytomegalovirus transcription from the UL127 promoter. J. Virol. 78 (10), 5113-5123]. However, the cellular factors which associate with the UR and FOX-like region remain to be determined. We reported previously that pancreatic-duodenal homeobox factor-1 (PDX1) bound to a 45-bp element located within the UR [Chao, S.H., Harada, J.N., Hyndman, F., Gao, X., Nelson, C.G., Chanda, S.K., Caldwell, J.S., 2004. PDX1, a Cellular Homeoprotein, Binds to and Regulates the Activity of Human Cytomegalovirus Immediate Early Promoter. J. Biol. Chem. 279 (16), 16111-16120]. Here we demonstrate that two additional cellular homeoproteins, special AT-rich sequence binding protein 1 (SATB1) and CCAAT displacement protein (CDP), bind to the human CMV UR in vitro and in vivo. Furthermore, CDP is identified as a FOX-like binding protein
Biological sex influences learning strategy preference and muscarinic receptor binding in specific brain regions of prepubertal rats.

Science.gov (United States)

Grissom, Elin M; Hawley, Wayne R; Hodges, Kelly S; Fawcett-Patel, Jessica M; Dohanich, Gary P

2013-04-01

According to the theory of multiple memory systems, specific brain regions interact to determine how the locations of goals are learned when rodents navigate a spatial environment. A number of factors influence the type of strategy used by rodents to remember the location of a given goal in space, including the biological sex of the learner. We recently found that prior to puberty male rats preferred a striatum-dependent stimulus-response strategy over a hippocampus-dependent place strategy when solving a dual-solution task, while age-matched females showed no strategy preference. Because the cholinergic system has been implicated in learning strategy and is known to be sexually dimorphic prior to puberty, we explored the relationship between learning strategy and muscarinic receptor binding in specific brain regions of prepubertal males and female rats. We confirmed our previous finding that at 28 days of age a significantly higher proportion of prepubertal males preferred a stimulus-response learning strategy than a place strategy to solve a dual-solution visible platform water maze task. Equal proportions of prepubertal females preferred stimulus-response or place strategies. Profiles of muscarinic receptor binding as assessed by autoradiography varied according to strategy preference. Regardless of biological sex, prepubertal rats that preferred stimulus-response strategy exhibited lower ratios of muscarinic receptor binding in the hippocampus relative to the dorsolateral striatum compared to rats that preferred place strategy. Importantly, much of the variance in this ratio was related to differences in the ventral hippocampus to a greater extent than the dorsal hippocampus. The ratios of muscarinic receptors in the hippocampus relative to the basolateral amygdala also were lower in rats that preferred stimulus-response strategy over place strategy. Results confirm that learning strategy preference varies with biological sex in prepubertal rats with males
ESA STSE “SST Diurnal Variability: Regional Extend - Implications in Atmospheric Modelling”

DEFF Research Database (Denmark)

Karagali, Ioanna

The diurnal variability of SST, driven by the coincident occurrence of low enough wind and solar heating, has been observed in various regions of the global ocean [4, 5, 6]. Atmospheric, oceanic and climate models are not adequately resolving the daily SST cycle, resulting in biases of the total...
Linking the uncertainty of low frequency variability in tropical forcing in regional climate change

Energy Technology Data Exchange (ETDEWEB)

Forest, Chris E. [Pennsylvania State Univ., University Park, PA (United States). Dept. of Meteorology; Barsugli, Joseph J. [Univ. of Colorado, Boulder, CO (United States). CIRES; Li, Wei [Pennsylvania State Univ., University Park, PA (United States). Dept. of Meteorology

2015-02-20

The project utilizes multiple atmospheric general circulation models (AGCMs) to examine the regional climate sensitivity to tropical sea surface temperature forcing through a series of ensemble experiments. The overall goal for this work is to use the global teleconnection operator (GTO) as a metric to assess the impact of model structural differences on the uncertainties in regional climate variability.
Relationship between Eurasian large-scale patterns and regional climate variability over the Black and Baltic Seas

Energy Technology Data Exchange (ETDEWEB)

Stankunavicius, G.; Pupienis, D. [Vilnius Univ. (Lithuania). Dept. of Hydrology and Climatology; Basharin, D. [National Academy of Science of Ukraine, Sevastopol (Ukraine). Sevastopol Marine Hydrophysical Inst.

2012-11-01

Using a NCEP/NCAR Reanalysis dataset and the empirical orthogonal function (EOF) analysis approach we studied interannual to decadal variabilities of the sea-level air pressure (SLP) and the surface air temperature (SAT) fields over Eurasia during the 2nd part of the 20th century. Our results agree with those of the previous studies, which conclude that Eurasian trends are the result of storm-path changes driven by the interdecadal behaviour of the NAO-like meridional dipole pattern in the Atlantic. On interannual and decadal time scales, significant synchronous correlations between correspondent modes of SAT and SLP EOF patterns were found. This fact suggests that there is a strong and stable Eurasian interrelationship between SAT and SLP large-scale fields which affects the local climate of two sub-regions: the Black and Baltic Seas. The climate variability in these sub-regions was studied in terms of Eurasian large-scale surface-temperature and air-pressure patterns responses. We concluded that the sub-regional climate variability substantially differs over the Black and Baltic Seas, and depends on different Eurasian large-scale patterns. We showed that the Baltic Sea region is influenced by the patterns arising primary from NAO-like meridional dipole, as well as Scandinavian patterns, while the Black Sea's SAT/SLP variability is influenced mainly by the second mode EOF (eastern Atlantic) and large scale tropospheric wave structures. (orig.)
The terroir of vineyards - climatic variability in an Austrian wine-growing region

Science.gov (United States)

Gerersdorfer, T.

2010-09-01

The description of a terroir is a concept in viticulture that relates the sensory attributes of wine to the environmental conditions in which the grapes grow. Many factors are involved including climate, soil, cultivar, human practices and all these factors interact manifold. The study area of Carnuntum is a small wine-growing region in the eastern part of Austria. It is rich of Roman remains which play a major role in tourism and the marketing strategies of the wines as well. An interdisciplinary study on the environmental characteristics particularly with regard to growing conditions of grapes was started in this region. The study is concerned with the description of the physiogeographic properties of the region and with the investigation of the dominating viticultural functions. Grape-vines depend on climatic conditions to a high extent. Compared to other influencing factors like soil, climate plays a significant role. In the framework of this interdisciplinary project climatic variability within the Carnuntum wine-growing region is investigated. On the one hand microclimatic variations are influenced by soil type and by canopy management. On the other hand the variability is a result of the topoclimate (altitude, aspect and slope) and therefore relief is a major terroir factor. Results of microclimatic measurements and variations are presented with focus on the interpretation of the relationship between relief, structure of the vineyards and the climatic conditions within the course of a full year period.
The T alpha 2 nuclear protein binding site from the human T cell receptor alpha enhancer functions as both a T cell-specific transcriptional activator and repressor

OpenAIRE

1990-01-01

T cell-specific expression of the human T cell receptor alpha (TCR- alpha) gene is regulated by the interaction of variable region promoter elements with a transcriptional enhancer that is located 4.5 kb 3' of the TCR-alpha constant region (C alpha) gene segment. The minimal TCR- alpha enhancer is composed of two nuclear protein binding sites, T alpha 1 and T alpha 2, that are both required for the T cell-specific activity of the enhancer. The T alpha 1 binding site contains a consensus cAMP ...
Similarities in transcription factor IIIC subunits that bind to the posterior regions of internal promoters for RNA polymerase III

OpenAIRE

Matsutani Sachiko

2004-01-01

Abstract Background In eukaryotes, RNA polymerase III (RNAP III) transcribes the genes for small RNAs like tRNAs, 5S rRNA, and several viral RNAs, and short interspersed repetitive elements (SINEs). The genes for these RNAs and SINEs have internal promoters that consist of two regions. These two regions are called the A and B blocks. The multisubunit transcription factor TFIIIC is required for transcription initiation of RNAP III; in transcription of tRNAs, the B-block binding subunit of TFII...
Calcium binding to an elastic portion of connectin/titin filaments.

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Tatsumi, R; Maeda, K; Hattori, A; Takahashi, K

2001-01-01

Alpha-connectin/titin-1 exists as an elastic filament that links a thick filament with the Z-disk, keeping thick filaments centered within the sarcomere during force generation. We have shown that the connectin filament has an affinity for calcium ions and its binding site(s) is restricted to the beta-connectin/titin-2 portion. We now report the localization and the characterization of calcium-binding sites on beta-connectin. Purified beta-connectin was digested by trypsin into 1700- and 400-kDa fragments. which were then subjected to fluorescence calcium-binding assays. The 400-kDa fragment possesses calcium-binding activity; the binding constant was 1.0 x 10(7) M(-1) and the molar ratio of bound calcium ions to the 400-kDa fragment reached a maximum of 12 at a free calcium ion concentration of approximately 1.0 microM. Antibodies against the 400-kDa fragment formed a sharp dense stripe at the boundary of the A and the I bands, indicating that the calcium-binding domain constitutes the N-terminal region of beta-connectin, that is, the elastic portion of connectin filaments. Furthermore, we estimated the N-terminal location of beta-connectin of various origins (n = 26). Myofibrils were treated with a solution containing 0.1 mM CaCl2 and 70 microM leupeptin to split connectin filaments into beta-connectin and a subfragment, and chain weights of these polypeptides were estimated according to their mobility in 2% polyacrylamide slab gels. The subfragment exhibited a similar chain weight of 1200+/-33 kDa (mean+/-SD), while alpha- and beta-connectins were variable in size according to their origin. These results suggest that the apparent length of the 1200-kDa subfragment portion is almost constant in all instances, about 0.34 microm at the slack condition, therefore that the C-terminus of the 1200-kDa subfragment, that is, the N-terminus of the calcium-binding domain, is at the N2 line region of parent filaments in situ. Because the secondary structure of the 400-k
Internal and external variability in regional simulations of the Iberian Peninsula climate over the last millennium

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J. J. Gómez-Navarro

2012-01-01

Full Text Available In this study we analyse the role of internal variability in regional climate simulations through a comparison of two regional paleoclimate simulations for the last millennium. They share the same external forcings and model configuration, differing only in the initial condition used to run the driving global model simulation. A comparison of these simulations allows us to study the role of internal variability in climate models at regional scales, and how it affects the long-term evolution of climate variables such as temperature and precipitation. The results indicate that, although temperature is homogeneously sensitive to the effect of external forcings, the evolution of precipitation is more strongly governed by random unpredictable internal dynamics. There are, however, some areas where the role of internal variability is lower than expected, allowing precipitation to respond to the external forcings. In this respect, we explore the underlying physical mechanisms responsible for it. This study identifies areas, depending on the season, in which a direct comparison between model simulations of precipitation and climate reconstructions would be meaningful, but also other areas where good agreement between them should not be expected even if both are perfect.

C-terminal region of MAP7 domain containing protein 3 (MAP7D3 promotes microtubule polymerization by binding at the C-terminal tail of tubulin.

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Saroj Yadav

Full Text Available MAP7 domain containing protein 3 (MAP7D3, a newly identified microtubule associated protein, has been shown to promote microtubule assembly and stability. Its microtubule binding region has been reported to consist of two coiled coil motifs located at the N-terminus. It possesses a MAP7 domain near the C-terminus and belongs to the microtubule associated protein 7 (MAP7 family. The MAP7 domain of MAP7 protein has been shown to bind to kinesin-1; however, the role of MAP7 domain in MAP7D3 remains unknown. Based on the bioinformatics analysis of MAP7D3, we hypothesized that the MAP7 domain of MAP7D3 may have microtubule binding activity. Indeed, we found that MAP7 domain of MAP7D3 bound to microtubules as well as enhanced the assembly of microtubules in vitro. Interestingly, a longer fragment MDCT that contained the MAP7 domain (MD with the C-terminal tail (CT of the protein promoted microtubule polymerization to a greater extent than MD and CT individually. MDCT stabilized microtubules against dilution induced disassembly. MDCT bound to reconstituted microtubules with an apparent dissociation constant of 3.0 ± 0.5 µM. An immunostaining experiment showed that MDCT localized along the length of the preassembled microtubules. Competition experiments with tau indicated that MDCT shares its binding site on microtubules with tau. Further, we present evidence indicating that MDCT binds to the C-terminal tail of tubulin. In addition, MDCT could bind to tubulin in HeLa cell extract. Here, we report a microtubule binding region in the C-terminal region of MAP7D3 that may have a role in regulating microtubule assembly dynamics.
Uncertainties in Future Regional Sea Level Trends: How to Deal with the Internal Climate Variability?

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Becker, M.; Karpytchev, M.; Hu, A.; Deser, C.; Lennartz-Sassinek, S.

2017-12-01

Today, the Climate models (CM) are the main tools for forecasting sea level rise (SLR) at global and regional scales. The CM forecasts are accompanied by inherent uncertainties. Understanding and reducing these uncertainties is becoming a matter of increasing urgency in order to provide robust estimates of SLR impact on coastal societies, which need sustainable choices of climate adaptation strategy. These CM uncertainties are linked to structural model formulation, initial conditions, emission scenario and internal variability. The internal variability is due to complex non-linear interactions within the Earth Climate System and can induce diverse quasi-periodic oscillatory modes and long-term persistences. To quantify the effects of internal variability, most studies used multi-model ensembles or sea level projections from a single model ran with perturbed initial conditions. However, large ensembles are not generally available, or too small, and computationally expensive. In this study, we use a power-law scaling of sea level fluctuations, as observed in many other geophysical signals and natural systems, which can be used to characterize the internal climate variability. From this specific statistical framework, we (1) use the pre-industrial control run of the National Center for Atmospheric Research Community Climate System Model (NCAR-CCSM) to test the robustness of the power-law scaling hypothesis; (2) employ the power-law statistics as a tool for assessing the spread of regional sea level projections due to the internal climate variability for the 21st century NCAR-CCSM; (3) compare the uncertainties in predicted sea level changes obtained from a NCAR-CCSM multi-member ensemble simulations with estimates derived for power-law processes, and (4) explore the sensitivity of spatial patterns of the internal variability and its effects on regional sea level projections.
Switch control pocket inhibitors of p38-MAP kinase. Durable type II inhibitors that do not require binding into the canonical ATP hinge region.

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Ahn, Yu Mi; Clare, Michael; Ensinger, Carol L; Hood, Molly M; Lord, John W; Lu, Wei-Ping; Miller, David F; Patt, William C; Smith, Bryan D; Vogeti, Lakshminarayana; Kaufman, Michael D; Petillo, Peter A; Wise, Scott C; Abendroth, Jan; Chun, Lawrence; Clark, Robin; Feese, Michael; Kim, Hidong; Stewart, Lance; Flynn, Daniel L

2010-10-01

Switch control pocket inhibitors of p38-alpha kinase are described. Durable type II inhibitors were designed which bind to arginines (Arg67 or Arg70) that function as key residues for mediating phospho-threonine 180 dependant conformational fluxing of p38-alpha from an inactive type II state to an active type I state. Binding to Arg70 in particular led to potent inhibitors, exemplified by DP-802, which also exhibited high kinase selectivity. Binding to Arg70 obviated the requirement for binding into the ATP Hinge region. X-ray crystallography revealed that DP-802 and analogs induce an enhanced type II conformation upon binding to either the unphosphorylated or the doubly phosphorylated form of p38-alpha kinase. Copyright © 2010 Elsevier Ltd. All rights reserved.
Regional and landscape-scale variability of Landsat-observed vegetation dynamics in northwest Siberian tundra

International Nuclear Information System (INIS)

Frost, Gerald V; Epstein, Howard E; Walker, Donald A

2014-01-01

Widespread increases in Arctic tundra productivity have been documented for decades using coarse-scale satellite observations, but finer-scale observations indicate that changes have been very uneven, with a high degree of landscape- and regional-scale heterogeneity. Here we analyze time-series of the Normalized Difference Vegetation Index (NDVI) observed by Landsat (1984–2012), to assess landscape- and regional-scale variability of tundra vegetation dynamics in the northwest Siberian Low Arctic, a little-studied region with varied soils, landscape histories, and permafrost attributes. We also estimate spatio-temporal rates of land-cover change associated with expansion of tall alder (Alnus) shrublands, by integrating Landsat time-series with very-high-resolution imagery dating to the mid-1960s. We compiled Landsat time-series for eleven widely-distributed landscapes, and performed linear regression of NDVI values on a per-pixel basis. We found positive net NDVI trends (‘greening’) in nine of eleven landscapes. Net greening occurred in alder shrublands in all landscapes, and strong greening tended to correspond to shrublands that developed since the 1960s. Much of the spatial variability of greening within landscapes was linked to landscape physiography and permafrost attributes, while between-landscape variability largely corresponded to differences in surficial geology. We conclude that continued increases in tundra productivity in the region are likely in upland tundra landscapes with fine-textured, cryoturbated soils; these areas currently tend to support discontinuous vegetation cover, but are highly susceptible to rapid increases in vegetation cover, as well as land-cover changes associated with the development of tall shrublands. (paper)
Tannat grape composition responses to spatial variability of temperature in an Uruguay's coastal wine region

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Fourment, Mercedes; Ferrer, Milka; González-Neves, Gustavo; Barbeau, Gérard; Bonnardot, Valérie; Quénol, Hervé

2017-09-01

Spatial variability of temperature was studied in relation to the berry basic composition and secondary compounds of the Tannat cultivar at harvest from vineyards located in Canelones and Montevideo, the most important wine region of Uruguay. Monitoring of berries and recording of temperature were performed in 10 commercial vineyards of Tannat situated in the southern coastal wine region of the country for three vintages (2012, 2013, and 2014). Results from a multivariate correlation analysis between berry composition and temperature over the three vintages showed that (1) Tannat responses to spatial variability of temperature were different over the vintages, (2) correlations between secondary metabolites and temperature were higher than those between primary metabolites, and (3) correlation values between berry composition and climate variables increased when ripening occurred under dry conditions (below average rainfall). For a particular studied vintage (2013), temperatures explained 82.5% of the spatial variability of the berry composition. Daily thermal amplitude was found to be the most important spatial mode of variability with lower values recorded at plots nearest to the sea and more exposed to La Plata River. The highest levels in secondary compounds were found in berries issued from plots situated as far as 18.3 km from La Plata River. The increasing knowledge of temperature spatial variability and its impact on grape berry composition contributes to providing possible issues to adapt grapevine to climate change.
Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver

DEFF Research Database (Denmark)

Gao, Hui; Fält, Susann; Sandelin, Albin

2007-01-01

We report the genome-wide identification of estrogen receptor alpha (ERalpha)-binding regions in mouse liver using a combination of chromatin immunoprecipitation and tiled microarrays that cover all nonrepetitive sequences in the mouse genome. This analysis identified 5568 ERalpha-binding regions...... genes. The majority of ERalpha-binding regions lie in regions that are evolutionarily conserved between human and mouse. Motif-finding algorithms identified the estrogen response element, and variants thereof, together with binding sites for activator protein 1, basic-helix-loop-helix proteins, ETS...... signaling in mouse liver, by characterizing the first step in this signaling cascade, the binding of ERalpha to DNA in intact chromatin....
Structural determination of functional units of the nucleotide binding domain (NBD94 of the reticulocyte binding protein Py235 of Plasmodium yoelii.

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Ardina Grüber

2010-02-01

Full Text Available Invasion of the red blood cells (RBC by the merozoite of malaria parasites involves a large number of receptor ligand interactions. The reticulocyte binding protein homologue family (RH plays an important role in erythrocyte recognition as well as virulence. Recently, it has been shown that members of RH in addition to receptor binding may also have a role as ATP/ADP sensor. A 94 kDa region named Nucleotide-Binding Domain 94 (NBD94 of Plasmodium yoelii YM, representative of the putative nucleotide binding region of RH, has been demonstrated to bind ATP and ADP selectively. Binding of ATP or ADP induced nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94, and directly impacted on the RBC binding ability of RH.In order to find the smallest structural unit, able to bind nucleotides, and its coupling module, the hinge region, three truncated domains of NBD94 have been generated, termed NBD94(444-547, NBD94(566-663 and NBD94(674-793, respectively. Using fluorescence correlation spectroscopy NBD94(444-547 has been identified to form the smallest nucleotide binding segment, sensitive for ATP and ADP, which became inhibited by 4-Chloro-7-nitrobenzofurazan. The shape of NBD94(444-547 in solution was calculated from small-angle X-ray scattering data, revealing an elongated molecule, comprised of two globular domains, connected by a spiral segment of about 73.1 A in length. The high quality of the constructs, forming the hinge-region, NBD94(566-663 and NBD94(674-793 enabled to determine the first crystallographic and solution structure, respectively. The crystal structure of NBD94(566-663 consists of two helices with 97.8 A and 48.6 A in length, linked by a loop. By comparison, the low resolution structure of NBD94(674-793 in solution represents a chair-like shape with three architectural segments.These structures give the first insight into how nucleotide binding impacts on the overall structure of RH and demonstrates the
Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

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Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

2017-11-23

Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.
Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses

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Zhou Bin

2005-04-01

Full Text Available Abstract Background Flaviviruses, which include Dengue (DV and West Nile (WN, mutate in response to immune system pressure. Identifying escape mutants, variant progeny that replicate in the presence of neutralizing antibodies, is a common way to identify functionally important residues of viral proteins. However, the mutations typically occur at variable positions on the viral surface that are not essential for viral replication. Methods are needed to determine the true targets of the neutralizing antibodies. Results Stereophysicochemical variability plots (SVPs, 3-D images of protein structures colored according to variability, as determined by our PCPMer program, were used to visualize residues conserved in their physical chemical properties (PCPs near escape mutant positions. The analysis showed 1 that escape mutations in the flavivirus envelope protein are variable residues by our criteria and 2 two escape mutants found at the same position in many flaviviruses sit above clusters of conserved residues from different regions of the linear sequence. Conservation patterns in T-cell epitopes in the NS3- protease suggest a similar mechanism of immune system evasion. Conclusion The SVPs add another dimension to structurally defining the binding sites of neutralizing antibodies. They provide a useful aid for determining antigenically important regions and designing vaccines.
Characterization of breakpoint cluster region kinase and SH2-binding activities.

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Afar, D E; Witte, O N

1995-01-01

BCR is an interesting signaling protein, whose cellular function is currently unknown. Its biochemical properties include serine kinase activity, SH2-binding activity, and a GTPase-activating activity. The SH2-binding activity is particularly interesting because it may link BCR to signaling pathways involving SH2-containing molecules. Since tyrosine phosphorylation of BCR has been detected in CML-derived cell lines and since tyrosine-phosphorylated BCR shows increased affinity toward certain SH2 domains, it seems particularly important to further characterize this activity. This chapter described a simple purification scheme for partial purification of BCR, which can be used to assess in vitro kinase and SH2-binding activities.
Regional climate change: Precipitation variability in mountainous part of Bulgaria

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Nikolova Nina

2007-01-01

Full Text Available The aim of paper is to analyze temporal and spatial changes in monthly precipitation as well as extremely dry and wet months in mountainous part of Bulgaria. Study precipitation variability in mountainous part is very important because this part is the region where the rivers take its source from. Extreme values of monthly precipitation are important information for better understanding of the whole variability and trends in precipitation time series. The mean investigated period is 1951-2005 and the reference period is so called temporary climate - 1961- 1990. Extreme dry precipitation months are defined as a month whose monthly precipitation is lower than 10% of gamma distribution in the reference period 1961-1990. Extreme wet months are determined with respect to 90% percentiles of gamma distribution (monthly precipitation is higher than 90%. The result of the research show that in mountainous part of Bulgaria during 1950s and 1960s number of extremely wet months is higher than number of dry months. Decreasing of monthly precipitation is a feature for 1980s. This dry period continues till 2004. The years 2000 makes impression as driest year in high mountains with about 7 extremely dry months. The second dry year is 1993. The negative precipitation anomaly is most clearly determined during last decade at study area. The present research points out that fluctuation of precipitation in mountainous part of Bulgaria are coinciding with regional and global climate trends.
Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

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Endres, Christopher J; Pomper, Martin G [Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Hammoud, Dima A, E-mail: endres@jhmi.edu [Radiology and Imaging Sciences, National Institutes of Health/Clinical Center, Bethesda, MD (United States)

2011-04-21

When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [{sup 11}C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (k{sup r}{sub 2}) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BP{sub ND}). Compared with standard SRTM, either coupling of k{sup r}{sub 2} across regions or constraining k{sup r}{sub 2} to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BP{sub ND} between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining k{sup r}{sub 2} to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the
Number of active transcription factor binding sites is essential for the Hes7 oscillator

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de Angelis Martin

2006-02-01

Full Text Available Abstract Background It is commonly accepted that embryonic segmentation of vertebrates is regulated by a segmentation clock, which is induced by the cycling genes Hes1 and Hes7. Their products form dimers that bind to the regulatory regions and thereby repress the transcription of their own encoding genes. An increase of the half-life of Hes7 protein causes irregular somite formation. This was shown in recent experiments by Hirata et al. In the same work, numerical simulations from a delay differential equations model, originally invented by Lewis, gave additional support. For a longer half-life of the Hes7 protein, these simulations exhibited strongly damped oscillations with, after few periods, severely attenuated the amplitudes. In these simulations, the Hill coefficient, a crucial model parameter, was set to 2 indicating that Hes7 has only one binding site in its promoter. On the other hand, Bessho et al. established three regulatory elements in the promoter region. Results We show that – with the same half life – the delay system is highly sensitive to changes in the Hill coefficient. A small increase changes the qualitative behaviour of the solutions drastically. There is sustained oscillation and hence the model can no longer explain the disruption of the segmentation clock. On the other hand, the Hill coefficient is correlated with the number of active binding sites, and with the way in which dimers bind to them. In this paper, we adopt response functions in order to estimate Hill coefficients for a variable number of active binding sites. It turns out that three active transcription factor binding sites increase the Hill coefficient by at least 20% as compared to one single active site. Conclusion Our findings lead to the following crucial dichotomy: either Hirata's model is correct for the Hes7 oscillator, in which case at most two binding sites are active in its promoter region; or at least three binding sites are active, in which
Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication

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Belhumeur Pierre

2008-11-01

Full Text Available Abstract Background HIV-1 integrase (IN is a key viral enzymatic molecule required for the integration of the viral cDNA into the genome. Additionally, HIV-1 IN has been shown to play important roles in several other steps during the viral life cycle, including reverse transcription, nuclear import and chromatin targeting. Interestingly, previous studies have demonstrated that the expression of HIV-1 IN induces the lethal phenotype in some strains of Saccharomyces cerevisiae. In this study, we performed mutagenic analyses of the C-terminal region of the catalytic core domain of HIV-1 IN in order to delineate the critical amino acid(s and/or motif(s required for the induction of the lethal phenotype in the yeast strain HP16, and to further elucidate the molecular mechanism which causes this phenotype. Results Our study identified three HIV-1 IN mutants, V165A, A179P and KR186,7AA, located in the C-terminal region of the catalytic core domain of IN that do not induce the lethal phenotype in yeast. Chromatin binding assays in yeast and mammalian cells demonstrated that these IN mutants were impaired for the ability to bind chromatin. Additionally, we determined that while these IN mutants failed to interact with LEDGF/p75, they retained the ability to bind Integrase interactor 1. Furthermore, we observed that VSV-G-pseudotyped HIV-1 containing these IN mutants was unable to replicate in the C8166 T cell line and this defect was partially rescued by complementation with the catalytically inactive D64E IN mutant. Conclusion Overall, this study demonstrates that three mutations located in the C-terminal region of the catalytic core domain of HIV-1 IN inhibit the IN-induced lethal phenotype in yeast by inhibiting the binding of IN to the host chromatin. These results demonstrate that the C-terminal region of the catalytic core domain of HIV-1 IN is important for binding to host chromatin and is crucial for both viral replication and the promotion of
Climatological variability in modeling of long-term regional transport and deposition of air pollutants

International Nuclear Information System (INIS)

Shannon, J.D.

1984-01-01

In a growing number of emission policy analyses, regulatory proceedings, and cost/benefit assessments, numerical models of long-range transport and deposition of air pollutants have been exercised to estimate source-receptor (S-R) relationships--for the particular meteorological conditions input to the model. The representativeness of the meteorological conditions, or the variability of the model estimates with climatological input from different years or corresponding seasons from different years, is seldom evaluated. Here, two full years (1980 and 1981) of meteorological data, as well as data from January and July of 1978, are used in the Advanced Statistical Trajectory Regional Air Pollution (ASTRAP) model (Shannon, 1981), one of the eight Memorandum of Intent (MOI) models, to estimate deposition for the S-R matrix combination of eleven source regions and nine receptors used in the MOI reports. (S-R matrices of dimensions 40 by 9 were also examined in the MOI reports.) Improvements in the ASTRAP model and in the emission inventory since the earlier work require recalculation of the two-month 1978 simulation in order for the comparison to isolate the effect of meteorological variability. The source regions are listed, and the receptor regions are provide. For completeness, an additional source region, the western states and provinces, has been added, as well as a total for the 48 contiguous states and 10 provinces. 4 references, 9 tables
Interannual variability of mass transport in the Canary region from LADCP data

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Comas-Rodríguez, Isis; Hernández-Guerra, Alonso; Vélez-Belchí, Pedro; Fraile-Nuez, Eugenio

2010-05-01

The variability of the Canary Current is a widely studied topic regarding its role as eastern boundary of the North Atlantic Subtropical Gyre. The Canary region provides indeed an interesting study area in terms of estimating variability scales of the Subtropical Gyre as well as the water masses dynamics. RAPROCAN (RAdial PROfunda de CANarias - Canary deep hydrographic section) is a project based on the reaching of these goals through the obtaining of hydrographic measures during cruises taking place approximately along 29°N, to the North of the Canary Archipelago, twice a year since 2006. The full depth sampling carried out allows the study of temperature and salinity distribution and the calculation of mass transports across the section. The transport estimates are compared to those obtained from previous measurements and estimates in the region. Therefore, transports and their variability through the last decade are quantified. The most significant advance made to previous works is the use of LADCP (Lowered Acoustic Doppler Current Profiler) data informing the initial geostrophic calculations. Thus, corrections are applied to each geostrophic profile considering the reference velocity obtained from LADCP data. ADCP-referenced transport estimates are obtained, providing a successful comparison between the velocity fields obtained from the hydrographic measures. While this work shows the interannual variability observed in winter since 1997, preliminary results confirm previous hypotheses about the magnitude of the Canary Current. Those results including LADCP data also provide new aspects in the circulation distribution across the Canary Archipelago. Also moored current meter data were taken into account in the up close study of the Current through the Lanzarote Passage. Interesting conclusions were drawn that certify the usefulness of LADCP data in referencing geostrophic calculations, while corroborating the results obtained through this methodology. Hence
Long term precipitation trends and variability within the Mediterranean region

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C. M. Philandras

2011-12-01

Full Text Available In this study, the trends and variability of annual precipitation totals and annual rain days over land within the Mediterranean region are analyzed. Long term ground-based observations concerning, on one hand, monthly precipitation totals (1900–2010 and rain days (1965–2010 from 40 meteorological stations within the Mediterranean region were obtained from the Hellenic National Meteorological Service and the World Climate Data and Monitoring Programme (WCDMP of the World Meteorological Organization. On the other hand, high spatial resolution (0.5° × 0.5° gridded monthly data CRU TS 3.1 were acquired from the Climatic Research Unit, University of East Anglia, for the period 1901–2009. The two datasets were compared by means of trends and variability, while the influence of the North Atlantic Oscillation (NAO in the Mediterranean precipitation was examined. In the process, the climatic changes in the precipitation regime between the period 1961–1990 (reference period and the period 2071–2100 (future climate were presented using climate model simulations (RACMO2.1/KNMI. The future climate projections were based on SRES A1B.

The findings of the analysis showed that statistically significant (95% confidence level negative trends of the annual precipitation totals exist in the majority of Mediterranean regions during the period 1901–2009, with an exception of northern Africa, southern Italy and western Iberian peninsula, where slight positive trends (not statistically significant at 95% CL appear. Concerning the annual number of rain days, a pronounced decrease of 20 %, statistically significant (95% confidence level, appears in representative meteorological stations of east Mediterranean, while the trends are insignificant for west and central Mediterranean. Additionally, NAO index was found to be anticorrelated with the precipitation totals and the number of rain days mainly in Spain, southern France, Italy and Greece. These
Climate change/variability science and adaptive strategies for state and regional transportation decision making.

Science.gov (United States)

2010-04-01

The objective of this study was to generate a baseline understanding of current policy responses to climate : change/variability at the state and regional transportation-planning and -decision levels. Specifically, : researchers were interested in th...
Influence of Climate Variability on US Regional Homicide Rates

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Harp, R. D.; Karnauskas, K. B.

2017-12-01

Recent studies have found consistent evidence of a relationship between temperature and criminal behavior. However, despite agreement in the overall relationship, little progress has been made in distinguishing between two proposed explanatory theories. The General Affective Aggression Model (GAAM) suggests that high temperatures create periods of higher heat stress that enhance individual aggressiveness, whereas the Routine Activities Theory (RAT) theorizes that individuals are more likely to be outdoors interacting with others during periods of pleasant weather with a resulting increase in both interpersonal interactions and victim availability. Further, few studies have considered this relationship within the context of climate change in a quantitative manner. In an effort to distinguish between the two theories, and to examine the statistical relationships on a broader spatial scale than previously, we combined data from the Supplementary Homicide Report (SHR—compiled by the Federal Bureau of Investigation) and the North American Regional Reanalysis (NARR—compiled by the National Centers for Environmental Protection, a branch of the National Oceanic and Atmospheric Administration). US homicide data described by the SHR was compared with seven relevant observed climate variables (temperature, dew point, relative humidity, accumulated precipitation, accumulated snowfall, snow cover, and snow depth) provided by the NARR atmospheric reanalysis. Relationships between homicide rates and climate variables, as well as reveal regional spatial patterns will be presented and discussed, along with the implications due to future climate change. This research lays the groundwork for the refinement of estimates of an oft-overlooked climate change impact, which has previously been estimated to cause an additional 22,000 murders between 2010 and 2099, including providing important constraints for empirical models of future violent crime incidences in the face of global
The egg coat zona pellucida 3 glycoprotein - evolution of its putative sperm-binding region in Old World murine rodents (Rodentia: Muridae).

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Swann, Christine A; Cooper, Steven J B; Breed, William G

2017-11-01

In eutherian mammals, before fertilisation can occur the spermatozoon has to bind to, and penetrate, the egg coat, the zona pellucida (ZP). In the laboratory mouse there is good evidence that the primary sperm-binding site is a protein region encoded by Exon 7 of the ZP3 gene and it has been proposed that binding is species specific and evolves by sexual selection. In the present study we investigate these hypotheses by comparing Exon 6 and 7 sequences of ZP3 in 28 species of murine rodents of eight different divisions from Asia, Africa and Australasia, in which a diverse array of sperm morphologies occurs. We found considerable nucleotide (and corresponding amino acid) sequence divergence in Exon 7, but not in Exon 6, across these species, with evidence for positive selection at five codon positions. This molecular divergence does not appear to be due to reinforcement to reduce hybridisation, nor does it correlate with divergence in sperm head morphology or tail length, thus it is unlikely to be driven by inter-male sperm competition. Other forms of post-copulatory sexual selection therefore appear to have resulted in the molecular divergence of this region of ZP3 in this highly speciose group of mammals.

Complement activating soluble pattern recognition molecules with collagen-like regions, mannan-binding lectin, ficolins and associated proteins

DEFF Research Database (Denmark)

Thiel, Steffen

2007-01-01

Mannan-binding lectin (MBL), L-ficolin, M-ficolin and H-ficolin are all complement activating soluble pattern recognition molecules with recognition domains linked to collagen-like regions. All four may form complexes with four structurally related proteins, the three MBL-associated serine...... proteases (MASPs), MASP-1, MASP-2 and MASP-3, and a smaller MBL-associated protein (MAp19). The four recognition molecules recognize patterns of carbohydrate or acetyl-group containing ligands. After binding to the relevant targets all four are able to activate the complement system. We thus have a system...... where four different and/or overlapping patterns of microbial origin or patterns of altered-self may be recognized, but in all cases the signalling molecules, the MASPs, are shared. MASP-1 and MASP-3 are formed from one gene, MASP1/3, by alternative splicing generating two different mRNAs from a single...
A Conservative Look at Term Deduction Systems with Variable Binding

NARCIS (Netherlands)

Fokkink, W.J.; Verhoef, C.

We set up a formal framework to describe term deduction systems, such as transition system specifications in the style of Plotkin, and conditional term rewriting systems. This framework has the power to express many-sortedness, general binding mechanisms and substitutions, among other notions such
Transcription factor binding sites prediction based on modified nucleosomes.

Directory of Open Access Journals (Sweden)

Mohammad Talebzadeh

Full Text Available In computational methods, position weight matrices (PWMs are commonly applied for transcription factor binding site (TFBS prediction. Although these matrices are more accurate than simple consensus sequences to predict actual binding sites, they usually produce a large number of false positive (FP predictions and so are impoverished sources of information. Several studies have employed additional sources of information such as sequence conservation or the vicinity to transcription start sites to distinguish true binding regions from random ones. Recently, the spatial distribution of modified nucleosomes has been shown to be associated with different promoter architectures. These aligned patterns can facilitate DNA accessibility for transcription factors. We hypothesize that using data from these aligned and periodic patterns can improve the performance of binding region prediction. In this study, we propose two effective features, "modified nucleosomes neighboring" and "modified nucleosomes occupancy", to decrease FP in binding site discovery. Based on these features, we designed a logistic regression classifier which estimates the probability of a region as a TFBS. Our model learned each feature based on Sp1 binding sites on Chromosome 1 and was tested on the other chromosomes in human CD4+T cells. In this work, we investigated 21 histone modifications and found that only 8 out of 21 marks are strongly correlated with transcription factor binding regions. To prove that these features are not specific to Sp1, we combined the logistic regression classifier with the PWM, and created a new model to search TFBSs on the genome. We tested the model using transcription factors MAZ, PU.1 and ELF1 and compared the results to those using only the PWM. The results show that our model can predict Transcription factor binding regions more successfully. The relative simplicity of the model and capability of integrating other features make it a superior method
The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange*

Science.gov (United States)

Fenyk, Stepan; Dixon, Christopher H.; Gittens, William H.; Townsend, Philip D.; Sharples, Gary J.; Pålsson, Lars-Olof; Takken, Frank L. W.; Cann, Martin J.

2016-01-01

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA. PMID:26601946
The Tomato Nucleotide-binding Leucine-rich Repeat Immune Receptor I-2 Couples DNA-binding to Nucleotide-binding Domain Nucleotide Exchange.

Science.gov (United States)

Fenyk, Stepan; Dixon, Christopher H; Gittens, William H; Townsend, Philip D; Sharples, Gary J; Pålsson, Lars-Olof; Takken, Frank L W; Cann, Martin J

2016-01-15

Plant nucleotide-binding leucine-rich repeat (NLR) proteins enable plants to recognize and respond to pathogen attack. Previously, we demonstrated that the Rx1 NLR of potato is able to bind and bend DNA in vitro. DNA binding in situ requires its genuine activation following pathogen perception. However, it is unknown whether other NLR proteins are also able to bind DNA. Nor is it known how DNA binding relates to the ATPase activity intrinsic to NLR switch function required to immune activation. Here we investigate these issues using a recombinant protein corresponding to the N-terminal coiled-coil and nucleotide-binding domain regions of the I-2 NLR of tomato. Wild type I-2 protein bound nucleic acids with a preference of ssDNA ≈ dsDNA > ssRNA, which is distinct from Rx1. I-2 induced bending and melting of DNA. Notably, ATP enhanced DNA binding relative to ADP in the wild type protein, the null P-loop mutant K207R, and the autoactive mutant S233F. DNA binding was found to activate the intrinsic ATPase activity of I-2. Because DNA binding by I-2 was decreased in the presence of ADP when compared with ATP, a cyclic mechanism emerges; activated ATP-associated I-2 binds to DNA, which enhances ATP hydrolysis, releasing ADP-bound I-2 from the DNA. Thus DNA binding is a general property of at least a subset of NLR proteins, and NLR activation is directly linked to its activity at DNA. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Regional specific binding of [11C]RO 15 1788 to central type benzodiazepine receptors in human brain: quantitative evaluation by PET

International Nuclear Information System (INIS)

Pappata, S.; Samson, Y.; Chavoix, C.; Prenant, C.; Maziere, M.; Baron, J.C.

1988-01-01

The central type benzodiazepine receptors were studied in 17 healthy human subjects with 11 C-RO 15 1788 and positron emission tomography (PET). The brain regional distribution of the tracer in eight control studies performed after injection of trace doses of 11 C-RO 15 1788 was consistent with that of benzodiazepine receptors. Saturation studies with co-injected cold RO 15 1788 in the remaining subjects showed a dose-dependent decrease of brain radiotracer until full inhibition of specific binding was achieved with doses above 0.1 mg/kg (four studies). Based on the results, a simple method to estimate the specifically bound 11 C-RO 15 1788 regionally in a single PET study is proposed, using the data from the full-saturation studies as a stable estimate of the nondisplaceable radioligand concentration. Using this method, it was found that quasiequilibrium between the estimated specifically bound and nondisplaceable components was achieved at times equal to or longer than 20 min after tracer administration. The validity of this method was partly supported by further results, showing a good agreement between the regional specific binding so calculated and postmortem data of receptor density
Adaptive evolution of transcription factor binding sites

Directory of Open Access Journals (Sweden)

Berg Johannes

2004-10-01

Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.
Neuronal Calcium Sensor-1 Binds the D2 Dopamine Receptor and G-protein-coupled Receptor Kinase 1 (GRK1) Peptides Using Different Modes of Interactions.

Science.gov (United States)

Pandalaneni, Sravan; Karuppiah, Vijaykumar; Saleem, Muhammad; Haynes, Lee P; Burgoyne, Robert D; Mayans, Olga; Derrick, Jeremy P; Lian, Lu-Yun

2015-07-24

Neuronal calcium sensor-1 (NCS-1) is the primordial member of the neuronal calcium sensor family of EF-hand Ca(2+)-binding proteins. It interacts with both the G-protein-coupled receptor (GPCR) dopamine D2 receptor (D2R), regulating its internalization and surface expression, and the cognate kinases GRK1 and GRK2. Determination of the crystal structures of Ca(2+)/NCS-1 alone and in complex with peptides derived from D2R and GRK1 reveals that the differential recognition is facilitated by the conformational flexibility of the C-lobe-binding site. We find that two copies of the D2R peptide bind within the hydrophobic crevice on Ca(2+)/NCS-1, but only one copy of the GRK1 peptide binds. The different binding modes are made possible by the C-lobe-binding site of NCS-1, which adopts alternative conformations in each complex. C-terminal residues Ser-178-Val-190 act in concert with the flexible EF3/EF4 loop region to effectively form different peptide-binding sites. In the Ca(2+)/NCS-1·D2R peptide complex, the C-terminal region adopts a 310 helix-turn-310 helix, whereas in the GRK1 peptide complex it forms an α-helix. Removal of Ser-178-Val-190 generated a C-terminal truncation mutant that formed a dimer, indicating that the NCS-1 C-terminal region prevents NCS-1 oligomerization. We propose that the flexible nature of the C-terminal region is essential to allow it to modulate its protein-binding sites and adapt its conformation to accommodate both ligands. This appears to be driven by the variability of the conformation of the C-lobe-binding site, which has ramifications for the target specificity and diversity of NCS-1. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Brain serotonin 4 receptor binding is inversely associated with verbal memory recall.

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Stenbæk, Dea S; Fisher, Patrick M; Ozenne, Brice; Andersen, Emil; Hjordt, Liv V; McMahon, Brenda; Hasselbalch, Steen G; Frokjaer, Vibe G; Knudsen, Gitte M

2017-04-01

We have previously identified an inverse relationship between cerebral serotonin 4 receptor (5-HT 4 R) binding and nonaffective episodic memory in healthy individuals. Here, we investigate in a novel sample if the association is related to affective components of memory, by examining the association between cerebral 5-HT 4 R binding and affective verbal memory recall. Twenty-four healthy volunteers were scanned with the 5-HT 4 R radioligand [ 11 C]SB207145 and positron emission tomography, and were tested with the Verbal Affective Memory Test-24. The association between 5-HT 4 R binding and affective verbal memory was evaluated using a linear latent variable structural equation model. We observed a significant inverse association across all regions between 5-HT 4 R binding and affective verbal memory performances for positive ( p = 5.5 × 10 -4 ) and neutral ( p = .004) word recall, and an inverse but nonsignificant association for negative ( p = .07) word recall. Differences in the associations with 5-HT 4 R binding between word categories (i.e., positive, negative, and neutral) did not reach statistical significance. Our findings replicate our previous observation of a negative association between 5-HT 4 R binding and memory performance in an independent cohort and provide novel evidence linking 5-HT 4 R binding, as a biomarker for synaptic 5-HT levels, to the mnestic processing of positive and neutral word stimuli in healthy humans.
Demonstration of a reduction in muscarinic receptor binding in early Alzheimer's disease using iodine-123 dexetimide single-photon emission tomography

International Nuclear Information System (INIS)

Claus, J.J.; Dubois, E.A.; Booij, J.; Habraken, J.; Munck, J.C. van; Herk, M. van; Verbeeten, B. Jr.; Royen, E.A. van

1997-01-01

Decreased muscarinic receptor binding has been suggested in single-photon emission tomography (SPET) studies of Alzheimer's disease. However, it remains unclear whether these changes are present in mildly demented patients, and the role of cortical atrophy in receptor binding assessment has not been investigated. We studied muscarinic receptor binding normalized to neostriatum with SPET using [ 123 I[4-iododexetimide in five mildly affected patients with probable Alzheimer's disease and in five age-matched control subjects. Region of interest (ROI) analysis was performed in a consensus procedure blind to clinical diagnosis using matched magnetic resonance (MRI) images. Cortical atrophy was assessed by calculating percentages of cerebrospinal fluid in each ROI. An observer study with three observers was conducted to validate this method. Alzheimer patients showed statistically significantly less [ 123 I[4-iododexetimide binding in left temporal and right temporo-parietal cortex compared with controls, independent of age, sex and cortical atrophy. Mean intra-observer variability was 3.6% and inter-observer results showed consistent differences in [ 123 I[4-iododexetimide binding between observers. However, differences between patients and controls were comparable among observers and statistically significant in the same regions as in the consensus procedure. Using an MRI-SPET matching technique, we conclude that [ 123 I[4-iododexetimide binding is reduced in patients with mild probable Alzheimer's disease in areas of temporal and temporo-parietal cortex. (orig.). With 1 fig., 4 tabs
Preliminary crystallographic analysis of the RNA-binding domain of HuR and its poly(U)-binding properties

International Nuclear Information System (INIS)

Wang, Hong; Li, Heng; Shi, Hui; Liu, Yang; Liu, Huihui; Zhao, Hui; Niu, Liwen; Teng, Maikun; Li, Xu

2011-01-01

Here, the recombinant ARE-binding region of HuR (residues 18–186) was crystallized in space group P2 1 2 1 2, with unit-cell parameters a = 41.2, b = 133.1, c = 31.4 Å. Human antigen R (HuR), a ubiquitously expressed member of the Hu protein family, is an important post-transcriptional regulator which has three RNA-recognition motif (RRM) domains. The two tandem N-terminal RRM domains can selectively bind to the AU-rich element (ARE), while the third one interacts with the poly(A) tail and other proteins. Here, the recombinant ARE-binding region of HuR (residues 18–186) was crystallized in space group P2 1 2 1 2, with unit-cell parameters a = 41.2, b = 133.1, c = 31.4 Å. X-ray diffraction data were collected to a resolution of 2.8 Å. Mutagenesis analysis and SPR assays revealed its poly(U)-binding properties
Molecular Dynamics Simulation Study on the Binding and Stabilization Mechanism of Antiprion Compounds to the "Hot Spot" Region of PrPC.

Science.gov (United States)

Zhou, Shuangyan; Liu, Xuewei; An, Xiaoli; Yao, Xiaojun; Liu, Huanxiang

2017-11-15

Structural transitions in the prion protein from the cellular form, PrP C , into the pathological isoform, PrP Sc , are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrP C to PrP Sc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrP C to PrP Sc conversion, stabilizing the native PrP C via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrP C is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrP C is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrP C that were previously reported to have specific binding to the "hot spot" region of PrP C . Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrP C by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrP C in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding
Serotonin-stimulated phosphoinositide turnover: mediation by the S2 binding site in rat cerebral cortex but not in subcortical regions

International Nuclear Information System (INIS)

Conn, P.J.; Sanders-Bush, E.

1985-01-01

In rat cerebral cortex, serotonin (5-HT) stimulates phosphoinositide turnover with an EC50 of 1 microM in the presence of pargyline. The EC50 is 16-fold higher in the absence of pargyline. Selective S2 antagonists inhibit 5-HT-stimulated phosphoinositide turnover. Schild analysis of the blockade by ketanserin of the 5-HT effect gives an estimated Kd of ketanserin for the phosphoinositide-linked receptor of 11.7 nM, which agrees with the Kd (3.5 nM) of [ 3 H]ketanserin for the S2 site. Furthermore, MK-212, 5-HT and 5-fluorotryptamine stimulate phosphoinositide turnover with potencies that resemble their potencies at the S2 but not the S1 binding site. Of 11 agonists tested, the tryptamine derivatives tend to be more efficacious than the piperazine derivatives. The selective S1 agonist 8-hydroxy-2-(di-N-propylamino)tetralin is inactive at stimulating phosphoinositide turnover. No significant relationship exists between the regional distributions of 5-HT-stimulated phosphoinositide turnover and S2 binding sites. Furthermore, the S2 antagonist ketanserin is less potent and less efficacious in hippocampus and limbic forebrain than in cerebral cortex. These data suggest that 5-HT-stimulated phosphoinositide turnover is linked to the S2 binding site in rat cerebral cortex. However, 5-HT increases phosphoinositide turnover in subcortical regions by mechanisms other than stimulation of the S2 receptor
Neural correlates of shape-color binding in visual working memory.

Science.gov (United States)

Parra, Mario A; Della Sala, Sergio; Logie, Robert H; Morcom, Alexa M

2014-01-01

The present study addressed an outstanding issue regarding feature binding in working memory (WM): whether this function engages specific resources relative to those required to process individual features. We investigated the brain regions supporting the encoding and maintenance of features and bindings in a change detection task, in which 22 healthy young volunteers remembered visual arrays of abstract shapes, colors or shape-color bindings while undergoing fMRI. After an unfilled delay they saw a second array and judged whether the features or combination of features presented across the two arrays were the same or different. Temporary retention of feature bindings was found to involve additional cortical regions compared with retaining single features, regardless of whether the number of objects or the number of features differed between feature-only and binding conditions. This binding-specific activation is consistent with the involvement of different neural generators that collectively support visual temporary memory for features and for feature bindings. Regions within the parietal, temporal and occipital cortex, but not within the prefrontal cortex or the medial temporal lobe, appear to support the integrated object binding function investigated in this study. Our findings suggest that both individual features and their binding within integrated objects are used to represent complex objects in WM. © 2013 Elsevier Ltd. All rights reserved.
Pressure locking and thermal binding of gate valves

Energy Technology Data Exchange (ETDEWEB)

Kelly, E.M.

1996-12-01

Pressure locking and thermal binding represent potential common mode failure mechanisms that can cause safety-related power-operated gate valves to fail in the closed position, thus rendering redundant safety-related systems incapable of performing their safety functions. Supplement 6 to Generic Letter 89-10, {open_quotes}Safety-Related Motor-Operated Gate Valve Testing and Surveillance,{close_quotes} provided an acceptable approach to addressing pressure locking and thermal binding of gate valves. More recently, the NRC has issued Generic Letter 95-07, {open_quotes}Pressure Locking and Thermal Binding of Safety-Related Power-Operated Gate Valves,{close_quotes} to request that licensees take certain actions to ensure that safety-related power-operated gate valves that are susceptible to pressure locking or thermal binding are capable of performing their safety functions within the current licensing bases. Over the past two years, several plants in Region I determined that valves in certain systems were potentially susceptible to pressure locking and thermal binding, and have taken various corrective actions. The NRC Region I Systems Engineering Branch has been actively involved in the inspection of licensee actions in response to the pressure locking and thermal binding issue. Region I continues to maintain an active involvement in this area, including participation with the Office of Nuclear Reactor Regulation in reviewing licensee responses to Generic Letter 95-07.
Binding of HIV-1 gp41-directed neutralizing and non-neutralizing fragment antibody binding domain (Fab and single chain variable fragment (ScFv antibodies to the ectodomain of gp41 in the pre-hairpin and six-helix bundle conformations.

Directory of Open Access Journals (Sweden)

John M Louis

Full Text Available We previously reported a series of antibodies, in fragment antigen binding domain (Fab formats, selected from a human non-immune phage library, directed against the internal trimeric coiled-coil of the N-heptad repeat (N-HR of HIV-1 gp41. Broadly neutralizing antibodies from that series bind to both the fully exposed N-HR trimer, representing the pre-hairpin intermediate state of gp41, and to partially-exposed N-HR helices within the context of the gp41 six-helix bundle. While the affinities of the Fabs for pre-hairpin intermediate mimetics vary by only 2 to 20-fold between neutralizing and non-neutralizing antibodies, differences in inhibition of viral entry exceed three orders of magnitude. Here we compare the binding of neutralizing (8066 and non-neutralizing (8062 antibodies, differing in only four positions within the CDR-H2 binding loop, in Fab and single chain variable fragment (ScFv formats, to several pre-hairpin intermediate and six-helix bundle constructs of gp41. Residues 56 and 58 of the mini-antibodies are shown to be crucial for neutralization activity. There is a large differential (≥ 150-fold in binding affinity between neutralizing and non-neutralizing antibodies to the six-helix bundle of gp41 and binding to the six-helix bundle does not involve displacement of the outer C-terminal helices of the bundle. The binding stoichiometry is one six-helix bundle to one Fab or three ScFvs. We postulate that neutralization by the 8066 antibody is achieved by binding to a continuum of states along the fusion pathway from the pre-hairpin intermediate all the way to the formation of the six-helix bundle, but prior to irreversible fusion between viral and cellular membranes.
Evaluating the Impact of Localized GCM Grid Refinement on Regional Tropical Cyclone Climatology and Synoptic Variability using Variable-Resolution CAM-SE

Science.gov (United States)

Zarzycki, C.; Jablonowski, C.

2013-12-01

Using General Circulation Models (GCMs) to resolve sub-synoptic features in climate simulations has traditionally been difficult due to a multitude of atmospheric processes operating at subgrid scales requiring significant parameterization. For example, at traditional GCM horizontal grid resolutions of 50-300 km, tropical cyclones are generally under-resolved. This paper explores a novel variable-resolution global modeling approach that allows for high spatial resolutions in areas of interest, such as low-latitude ocean basins where tropical cyclogenesis occurs. Such multi-resolution GCM designs allow for targeted use of computing resources at the regional level while maintaining a globally-continuous model domain and may serve to bridge the gap between GCMs with uniform grids and boundary-forced limited area models. A statically-nested, variable-resolution option has recently been introduced into the Community Atmosphere Model's (CAM) Spectral Element (SE) dynamical core. A 110 km CAM-SE grid with a 28 km nest over the Atlantic Ocean has been coupled to land, ocean, and ice components within the Community Earth System Model (CESM). We present the results of a multi-decadal climate simulation using Atmospheric Model Intercomparison Project (AMIP) protocols, which force the model with historical sea surface temperatures and airborne chemical species. To investigate whether refinement improves the representation of tropical cyclones, we compare Atlantic storm statistics to observations with specific focus paid to intensity profiles and track densities. The resolution dependance of both cyclone structure and objective detection between refined and unrefined basins is explored. In addition, we discuss the potential impact of using variable-resolution grids on the large-scale synoptic interannual variability by comparing refined grid simulations to reanalysis data as well as an unrefined, globally-uniform CAM-SE simulation with identical forcing. We also evaluate the
Climatic variability of river outflow in the Pantanal region and the influence of sea surface temperature

Science.gov (United States)

Silva, Carlos Batista; Silva, Maria Elisa Siqueira; Ambrizzi, Tércio

2017-07-01

This paper investigates possible linear relationships between climate, hydrology, and oceanic surface variability in the Pantanal region (in South America's central area), over interannual and interdecadal time ranges. In order to verify the mentioned relations, lagged correlation analysis and linear adjustment between river discharge at the Pantanal region and sea surface temperature were used. Composite analysis for atmospheric fields, air humidity flux divergence, and atmospheric circulation at low and high levels, for the period between 1970 and 2003, was analyzed. Results suggest that the river discharge in the Pantanal region is linearly associated with interdecadal and interannual oscillations in the Pacific and Atlantic oceans, making them good predictors to continental hydrological variables. Considering oceanic areas, 51 % of the annual discharge in the Pantanal region can be linearly explained by mean sea surface temperature (SST) in the Subtropical North Pacific, Tropical North Pacific, Extratropical South Pacific, and Extratropical North Atlantic over the period. Considering a forecast approach in seasonal scale, 66 % of the monthly discharge variance in Pantanal, 3 months ahead of SST, is explained by the oceanic variables, providing accuracy around 65 %. Annual discharge values in the Pantanal region are strongly related to the Pacific Decadal Oscillation (PDO) variability (with 52 % of linear correlation), making it possible to consider an interdecadal variability and a consequent subdivision of the whole period in three parts: 1st (1970-1977), 2nd (1978-1996), and 3rd (1997-2003) subperiods. The three subperiods coincide with distinct PDO phases: negative, positive, and negative, respectively. Convergence of humidity flux at low levels and the circulation pattern at high levels help to explain the drier and wetter subperiods. During the wetter 2nd subperiod, the air humidity convergence at low levels is much more evident than during the other two
Factor H binds to the hypervariable region of many Streptococcus pyogenes M proteins but does not promote phagocytosis resistance or acute virulence

DEFF Research Database (Denmark)

Gustafsson, Caj Ulrik Mattias; Lannergård, Jonas; Nilsson, Olof Rickard

2013-01-01

Many pathogens express a surface protein that binds the human complement regulator factor H (FH), as first described for Streptococcus pyogenes and the antiphagocytic M6 protein. It is commonly assumed that FH recruited to an M protein enhances virulence by protecting the bacteria against...... represents a distinct ligand-binding domain. The isolated HVRs specifically interacted with FH among all human serum proteins, interacted with the same region in FH and showed species specificity, but exhibited little or no antigenic cross-reactivity. Although these findings suggested that FH recruited...... to an M protein promotes virulence, studies in transgenic mice did not demonstrate a role for bound FH during acute infection. Moreover, phagocytosis tests indicated that ability to bind FH is neither sufficient nor necessary for S. pyogenes to resist killing in whole human blood. While these data shed...
Significant decreases in frontal and temporal [11C]-raclopride binding after THC challenge.

Science.gov (United States)

Stokes, Paul R A; Egerton, Alice; Watson, Ben; Reid, Alistair; Breen, Gerome; Lingford-Hughes, Anne; Nutt, David J; Mehta, Mitul A

2010-10-01

Delta9-tetrahydrocannabinol (THC) increases prefrontal cortical dopamine release in animals, but this is yet to be examined in humans. In man, striatal dopamine release can be indexed using [11C]-raclopride positron emission tomography (PET), and recent reports suggest that cortical [11C]-raclopride binding may also be sensitive to dopaminergic challenges. Using an existing dataset we examined whether THC alters [11C]-raclopride binding potential (BP(ND)) in cortical regions. Thirteen healthy volunteers underwent two [11C]-raclopride PET scans following either oral 10 mg THC or placebo. Significant areas of decreased cortical [11C]-raclopride BP(ND) were identified using whole brain voxel-wise analysis and quantified using a region of interest (ROI) ratio analysis. Effect of blood flow on binding was estimated using a simplified reference tissue model analysis. Results were compared to [11C]-raclopride test-retest reliability in the ROIs identified using a separate cohort of volunteers. Voxel-wise analysis identified three significant clusters of decreased [11C]-raclopride BP(ND) after THC in the right middle frontal gyrus, left superior frontal gyrus and left superior temporal gyrus. Decreases in [11C]-raclopride BPND following THC were greater than test-retest variability in these ROIs. R1, an estimate of blood flow, significantly decreased in the left superior frontal gyrus in the THC condition but was unchanged in the other ROIs. Decreased frontal binding significantly correlated to catechol-o-methyl transferase (COMT) val108 status. We have demonstrated for the first time significant decreases in bilateral frontopolar cortical and left superior temporal gyrus [11C]-raclopride binding after THC. The interpretation of these findings in relation to prefrontal dopamine release is discussed. Copyright 2010 Elsevier Inc. All rights reserved.

Climate variability and wine quality over Portuguese regions

Science.gov (United States)

Gouveia, Célia M.; Gani, Érico A.; Liberato, Margarida L. R.

2015-04-01

characterized in each region by high/low quality wines. Finally, we also investigated how climate variability is related to DOC wine quality for different regions using North Atlantic Oscillation (NAO) index. Results reveal a strong dependence of wine quality for all regions on maximum temperature and precipitation during spring and summer (the growing season) as expected. However the role of temperature on wine quality seems to be distinct among the diverse regions probably due to their different climate zoning. Moreover, it is shown that the differences associated with high/low quality wine are in agreement with different synoptic fields patterns. Our results suggest that this type of analysis may be used in developing a tool that may help anticipating a vintage/high quality year, based on already available seasonal climate outlooks. Santo F.E., de Lima M.I.P., Ramos A.M., Trigo R.M., Trends in seasonal surface air temperature in mainland Portugal, since 1941, International Journal Climatolology, 34: 1814-1837, doi: 10.1002/joc.3803 (2014) de Lima M.I.P., Santo F.E., Ramos A.M. , Trigo, R.M., Trends and correlations in annual extreme precipitation indices for mainland Portugal, 1941-2007, Theoretical and Applied Climatology, DOI:10.1007/s00704-013-1079-6 (2014) Acknowledgements: This work was partially supported by national funds through FCT (Fundação para a Ciência e a Tecnologia, Portugal) under project QSECA (PTDC/AAGGLO/4155/2012).
Vitronectin Binds to a Specific Stretch within the Head Region of Yersinia Adhesin A and Thereby Modulates Yersinia enterocolitica Host Interaction.

Science.gov (United States)

Mühlenkamp, Melanie C; Hallström, Teresia; Autenrieth, Ingo B; Bohn, Erwin; Linke, Dirk; Rinker, Janina; Riesbeck, Kristian; Singh, Birendra; Leo, Jack C; Hammerschmidt, Sven; Zipfel, Peter F; Schütz, Monika S

2017-01-01

Complement resistance is an important virulence trait of Yersinia enterocolitica (Ye). The predominant virulence factor expressed by Ye is Yersinia adhesin A (YadA), which enables bacterial attachment to host cells and extracellular matrix and additionally allows the acquisition of soluble serum factors. The serum glycoprotein vitronectin (Vn) acts as an inhibitory regulator of the terminal complement complex by inhibiting the lytic pore formation. Here, we show YadA-mediated direct interaction of Ye with Vn and investigated the role of this Vn binding during mouse infection in vivo. Using different Yersinia strains, we identified a short stretch in the YadA head domain of Ye O:9 E40, similar to the 'uptake region' of Y. pseudotuberculosis YPIII YadA, as crucial for efficient Vn binding. Using recombinant fragments of Vn, we found the C-terminal part of Vn, including heparin-binding domain 3, to be responsible for binding to YadA. Moreover, we found that Vn bound to the bacterial surface is still functionally active and thus inhibits C5b-9 formation. In a mouse infection model, we demonstrate that Vn reduces complement-mediated killing of Ye O:9 E40 and, thus, improved bacterial survival. Taken together, these findings show that YadA-mediated Vn binding influences Ye pathogenesis. © 2016 S. Karger AG, Basel.
TATA-binding protein and the retinoblastoma gene product bind to overlapping epitopes on c-Myc and adenovirus E1A protein

NARCIS (Netherlands)

Hateboer, G.; Timmers, H.T.M.; Rustgi, A.K.; Billaud, Marc; Veer, L.J. Van 't; Bernards, R.A.

1993-01-01

Using a protein binding assay, we show that the amino-teminal 204 amino acids of the c-Myc protein interact di y with a key component of the basal p tdon factor TFID, the TATA box-binding protein (TBP). Essentialy the same region of the c-Myc protein alo binds the product of the retinoblatoma
[3H]cytisine binding to nicotinic cholinergic receptors in brain

International Nuclear Information System (INIS)

Pabreza, L.A.; Dhawan, S.; Kellar, K.J.

1991-01-01

Cytisine, a ganglionic agonist, competes with high affinity for brain nicotinic cholinergic receptors labeled by any of several nicotinic 3 H-agonist ligands. Here we have examined the binding of [ 3 H]cytisine in rat brain homogenates. [ 3 H]Cytisine binds with high affinity (Kd less than 1 nM), and specific binding represented 60-90% of total binding at all concentrations examined up to 15 nM. The nicotinic cholinergic agonists nicotine, acetylcholine, and carbachol compete with high affinity for [ 3 H]cytisine binding sites, whereas among nicotinic receptor antagonists only dihydro-beta-erythroidine competes with high affinity (in the nanomolar range). Comparison of binding in several brain regions showed that [ 3 H]cytisine binding is higher in the thalamus, striatum, and cortex than in the hippocampus, cerebellum, or hypothalamus. The pharmacology and brain regional distribution of [ 3 H]cytisine binding sites are those predicted for neuronal nicotinic receptor agonist recognition sites. The high affinity and low nonspecific binding of [ 3 H]cytisine should make it a very useful ligand for studying neuronal nicotinic receptors
The involvement of coordinative interactions in the binding of dihydrolipoamide dehydrogenase to titanium dioxide-Localization of a putative binding site.

Science.gov (United States)

Dayan, Avraham; Babin, Gilad; Ganoth, Assaf; Kayouf, Nivin Samir; Nitoker Eliaz, Neta; Mukkala, Srijana; Tsfadia, Yossi; Fleminger, Gideon

2017-08-01

Titanium (Ti) and its alloys are widely used in orthodontic and orthopedic implants by virtue to their high biocompatibility, mechanical strength, and high resistance to corrosion. Biointegration of the implants with the tissue requires strong interactions, which involve biological molecules, proteins in particular, with metal oxide surfaces. An exocellular high-affinity titanium dioxide (TiO 2 )-binding protein (TiBP), purified from Rhodococcus ruber, has been previously studied in our lab. This protein was shown to be homologous with the orthologous cytoplasmic rhodococcal dihydrolipoamide dehydrogenase (rhDLDH). We have found that rhDLDH and its human homolog (hDLDH) share the TiO 2 -binding capabilities with TiBP. Intrigued by the unique TiO 2 -binding properties of hDLDH, we anticipated that it may serve as a molecular bridge between Ti-based medical structures and human tissues. The objective of the current study was to locate the region and the amino acids of the protein that mediate the protein-TiO 2 surface interaction. We demonstrated the role of acidic amino acids in the nonelectrostatic enzyme/dioxide interactions at neutral pH. The observation that the interaction of DLDH with various metal oxides is independent of their isoelectric values strengthens this notion. DLDH does not lose its enzymatic activity upon binding to TiO 2 , indicating that neither the enzyme undergoes major conformational changes nor the TiO 2 binding site is blocked. Docking predictions suggest that both rhDLDH and hDLDH bind TiO 2 through similar regions located far from the active site and the dimerization sites. The putative TiO 2 -binding regions of both the bacterial and human enzymes were found to contain a CHED (Cys, His, Glu, Asp) motif, which has been shown to participate in metal-binding sites in proteins. Copyright © 2017 John Wiley & Sons, Ltd.
Some aspects of regional flow of variable-density groundwater in crystalline basement rock of Sweden

International Nuclear Information System (INIS)

Voss, C.I.; Andersson, Johan

1991-12-01

The distribution of saltwaters in the Baltic shield in Sweden is consistent with ongoing but incomplete Holocene flushing and depends on the geometry and connectivity of conductive structures at both regional and local scales, and on the surface topography. Numerical simulation of regional variable-density fluid flow during Holocene land-rise and coastal regression shows that the existence of any old saltwater, whether derived from submarine recharge in regions below Sweden's highest post-glacial coastline or geochemical processes, is an indication either of slow fluid movements through the bedrock over long times, or of long travel distances through fracture systems before arriving at measurement points. During the land-rise period, regional flow is not affected by the variable density of fluids in the upper few kilometers of the shield and the topography of the water table is the only driving force. The spatial distribution of meteoric flushing water and pre-Holocene waters may be complex, with the possibility of relatively fresh water in fracture zones below salty units even at depths of a few kilometers. The domination of the topographic driving force implies that deep saltwater is not necessarily stagnant, and significant saltwater flows may be expected to occur in well-connected horizons even at depth. Local topography variation and fracture zone location combine to create a complex flow field in which local topographic driving forces extend to considerable depth in some areas, whereas regional topographic forces predominate in others. Thus, a pattern may be difficult to discern in measurements of the regional saltwater distribution, although it is clear that the coastal region is the major zone of discharge for deeper pre-Holocene fluids. During the land-rise period, regional flow equilibrates with changing climatic conditions and coastal positions, while the distribution of flushing water and older waters lags and will perpetually change between successive
Attenuating illusory binding with TMS of the right parietal cortex

OpenAIRE

Esterman, Michael; Verstynen, Timothy; Robertson, Lynn C.

2007-01-01

A number of neuroimaging and neuropsychology studies have implicated various regions of parietal cortex as playing a critical role in the binding of color and form into conjunctions. The current study investigates the role of two such regions by examining how parietal transcranial magnetic stimulation (TMS) influences binding errors known as ‘illusory conjunctions.’ Participants made fewer binding errors after 1 Hz rTMS of the right intraparietal sulcus (IPS), while basic perception of featur...
Regional Community Climate Simulations with variable resolution meshes in the Community Earth System Model

Science.gov (United States)

Zarzycki, C. M.; Gettelman, A.; Callaghan, P.

2017-12-01

Accurately predicting weather extremes such as precipitation (floods and droughts) and temperature (heat waves) requires high resolution to resolve mesoscale dynamics and topography at horizontal scales of 10-30km. Simulating such resolutions globally for climate scales (years to decades) remains computationally impractical. Simulating only a small region of the planet is more tractable at these scales for climate applications. This work describes global simulations using variable-resolution static meshes with multiple dynamical cores that target the continental United States using developmental versions of the Community Earth System Model version 2 (CESM2). CESM2 is tested in idealized, aquaplanet and full physics configurations to evaluate variable mesh simulations against uniform high and uniform low resolution simulations at resolutions down to 15km. Different physical parameterization suites are also evaluated to gauge their sensitivity to resolution. Idealized variable-resolution mesh cases compare well to high resolution tests. More recent versions of the atmospheric physics, including cloud schemes for CESM2, are more stable with respect to changes in horizontal resolution. Most of the sensitivity is due to sensitivity to timestep and interactions between deep convection and large scale condensation, expected from the closure methods. The resulting full physics model produces a comparable climate to the global low resolution mesh and similar high frequency statistics in the high resolution region. Some biases are reduced (orographic precipitation in the western United States), but biases do not necessarily go away at high resolution (e.g. summertime JJA surface Temp). The simulations are able to reproduce uniform high resolution results, making them an effective tool for regional climate studies and are available in CESM2.
Rational redesign of neutral endopeptidase binding to merlin and moesin proteins

Science.gov (United States)

Niv, Masha Y; Iida, Katsuyuki; Zheng, Rong; Horiguchi, Akio; Shen, Ruoqian; Nanus, David M

2009-01-01

Neutral endopeptidase (NEP) is a 90- to 110-kDa cell-surface peptidase that is normally expressed by numerous tissues but whose expression is lost or reduced in a variety of malignancies. The anti-tumorigenic function of NEP is mediated not only by its catalytic activity but also through direct protein–protein interactions of its cytosolic region with several binding partners, including Lyn kinase, PTEN, and ezrin/radixin/moesin (ERM) proteins. We have previously shown that mutation of the K19K20K21 basic cluster in NEPs' cytosolic region to residues QNI disrupts binding to the ERM proteins. Here we show that the ERM-related protein merlin (NF2) does not bind NEP or its cytosolic region. Using experimental data, threading, and sequence analysis, we predicted the involvement of moesin residues E159Q160 in binding to the NEP cytosolic domain. Mutation of these residues to NL (to mimic the corresponding N159L160 residues in the nonbinder merlin) disrupted moesin binding to NEP. Mutation of residues N159L160Y161K162M163 in merlin to the corresponding moesin residues resulted in NEP binding to merlin. This engineered NEP peptide–merlin interaction was diminished by the QNI mutation in NEP, supporting the role of the NEP basic cluster in binding. We thus identified the region of interaction between NEP and moesin, and engineered merlin into a NEP-binding protein. These data form the basis for further exploration of the details of NEP-ERM binding and function. PMID:19388049
[Effects of land use and environmental factors on the variability of soil quality indicators in hilly Loess Plateau region of China].

Science.gov (United States)

Xu, Ming-Xiang; Liu, Guo-Bin; Zhao, Yun-Ge

2011-02-01

Classical statistics methods were adopted to analyze the soil quality variability, its affecting factors, and affecting degree at a regional scale (700 km2) in the central part of hilly Loess Plateau region of China. There existed great differences in the variability of test soil quality indicators. Soil pH, structural coefficient, silt content, specific gravity, bulk density, total porosity, capillary porosity, and catalase activity were the indicators with weak variability; soil nutrients (N, P, and K) contents, CaCO3 content, cation exchange capacity (CEC), clay content, micro-aggregate mean mass diameter, aggregate mean mass diameter, water-stable aggregates, respiration rate, microbial quotient, invertase and phosphatase activities, respiratory quotient, and microbial carbon and nitrogen showed medium variation; while soil labile organic carbon and phosphorus contents, erosion-resistance, permeability coefficient, and urease activity were the indicators with strong variability. The variability of soil CaCO3, total P and K, CEC, texture, and specific gravity, etc. was correlated with topography and other environmental factors, while the variability of dynamic soil quality indicators, including soil organic matter content, nitrogen content, water-stable aggregates, permeability, microbial biomass carbon and nitrogen, enzyme activities, and respiration rate, was mainly correlated with land use type. Overall, land use pattern explained 97% of the variability of soil quality indicators in the region. It was suggested that in the evaluation of soil quality in hilly Loess Plateau region, land use type and environmental factors should be fully considered.
Consortium for Osteogenesis Imperfecta Mutations in the Helical Domain of Type I Collagen: Regions Rich in Lethal Mutations Align With Collagen Binding Sites for Integrins and Proteoglycans

Science.gov (United States)

Marini, Joan C.; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; San Antonio, James D.; Milgrom, Sarah; Hyland, James C.; Körkkö, Jarmo; Prockop, Darwin J.; De Paepe, Anne; Coucke, Paul; Symoens, Sofie; Glorieux, Francis H.; Roughley, Peter J.; Lund, Alan M.; Kuurila-Svahn, Kaija; Hartikka, Heini; Cohn, Daniel H.; Krakow, Deborah; Mottes, Monica; Schwarze, Ulrike; Chen, Diana; Yang, Kathleen; Kuslich, Christine; Troendle, James; Dalgleish, Raymond; Byers, Peter H.

2014-01-01

Osteogenesis imperfecta (OI) is a generalized disorder of connective tissue characterized by fragile bones and easy susceptibility to fracture. Most cases of OI are caused by mutations in type I collagen. We have identified and assembled structural mutations in type I collagen genes (COL1A1 and COL1A2, encoding the proα1(I) and proα2(I) chains, respectively) that result in OI. Quantitative defects causing type I OI were not included. Of these 832 independent mutations, 682 result in substitution for glycine residues in the triple helical domain of the encoded protein and 150 alter splice sites. Distinct genotype–phenotype relationships emerge for each chain. One-third of the mutations that result in glycine substitutions in α1(I) are lethal, especially when the substituting residues are charged or have a branched side chain. Substitutions in the first 200 residues are nonlethal and have variable outcome thereafter, unrelated to folding or helix stability domains. Two exclusively lethal regions (helix positions 691–823 and 910–964) align with major ligand binding regions (MLBRs), suggesting crucial interactions of collagen monomers or fibrils with integrins, matrix metalloproteinases (MMPs), fibronectin, and cartilage oligomeric matrix protein (COMP). Mutations in COL1A2 are predominantly nonlethal (80%). Lethal substitutions are located in eight regularly spaced clusters along the chain, supporting a regional model. The lethal regions align with proteoglycan binding sites along the fibril, suggesting a role in fibril–matrix interactions. Recurrences at the same site in α2(I) are generally concordant for outcome, unlike α1(I). Splice site mutations comprise 20% of helical mutations identified in OI patients, and may lead to exon skipping, intron inclusion, or the activation of cryptic splice sites. Splice site mutations in COL1A1 are rarely lethal; they often lead to frameshifts and the mild type I phenotype. In α2(I), lethal exon skipping events are
Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts.

Science.gov (United States)

Boehm, M K; Corper, A L; Wan, T; Sohi, M K; Sutton, B J; Thornton, J D; Keep, P A; Chester, K A; Begent, R H; Perkins, S J

2000-03-01

MFE-23 is the first single-chain Fv antibody molecule to be used in patients and is used to target colorectal cancer through its high affinity for carcinoembryonic antigen (CEA), a cell-surface member of the immunoglobulin superfamily. MFE-23 contains an N-terminal variable heavy-chain domain joined by a (Gly(4)Ser)(3) linker to a variable light-chain (V(L)) domain (kappa chain) with an 11-residue C-terminal Myc-tag. Its crystal structure was determined at 2.4 A resolution by molecular replacement with an R(cryst) of 19.0%. Five of the six antigen-binding loops, L1, L2, L3, H1 and H2, conformed to known canonical structures. The sixth loop, H3, displayed a unique structure, with a beta-hairpin loop and a bifurcated apex characterized by a buried Thr residue. In the crystal lattice, two MFE-23 molecules were associated back-to-back in a manner not seen before. The antigen-binding site displayed a large acidic region located mainly within the H2 loop and a large hydrophobic region within the H3 loop. Even though this structure is unliganded within the crystal, there is an unusually large region of contact between the H1, H2 and H3 loops and the beta-sheet of the V(L) domain of an adjacent molecule (strands DEBA) as a result of intermolecular packing. These interactions exhibited remarkably high surface and electrostatic complementarity. Of seven MFE-23 residues predicted to make contact with antigen, five participated in these lattice contacts, and this model for antigen binding is consistent with previously reported site-specific mutagenesis of MFE-23 and its effect on CEA binding.
Changes of extreme precipitation and nonlinear influence of climate variables over monsoon region in China

KAUST Repository

Gao, Tao; Wang, Huixia Judy; Zhou, Tianjun

2017-01-01

of precipitation extremes over monsoon regions in China (MRC). However, research on monsoon extremes in China and their associations with climate variables is limited. In this study, we examine the space-time variations of extreme precipitation across the MRC
Morphological variability, lectin binding and Na+,K+-activated adenosine triphosphatase activity of isolated Müller (glial) cells from the rabbit retina.

Science.gov (United States)

Reichenbach, A; Dettmer, D; Brückner, G; Neumann, M; Birkenmeyer, G

1985-03-22

Rabbit retinal Müller cells were isolated by means of papaine and mechanical dissociation. These cells were shown to have a well preserved morphology and to preserve viability for many hours. Intense wheat germ agglutinin binding occurs on the photoreceptor side of Müller cells, especially in the microvillous region. Rabbit retinal Müller cells have a Na+,K+-activated adenosine triphosphatase activity in the same order of magnitude as brain astroglial cells.
Immunization with influenza virus hemagglutinin globular region containing the receptor-binding pocket.

Science.gov (United States)

Jeon, Sung Ho; Arnon, Ruth

2002-01-01

The globular region of hemagglutinin (residues 91-261) membrane glycoprotein of influenza virus that encompasses the binding zone to the oligosaccharide receptor of target cells has been cloned by reverse transcriptase-polymerase chain reaction (RT-PCR). This protein segment (denoted HA91-261 peptide) induced significant immune response in mice. The serum antibodies and lung homogenates from the immunized mice cross-reacted with native virus particles. The cellular immunity was manifested by proliferative splenocyte responses and cytokine release indicating T helper type 1 activity. The plasmid DNA containing this segment (denoted pHA91-261) provoked, in addition, a significant cytotoxic T lymphocyte (CTL) response, whereas the HA91-261 protein fragment led to no such response. Both the DNA and the protein fragment of HA91-261 induced significant protection against viral challenge, although the immune response they induce might be along different pathways. Interestingly, the combined DNA priming-protein boosting immunization regimen did not induce protection against viral challenges even though it led to significant humoral immune responses similar to that induced by the peptide vaccine.
Identification of the promoter region required for human adiponectin gene transcription: Association with CCAAT/enhancer binding protein-β and tumor necrosis factor-α

International Nuclear Information System (INIS)

Kita, Atsushi; Yamasaki, Hironori; Kuwahara, Hironaga; Moriuchi, Akie; Fukushima, Keiko; Kobayashi, Masakazu; Fukushima, Tetsuya; Takahashi, Ryoko; Abiru, Norio; Uotani, Shigeo; Kawasaki, Eiji; Eguchi, Katsumi

2005-01-01

Adiponectin, an adipose tissue-specific plasma protein, is involved in insulin sensitizing and has anti-atherosclerotic properties. Plasma levels of adiponectin are decreased in obese individuals and patients with type 2 diabetes with insulin resistance. Tumor necrosis factor-α (TNF-α) decreases the expression of adiponectin in adipocytes. The aims of the present study were: (1) to identify the promoter region responsible for basal transcription of the human adiponectin gene, and (2) to investigate the mechanism by which adiponectin was regulated by TNF-α. The human adiponectin promoter (2.1 kb) was isolated and used for luciferase reporter analysis by transient transfection into 3T3-L1 adipocytes. Deletion analysis demonstrated that the promoter region from -676 to +41 was sufficient for basal transcriptional activity. Mutation analysis of putative response elements for sterol regulatory element binding protein (SREBP) (-431 to -423) and CCAAT/enhancer binding protein (C/EBP) (-230 to -224) showed that both elements were required for basal promoter activity. Adiponectin transcription was increased 3-fold in cells that over-expressed constitutively active C/EBP-β. Electrophoretic mobility shift assay, using nuclear extract from 3T3-L1 cells and the -258 to -199 region as a probe, demonstrated specific DNA-protein binding, which was abolished by TNF-α treatment. The present data indicate that the putative response elements for SREBP and C/EBP are required for human adiponectin promoter activity, and that suppression by TNF-α may, at least in part, be associated with inactivation of C/EBP-β
Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

Directory of Open Access Journals (Sweden)

Garry Robert F

2011-01-01

Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.
Variability in the Water Footprint of Arable Crop Production across European Regions

Directory of Open Access Journals (Sweden)

Anne Gobin

2017-02-01

Full Text Available Crop growth and yield are affected by water use during the season: the green water footprint (WF accounts for rain water, the blue WF for irrigation and the grey WF for diluting agri-chemicals. We calibrated crop yield for FAO’s water balance model “Aquacrop” at field level. We collected weather, soil and crop inputs for 45 locations for the period 1992–2012. Calibrated model runs were conducted for wheat, barley, grain maize, oilseed rape, potato and sugar beet. The WF of cereals could be up to 20 times larger than the WF of tuber and root crops; the largest share was attributed to the green WF. The green and blue WF compared favourably with global benchmark values (R2 = 0.64–0.80; d = 0.91–0.95. The variability in the WF of arable crops across different regions in Europe is mainly due to variability in crop yield ( c v ¯ = 45% and to a lesser extent to variability in crop water use ( c v ¯ = 21%. The WF variability between countries ( c v ¯ = 14% is lower than the variability between seasons ( c v ¯ = 22% and between crops ( c v ¯ = 46%. Though modelled yields increased up to 50% under sprinkler irrigation, the water footprint still increased between 1% and 25%. Confronted with drainage and runoff, the grey WF tended to overestimate the contribution of nitrogen to the surface and groundwater. The results showed that the water footprint provides a measurable indicator that may support European water governance.
Reliable cloning of functional antibody variable domains from hybridomas and spleen cell repertoires employing a reengineered phage display system.

Science.gov (United States)

Krebber, A; Bornhauser, S; Burmester, J; Honegger, A; Willuda, J; Bosshard, H R; Plückthun, A

1997-02-14

A prerequisite for the use of recombinant antibody technologies starting from hybridomas or immune repertoires is the reliable cloning of functional immunoglobulin genes. For this purpose, a standard phage display system was optimized for robustness, vector stability, tight control of scFv-delta geneIII expression, primer usage for PCR amplification of variable region genes, scFv assembly strategy and subsequent directional cloning using a single rare cutting restriction enzyme. This integrated cloning, screening and selection system allowed us to rapidly obtain antigen binding scFvs derived from spleen-cell repertoires of mice immunized with ampicillin as well as from all hybridoma cell lines tested to date. As representative examples, cloning of monoclonal antibodies against a his tag, leucine zippers, the tumor marker EGP-2 and the insecticide DDT is presented. Several hybridomas whose genes could not be cloned in previous experimental setups, but were successfully obtained with the present system, expressed high amounts of aberrant heavy and light chain mRNAs, which were amplified by PCR and greatly exceeded the amount of binding antibody sequences. These contaminating variable region genes were successfully eliminated by employing the optimized phage display system, thus avoiding time consuming sequencing of non-binding scFv genes. To maximize soluble expression of functional scFvs subsequent to cloning, a compatible vector series to simplify modification, detection, multimerization and rapid purification of recombinant antibody fragments was constructed.
Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor

Energy Technology Data Exchange (ETDEWEB)

Wu, Kailang; Li, Weikai; Peng, Guiqing; Li, Fang; (Harvard-Med); (UMM-MED)

2010-03-04

NL63 coronavirus (NL63-CoV), a prevalent human respiratory virus, is the only group I coronavirus known to use angiotensin-converting enzyme 2 (ACE2) as its receptor. Incidentally, ACE2 is also used by group II SARS coronavirus (SARS-CoV). We investigated how different groups of coronaviruses recognize the same receptor, whereas homologous group I coronaviruses recognize different receptors. We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. NL63-CoV RBD has a novel {beta}-sandwich core structure consisting of 2 layers of {beta}-sheets, presenting 3 discontinuous receptor-binding motifs (RBMs) to bind ACE2. NL63-CoV and SARS-CoV have no structural homology in RBD cores or RBMs; yet the 2 viruses recognize common ACE2 regions, largely because of a 'virus-binding hotspot' on ACE2. Among group I coronaviruses, RBD cores are conserved but RBMs are variable, explaining how these viruses recognize different receptors. These results provide a structural basis for understanding viral evolution and virus-receptor interactions.

Intraseasonal variability of organized convective systems in the Central Andes: Relationship to Regional Dynamical Features

Science.gov (United States)

Mohr, K. I.; Slayback, D. A.; Nicholls, S.; Yager, K.

2013-12-01

The Andes extend from the west coast of Colombia (10N) to the southern tip of Chile (53S). In southern Peru and Bolivia, the Central Andes is split into separate eastern and western cordilleras, with a high plateau (≥ 3000 m), the Altiplano, between them. Because 90% of the Earth's tropical mountain glaciers are located in the Central Andes, our study focuses on this region, defining its zonal extent as 7S-21S and the meridional extent as the terrain 1000 m and greater. Although intense convection occurs during the wet season in the Altiplano, it is not included in the lists of regions with frequent or the most intense convection. The scarcity of in-situ observations with sufficient density and temporal resolution to resolve individual storms or even mesoscale-organized cloud systems and documented biases in microwave-based rainfall products in poorly gauged mountainous regions have impeded the development of an extensive literature on convection and convective systems in this region. With the tropical glaciers receding at unprecedented rates, leaving seasonal precipitation as an increasingly important input to the water balance in alpine valley ecosystems and streams, understanding the nature and characteristics of the seasonal precipitation becomes increasingly important for the rural economies in this region. Previous work in analyzing precipitation in the Central Andes has emphasized interannual variability with respect to ENSO, this is the first study to focus on shorter scale variability with respect to organized convection. The present study took advantage of the University of Utah's Precipitation Features database compiled from 14 years of TRMM observations (1998-2012), supplemented by field observations of rainfall and streamflow, historical gauge data, and long-term WRF-simulations, to analyze the intraseasonal variability of precipitating systems and their relationship regional dynamical features such as the Bolivian High. Through time series and
Validation of EURO-CORDEX regional climate models in reproducing the variability of precipitation extremes in Romania

Science.gov (United States)

Dumitrescu, Alexandru; Busuioc, Aristita

2016-04-01

EURO-CORDEX is the European branch of the international CORDEX initiative that aims to provide improved regional climate change projections for Europe. The main objective of this paper is to document the performance of the individual models in reproducing the variability of precipitation extremes in Romania. Here three EURO-CORDEX regional climate models (RCMs) ensemble (scenario RCP4.5) are analysed and inter-compared: DMI-HIRHAM5, KNMI-RACMO2.2 and MPI-REMO. Compared to previous studies, when the RCM validation regarding the Romanian climate has mainly been made on mean state and at station scale, a more quantitative approach of precipitation extremes is proposed. In this respect, to have a more reliable comparison with observation, a high resolution daily precipitation gridded data set was used as observational reference (CLIMHYDEX project). The comparison between the RCM outputs and observed grid point values has been made by calculating three extremes precipitation indices, recommended by the Expert Team on Climate Change Detection Indices (ETCCDI), for the 1976-2005 period: R10MM, annual count of days when precipitation ≥10mm; RX5DAY, annual maximum 5-day precipitation and R95P%, precipitation fraction of annual total precipitation due to daily precipitation > 95th percentile. The RCMs capability to reproduce the mean state for these variables, as well as the main modes of their spatial variability (given by the first three EOF patterns), are analysed. The investigation confirms the ability of RCMs to simulate the main features of the precipitation extreme variability over Romania, but some deficiencies in reproducing of their regional characteristics were found (for example, overestimation of the mea state, especially over the extra Carpathian regions). This work has been realised within the research project "Changes in climate extremes and associated impact in hydrological events in Romania" (CLIMHYDEX), code PN II-ID-2011-2-0073, financed by the Romanian
RNA binding specificity of Ebola virus transcription factor VP30.

Science.gov (United States)

Schlereth, Julia; Grünweller, Arnold; Biedenkopf, Nadine; Becker, Stephan; Hartmann, Roland K

2016-09-01

The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.
Specific binding of 125I-salmon calcitonin to rat brain

International Nuclear Information System (INIS)

Nakamuta, Hiromichi; Furukawa, Shinichi; Koida, Masao; Yajima, Haruaki; Orlowski, R.C.

1981-01-01

Rat brain particulate fraction was found to contain binding sites for 125 I-Salmon Calcitonin-I ( 125 I-SCT). Maximum binding occurred in the physiological pH range of 7.25 - 7.5. The binding reaction proceeded in a temperature-dependent manner. Binding sites were broadly distributed among the various rat brain regions and considerable regional differences existed in the affinity and density as detected by Scatchard analysis. The highest affinity was recorded in the case of the hypothalamus and the lowest in the case of the cerebellum. The KD (nM) and Bmax (pmole/mg protein) estimated for the binding to four regions were as follows: hypothalamus: 1.4 and 0.19, midbrain, hippocampus plus striatum: 1.5 and 0.08, pon plus medulla oblongata: 3.0 and 0.15 and cerebellum: 8.3 and 0.20. Using a particulate fraction of rat brain void of cerebellum and cortices, a binding assay for calcitonins was developed. Binding of 125 I-SCT was inhibited by unlabeled salmon, [Asu sup(1,7)]-eel and porcine calcitonins in a dose-dependent manner and the IC50s were 2.0, 8.0 and 30 nM, respectively. The IC50s were comparable to those estimated using a kidney particulate fraction. Human calcitonin, β-endorphin and substance P were weak inhibitors of the binding. Other peptides, drugs and putative neurotransmitters tested (totally 23 substances) failed to inhibit the binding at concentrations of 1.0 μM. The physiological significance of brain binding sites for calcitonin, with the possibility that the brain may possess endogenous ligands for these sites are discussed. (author)
Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

OpenAIRE

Bolton, Michael J; Garry, Robert F

2011-01-01

Abstract Background The surface glycoprotein (SU, gp120) of the human immunodeficiency virus (HIV) must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP) to bind the Duffy Antigen Receptor for Chemokines (DARC) and invade reticulocytes. Results Variable loop 3 (V3) of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, ...
Coupled decadal variability of the North Atlantic Oscillation, regional rainfall and karst spring discharges in the Campania region (southern Italy

Directory of Open Access Journals (Sweden)

P. De Vita

2012-05-01

Full Text Available Thus far, studies on climate change have focused mainly on the variability of the atmospheric and surface components of the hydrologic cycle, investigating the impact of this variability on the environment, especially with respect to the risks of desertification, droughts and floods. Conversely, the impacts of climate change on the recharge of aquifers and on the variability of groundwater flow have been less investigated, especially in Mediterranean karst areas whose water supply systems depend heavily upon groundwater exploitation.

In this paper, long-term climatic variability and its influence on groundwater recharge were analysed by examining decadal patterns of precipitation, air temperature and spring discharges in the Campania region (southern Italy, coupled with the North Atlantic Oscillation (NAO.

The time series of precipitation and air temperature were gathered over 90 yr, from 1921 to 2010, using 18 rain gauges and 9 air temperature stations with the most continuous functioning. The time series of the winter NAO index and of the discharges of 3 karst springs, selected from those feeding the major aqueducts systems, were collected for the same period.

Regional normalised indexes of the precipitation, air temperature and karst spring discharges were calculated, and different methods were applied to analyse the related time series, including long-term trend analysis using smoothing numerical techniques, cross-correlation and Fourier analysis.

The investigation of the normalised indexes highlighted the existence of long-term complex periodicities, from 2 to more than 30 yr, with differences in average values of up to approximately ±30% for precipitation and karst spring discharges, which were both strongly correlated with the winter NAO index.

Although the effects of the North Atlantic Oscillation (NAO had already been demonstrated in the long-term precipitation and streamflow patterns of
Near-surface wind variability over the broader Adriatic region: insights from an ensemble of regional climate models

Science.gov (United States)

Belušić, Andreina; Prtenjak, Maja Telišman; Güttler, Ivan; Ban, Nikolina; Leutwyler, David; Schär, Christoph

2018-06-01

Over the past few decades the horizontal resolution of regional climate models (RCMs) has steadily increased, leading to a better representation of small-scale topographic features and more details in simulating dynamical aspects, especially in coastal regions and over complex terrain. Due to its complex terrain, the broader Adriatic region represents a major challenge to state-of-the-art RCMs in simulating local wind systems realistically. The objective of this study is to identify the added value in near-surface wind due to the refined grid spacing of RCMs. For this purpose, we use a multi-model ensemble composed of CORDEX regional climate simulations at 0.11° and 0.44° grid spacing, forced by the ERA-Interim reanalysis, a COSMO convection-parameterizing simulation at 0.11° and a COSMO convection-resolving simulation at 0.02° grid spacing. Surface station observations from this region and satellite QuikSCAT data over the Adriatic Sea have been compared against daily output obtained from the available simulations. Both day-to-day wind and its frequency distribution are examined. The results indicate that the 0.44° RCMs rarely outperform ERA-Interim reanalysis, while the performance of the high-resolution simulations surpasses that of ERA-Interim. We also disclose that refining the grid spacing to a few km is needed to properly capture the small-scale wind systems. Finally, we show that the simulations frequently yield the accurate angle of local wind regimes, such as for the Bora flow, but overestimate the associated wind magnitude. Finally, spectral analysis shows good agreement between measurements and simulations, indicating the correct temporal variability of the wind speed.
Kinetic analysis of [11C]vorozole binding in the human brain with positron emission tomography.

Science.gov (United States)

Logan, Jean; Kim, Sung Won; Pareto, Deborah; Telang, Frank; Wang, Gene-Jack; Fowler, Joanna S; Biegon, Anat

2014-01-01

Using positron emission tomography, we investigated the kinetics of [11C]vorozole ([11C]VOR), a radiotracer for the enzyme aromatase that catalyzes the last step in estrogen biosynthesis. Six subjects were scanned under baseline conditions followed by retest 2 weeks later. The retest was followed by a blocking study with 2.5 mg of the aromatase inhibitor letrozole. The binding potential (BP(A)ND) was estimated from a Lassen plot using the total tissue distribution volume (VT) for baseline and blocked. for the thalamus was found to be 15 times higher than that for the cerebellum. From the letrozole studies, we found that [11C]VOR exhibits a slow binding compartment (small k4) that has a nonspecific and a blockable component. Because of the sensitivity of VT to variations in k4, a common value was used for the four highest binding regions. We also considered the tissue uptake to plasma ratio for 60 to 90 minutes as an outcome measure. Using the ratio method, the difference between the highest and lowest was 2.4 compared to 3.5 for the VT. The ratio method underestimates the high regions but is less variable and may be more suitable for patient studies. Because of its kinetics and distribution, this tracer is not a candidate for a bolus infusion or reference tissue methods.
Analysis of source regions and meteorological factors for the variability of spring PM10 concentrations in Seoul, Korea

Science.gov (United States)

Lee, Jangho; Kim, Kwang-Yul

2018-02-01

CSEOF analysis is applied for the springtime (March, April, May) daily PM10 concentrations measured at 23 Ministry of Environment stations in Seoul, Korea for the period of 2003-2012. Six meteorological variables at 12 pressure levels are also acquired from the ERA Interim reanalysis datasets. CSEOF analysis is conducted for each meteorological variable over East Asia. Regression analysis is conducted in CSEOF space between the PM10 concentrations and individual meteorological variables to identify associated atmospheric conditions for each CSEOF mode. By adding the regressed loading vectors with the mean meteorological fields, the daily atmospheric conditions are obtained for the first five CSEOF modes. Then, HYSPLIT model is run with the atmospheric conditions for each CSEOF mode in order to back trace the air parcels and dust reaching Seoul. The K-means clustering algorithm is applied to identify major source regions for each CSEOF mode of the PM10 concentrations in Seoul. Three main source regions identified based on the mean fields are: (1) northern Taklamakan Desert (NTD), (2) Gobi Desert and (GD), and (3) East China industrial area (ECI). The main source regions for the mean meteorological fields are consistent with those of previous study; 41% of the source locations are located in GD followed by ECI (37%) and NTD (21%). Back trajectory calculations based on CSEOF analysis of meteorological variables identify distinct source characteristics associated with each CSEOF mode and greatly facilitate the interpretation of the PM10 variability in Seoul in terms of transportation route and meteorological conditions including the source area.
YSOVAR: MID-INFRARED VARIABILITY AMONG YSOs IN THE STAR FORMATION REGION GGD12-15

Energy Technology Data Exchange (ETDEWEB)

Wolk, Scott J.; Günther, H. Moritz; Poppenhaeger, Katja; Forbrich, J. [Harvard–Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Cody, A. M. [NASA Ames Research Center, M/S 244-5 Moffett Field, CA 94035 (United States); Rebull, L. M.; Stauffer, J. R. [Spitzer Science Center/Caltech, 1200 E. California Blvd., Pasadena, CA 91125 (United States); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA 01003 (United States); Hillenbrand, L. A. [Department of Astronomy, California Institute of Technology, Pasadena, CA 91125 (United States); Plavchan, P. [Department of Physics Astronomy and Materials Science, Missouri State University, Springfield, MO 65897 (United States); Covey, K. R. [Department of Physics and Astronomy, Western Washington Univ., Bellingham, WA 98225-9164 (United States); Song, Inseok, E-mail: swolk@cfa.harvard.edu [Physics and Astronomy Department, University of Georgia, Athens, GA 30602-2451 (United States)

2015-11-15

We present an IR-monitoring survey with the Spitzer Space Telescope of the star-forming region GGD 12-15. More than 1000 objects were monitored, including about 350 objects within the central 5′, which is found to be especially dense in cluster members. The monitoring took place over 38 days and is part of the Young Stellar Object VARiability project. The region was also the subject of a contemporaneous 67 ks Chandra observation. The field includes 119 previously identified pre-main sequence star candidates. X-rays are detected from 164 objects, 90 of which are identified with cluster members. Overall, we find that about half the objects in the central 5′ are young stellar objects (YSOs) based on a combination of their spectral energy distribution, IR variability, and X-ray emission. Most of the stars with IR excess relative to a photosphere show large amplitude (>0.1 mag) mid-infrared (mid-IR) variability. There are 39 periodic sources, and all but one is found to be a cluster member. Almost half of the periodic sources do not show IR excesses. Overall, more than 85% of the Class I, flat spectrum, and Class II sources are found to vary. The amplitude of the variability is larger in more embedded YSOs. Most of the Class I/II objects exhibit redder colors in a fainter state, which is compatible with time-variable extinction. A few become bluer when fainter, which can be explained with significant changes in the structure of the inner disk. A search for changes in the IR due to X-ray events is carried out, but the low number of flares prevented an analysis of the direct impact of X-ray flares on the IR light curves. However, we find that X-ray detected Class II sources have longer timescales for change in the MIR than a similar set of non-X-ray detected Class IIs.
Understanding Short-Term Nonmigrating Tidal Variability in the Ionospheric Dynamo Region from SABER Using Information Theory and Bayesian Statistics

Science.gov (United States)

Kumari, K.; Oberheide, J.

2017-12-01

Nonmigrating tidal diagnostics of SABER temperature observations in the ionospheric dynamo region reveal a large amount of variability on time-scales of a few days to weeks. In this paper, we discuss the physical reasons for the observed short-term tidal variability using a novel approach based on Information theory and Bayesian statistics. We diagnose short-term tidal variability as a function of season, QBO, ENSO, and solar cycle and other drivers using time dependent probability density functions, Shannon entropy and Kullback-Leibler divergence. The statistical significance of the approach and its predictive capability is exemplified using SABER tidal diagnostics with emphasis on the responses to the QBO and solar cycle. Implications for F-region plasma density will be discussed.
Climate variability and land cover change over the North American monsoon region (Invited)

Science.gov (United States)

Zeng, X.; Scheftic, W. D.; Broxton, P. D.

2013-12-01

The North American Monsoon System over Mexico and southwestern United States represents a weather/climate and ecosystem coupled "macrosystem". The weather and climate affect the seasonal and interannual variability of ecosystem, while the ecosystem change affects surface energy, water, and carbon fluxes that, in turn, affect weather and climate. Furthermore, long-term weather/climate data have a much coarser horizontal resolution than the satellite land cover data. Here the North American Regional Reanalysis (NARR) data at 32 km grid spacing will be combined with various satellite remote sensing products at 1 km and/or 8 km resolution from AVHRR, MODIS, and SPOT for the period of 1982 to present. Our analysis includes: a) precipitation, wind, and precipitable water data from NARR to characterize the North American monsoon; b) land cover type, normalized difference vegetation index (NDVI), green vegetation fraction, and leaf-area index (LAI) data to characterize the seasonal and interannual variability of ecosystem; c) assessing the consistency of various satellite products; and d) testing the coherence in the weather/climate and ecosystem variability.
Ribosomal binding region for the antibiotic tiamulin: stoichiometry, subunit location, and affinity for various analogs.

Science.gov (United States)

Högenauer, G; Ruf, C

1981-01-01

Equilibrium dialysis experiments with a highly purified preparation of labeled tiamulin, a semisynthetic derivative of the antibiotic pleuromutilin, and Escherichia coli ribosomes allowed the determination of two binding sites for the drug. The binding reaction showed a cooperative effect. Of the two subunits, the 50S particle was able to bind the antibiotic in a 1:1 stoichiometry. Hence, the 50S subunit contributed predominantly to the binding energy which held the antibiotic to the ribosomes. The 30S subunit, showing no strong affinity for the drug, may be needed for the generation of the second binding site in the 70S particle. If depleted of ammonium ions, 70S ribosomes lost their binding capacity for the antibiotic. The attachment sites for tiamulin could be restored by heating the ribosomes to 40 degrees C in the presence of either ammonium ions or the antibiotic. Other pleuromutilin derivatives displaced labeled tiamulin from its ribosomal binding sites. By quantifying this competition, the relative affinity of various pleuromutilin derivatives for E. coli ribosomes was determined. The binding correlated with the minimal inhibitory concentrations of these compounds against E. coli. When compared with the minimal inhibitory concentrations of these compounds against E. coli. When compared with the minimal inhibitory concentrations against E. coli. When compared with the minimal inhibitory concentrations against Staphylococcus aureus, the correlation was less strict, but the same trend prevailed. These results suggest that the antibacterial activities of various pleuromutilin derivatives on a given test organism are mainly determined by the strength of binding to the ribosomes within the bacterial cell. PMID:6751216
Regional regression models of percentile flows for the contiguous United States: Expert versus data-driven independent variable selection

Directory of Open Access Journals (Sweden)

Geoffrey Fouad

2018-06-01

New hydrological insights for the region: A set of three variables selected based on an expert assessment of factors that influence percentile flows performed similarly to larger sets of variables selected using a data-driven method. Expert assessment variables included mean annual precipitation, potential evapotranspiration, and baseflow index. Larger sets of up to 37 variables contributed little, if any, additional predictive information. Variables used to describe the distribution of basin data (e.g. standard deviation were not useful, and average values were sufficient to characterize physical and climatic basin conditions. Effectiveness of the expert assessment variables may be due to the high degree of multicollinearity (i.e. cross-correlation among additional variables. A tool is provided in the Supplementary material to predict percentile flows based on the three expert assessment variables. Future work should develop new variables with a strong understanding of the processes related to percentile flows.
Analysis of the diversity of murine antibodies to dextran B1355. II. Demonstration of multiple idiotypes with variable expression in several strains

International Nuclear Information System (INIS)

Hansburg, D.; Briles, D.E.; Davie, J.M.

1977-01-01

We have developed radioimmunoassays that detect idiotypic (variable region) differences among the α(1 → 3) dextran-binding myeloma proteins U102, J558, and M104 as well as an assay that detects variable region determinants common to all three proteins. Using these assays, we have examined 7S and 19S anti-α(1 → 3) dextran antibodies induced in five murine strains of the a 1 I/sub g/C/sub H/ linkage group and the recombinant strain BAB/14. All idiotypes were expressed in both 19S and 7S antibodies from all strains, but with considerable strain-specific variability in penetrance. In two strains, one additional type of antibody, which lacked all four idiotypic determinants, generally constituted the bulk of total anti-α(1 → 3) dextran antibodies
Intraseasonal variability in the far-east pacific: investigation of the role of air-sea coupling in a regional coupled model

Energy Technology Data Exchange (ETDEWEB)

Small, R.J. [Naval Research Laboratory, Jacobs Technology, Stennis Space Center, MS (United States); University of Hawaii, International Pacific Research Center, POST 401, Honolulu, HI (United States); Xie, Shang-Ping [University of Hawaii, International Pacific Research Center, POST 401, Honolulu, HI (United States); University of Hawaii, Department of Meteorology, School of Ocean and Earth Science and Technology, Honolulu, HI (United States); Maloney, Eric D. [Colorado State University, Department of Atmospheric Science, Fort Collins, CO (United States); Szoeke, Simon P. de [Oregon State University, College of Oceanic and Atmospheric Sciences, Corvallis, OR (United States); Miyama, Toru [Frontier Research for Global Change, Yokohama (Japan)

2011-03-15

Intraseasonal variability in the eastern Pacific warm pool in summer is studied, using a regional ocean-atmosphere model, a linear baroclinic model (LBM), and satellite observations. The atmospheric component of the model is forced by lateral boundary conditions from reanalysis data. The aim is to quantify the importance to atmospheric deep convection of local air-sea coupling. In particular, the effect of sea surface temperature (SST) anomalies on surface heat fluxes is examined. Intraseasonal (20-90 day) east Pacific warm-pool zonal wind and outgoing longwave radiation (OLR) variability in the regional coupled model are correlated at 0.8 and 0.6 with observations, respectively, significant at the 99% confidence level. The strength of the intraseasonal variability in the coupled model, as measured by the variance of outgoing longwave radiation, is close in magnitude to that observed, but with a maximum located about 10 further west. East Pacific warm pool intraseasonal convection and winds agree in phase with those from observations, suggesting that remote forcing at the boundaries associated with the Madden-Julian oscillation determines the phase of intraseasonal convection in the east Pacific warm pool. When the ocean model component is replaced by weekly reanalysis SST in an atmosphere-only experiment, there is a slight improvement in the location of the highest OLR variance. Further sensitivity experiments with the regional atmosphere-only model in which intraseasonal SST variability is removed indicate that convective variability has only a weak dependence on the SST variability, but a stronger dependence on the climatological mean SST distribution. A scaling analysis confirms that wind speed anomalies give a much larger contribution to the intraseasonal evaporation signal than SST anomalies, in both model and observations. A LBM is used to show that local feedbacks would serve to amplify intraseasonal convection and the large-scale circulation. Further
IDENTIFICATION OF THOSE VARIABLES THAT HAVE A SIGNIFICANT INFLUENCE ON THE EXPECTED NUMBER OF DAYS OF STAYING IN THE CENTRE DEVELOPMENT REGION OF ROMANIA

Directory of Open Access Journals (Sweden)

Erika KULCSÁR

2010-06-01

Full Text Available I started from the assumption that there are more variables that have a significant influence on the expected number of days of staying in the Centre Development Region. To identify those variables this paper includes the analysis of variance with two variables that are not interacting, in this case the dependent variable is the question "How many days did you plan to stay in Centre Development Region?" and the independent variables are: "What is the purpose of your stay?" "What is the highest level of education?". Given that there are cases when interactions occur between variables, I also analyzed the interaction effects between the two independent variables. The paper also includes an ANOVA analysis with three variables between which interactions relationships occur. After identifying the dependency relations between the variables I found that the inclusion of the third variable, namely the "Marital status" of respondents, adds value to the model. Following the results obtained by ANOVA analysis, I identified those socio-demographic characteristics that, in my opinion, companies that operate on tourist market in the Center Development Region should consider when fundamenting marketing strategies in tourism.
Exploring the Links in Monthly to Decadal Variability of the Atmospheric Water Balance Over the Wettest Regions in ERA-20C

Science.gov (United States)

Nogueira, M.

2017-10-01

Monthly-to-decadal variability of the regional precipitation over Intertropical Convergence Zone and north-Atlantic and north-Pacific storm tracks was investigated using ERA-20C reanalysis. Satellite-based precipitation (P) and evaporation (E) climatological patterns were well reproduced by ERA-20C. Regional P and E monthly time series displayed 20% differences, but these decreased rapidly with time scale ( 10% at yearly time scales). Spectral analysis showed good scale-by-scale statistical agreement between ERA-20C and observations. Using ERA-Interim showed no improvement despite the much wider range of information assimilated (including satellites). Remarkably high Detrended Cross-Correlation Analysis coefficients (ρDCCA > 0.7 and often ρDCCA > 0.9) revealed tight links between the nonperiodic variability of P, moisture divergence (DIV), and pressure velocity (ω) at monthly-to-decadal time scales over all the wet regions. In contrast, ρDCCA was essentially nonsignificant between nonperiodic P and E or sea surface temperature (SST). Thus, the nonperiodic monthly-to-decadal variability of precipitation in these regions is almost fully controlled by dynamics and not by local E or SST (suggested by Clausius-Clapeyron relation). Analysis of regional nonperiodic standard deviations and power spectra (and respective spectral exponents, β) provided further robustness to this conclusion. Finally, clear transitions in β for P, DIV, and ω between tropical and storm track regions were found. The latter is dominated by transient storms, with energy accumulation at synoptic scales and β β values (0.2 to 0.4) were found in the tropics, implying longer-range autocorrelations and slower decreasing variability and information creation with time scale, consistent with the important forcing from internal modes of variability (e.g., El Niño-Southern Oscillation).
Climate related diseases. Current regional variability and projections to the year 2100

Directory of Open Access Journals (Sweden)

Błażejczyk Krzysztof

2018-03-01

Full Text Available The health of individuals and societies depends on different factors including atmospheric conditions which influence humans in direct and indirect ways. The paper presents regional variability of some climate related diseases (CRD in Poland: salmonellosis intoxications, Lyme boreliosis, skin cancers (morbidity and mortality, influenza, overcooling deaths, as well as respiratory and circulatory mortality. The research consisted of two stages: 1 statistical modelling basing on past data and 2 projections of CRD for three SRES scenarios of climate change (A1B, A2, B1 to the year 2100. Several simple and multiply regression models were found for the relationships between climate variables and CRD. The models were applied to project future levels of CRD. At the end of 21st century we must expect increase in: circulatory mortality, Lyme boreliosis infections and skin cancer morbidity and mortality. There is also projected decrease in: respiratory mortality, overcooling deaths and influenza infections.
Screening the sequence selectivity of DNA-binding molecules using a gold nanoparticle-based colorimetric approach.

Science.gov (United States)

Hurst, Sarah J; Han, Min Su; Lytton-Jean, Abigail K R; Mirkin, Chad A

2007-09-15

We have developed a novel competition assay that uses a gold nanoparticle (Au NP)-based, high-throughput colorimetric approach to screen the sequence selectivity of DNA-binding molecules. This assay hinges on the observation that the melting behavior of DNA-functionalized Au NP aggregates is sensitive to the concentration of the DNA-binding molecule in solution. When short, oligomeric hairpin DNA sequences were added to a reaction solution consisting of DNA-functionalized Au NP aggregates and DNA-binding molecules, these molecules may either bind to the Au NP aggregate interconnects or the hairpin stems based on their relative affinity for each. This relative affinity can be measured as a change in the melting temperature (Tm) of the DNA-modified Au NP aggregates in solution. As a proof of concept, we evaluated the selectivity of 4',6-diamidino-2-phenylindone (an AT-specific binder), ethidium bromide (a nonspecific binder), and chromomycin A (a GC-specific binder) for six sequences of hairpin DNA having different numbers of AT pairs in a five-base pair variable stem region. Our assay accurately and easily confirmed the known trends in selectivity for the DNA binders in question without the use of complicated instrumentation. This novel assay will be useful in assessing large libraries of potential drug candidates that work by binding DNA to form a drug/DNA complex.

Collaborative Research: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic

Energy Technology Data Exchange (ETDEWEB)

Gutowski, William J. [Iowa State Univ., Ames, IA (United States)

2017-12-28

This project developed and applied a regional Arctic System model for enhanced decadal predictions. It built on successful research by four of the current PIs with support from the DOE Climate Change Prediction Program, which has resulted in the development of a fully coupled Regional Arctic Climate Model (RACM) consisting of atmosphere, land-hydrology, ocean and sea ice components. An expanded RACM, a Regional Arctic System Model (RASM), has been set up to include ice sheets, ice caps, mountain glaciers, and dynamic vegetation to allow investigation of coupled physical processes responsible for decadal-scale climate change and variability in the Arctic. RASM can have high spatial resolution (~4-20 times higher than currently practical in global models) to advance modeling of critical processes and determine the need for their explicit representation in Global Earth System Models (GESMs). The pan-Arctic region is a key indicator of the state of global climate through polar amplification. However, a system-level understanding of critical arctic processes and feedbacks needs further development. Rapid climate change has occurred in a number of Arctic System components during the past few decades, including retreat of the perennial sea ice cover, increased surface melting of the Greenland ice sheet, acceleration and thinning of outlet glaciers, reduced snow cover, thawing permafrost, and shifts in vegetation. Such changes could have significant ramifications for global sea level, the ocean thermohaline circulation and heat budget, ecosystems, native communities, natural resource exploration, and commercial transportation. The overarching goal of the RASM project has been to advance understanding of past and present states of arctic climate and to improve seasonal to decadal predictions. To do this the project has focused on variability and long-term change of energy and freshwater flows through the arctic climate system. The three foci of this research are: - Changes
The spread amongst ENSEMBLES regional scenarios: regional climate models, driving general circulation models and interannual variability

Energy Technology Data Exchange (ETDEWEB)

Deque, M.; Somot, S. [Meteo-France, Centre National de Recherches Meteorologiques, CNRS/GAME, Toulouse Cedex 01 (France); Sanchez-Gomez, E. [Cerfacs/CNRS, SUC URA1875, Toulouse Cedex 01 (France); Goodess, C.M. [University of East Anglia, Climatic Research Unit, Norwich (United Kingdom); Jacob, D. [Max Planck Institute for Meteorology, Hamburg (Germany); Lenderink, G. [KNMI, Postbus 201, De Bilt (Netherlands); Christensen, O.B. [Danish Meteorological Institute, Copenhagen Oe (Denmark)

2012-03-15

Various combinations of thirteen regional climate models (RCM) and six general circulation models (GCM) were used in FP6-ENSEMBLES. The response to the SRES-A1B greenhouse gas concentration scenario over Europe, calculated as the difference between the 2021-2050 and the 1961-1990 means can be viewed as an expected value about which various uncertainties exist. Uncertainties are measured here by variance explained for temperature and precipitation changes over eight European sub-areas. Three sources of uncertainty can be evaluated from the ENSEMBLES database. Sampling uncertainty is due to the fact that the model climate is estimated as an average over a finite number of years (30) despite a non-negligible interannual variability. Regional model uncertainty is due to the fact that the RCMs use different techniques to discretize the equations and to represent sub-grid effects. Global model uncertainty is due to the fact that the RCMs have been driven by different GCMs. Two methods are presented to fill the many empty cells of the ENSEMBLES RCM x GCM matrix. The first one is based on the same approach as in FP5-PRUDENCE. The second one uses the concept of weather regimes to attempt to separate the contribution of the GCM and the RCM. The variance of the climate response is analyzed with respect to the contribution of the GCM and the RCM. The two filling methods agree that the main contributor to the spread is the choice of the GCM, except for summer precipitation where the choice of the RCM dominates the uncertainty. Of course the implication of the GCM to the spread varies with the region, being maximum in the South-western part of Europe, whereas the continental parts are more sensitive to the choice of the RCM. The third cause of spread is systematically the interannual variability. The total uncertainty about temperature is not large enough to mask the 2021-2050 response which shows a similar pattern to the one obtained for 2071-2100 in PRUDENCE. The uncertainty
Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

Science.gov (United States)

Marsh, Lorraine

2015-01-01

Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function.
Immune recognition of botulinum neurotoxin B: antibody-binding regions on the heavy chain of the toxin.

Science.gov (United States)

Dolimbek, Behzod Z; Steward, Lance E; Aoki, K Roger; Atassi, M Zouhair

2008-02-01

The purpose of this work was to map the continuous regions recognized by human, horse and mouse anti-botulinum neurotoxin B (BoNT/B) antibodies (Abs). We synthesized a panel of sixty 19-residue peptides (peptide C31 was 24 residues) that overlapped consecutively by 5 residues and together encompassed the entire heavy chain of BoNT/B (H/B, residues 442-1291). Abs from the three host species recognized similar, but not identical, peptides. There were also peptides recognized by two or only by one host species. Where a peptide was recognized by Abs of more than one host species, these Abs were at different levels among the species. Human, horse and mouse Abs bound, although in different amounts, to regions within peptides 736-754, 778-796, 848-866, 932-950, 974-992, 1058-1076 and 1128-1146. Human and horse Abs bound to peptides 890-908 and 1170-1188. Human and mouse Abs recognized peptides 470-488/484-502 overlap, 638-656, 722-740, 862-880, 1030-1048, 1072-1090, 1240-1258 and 1268-1291. We concluded that the antigenic regions localized with the three antisera are quite similar, exhibiting in some cases a small shift to the left or to the right. This is consistent with what is known about protein immune recognition. In the three-dimensional structure, the regions recognized on H/B by anti-BoNT/B Abs occupied surface locations and analysis revealed no correlation between these surface locations and surface electrostatic potential, hydrophilicity, hydrophobicity, or temperature factor. A region that bound mouse Abs overlapped with a recently defined site on BoNT/B that binds to mouse and rat synaptotagmin II, thus providing a molecular explanation for the blocking (protecting) activity of these Abs. The regions thus localized afford candidates for incorporation into a synthetic vaccine design.
Rapid isolation of IgNAR variable single-domain antibody fragments from a shark synthetic library.

Science.gov (United States)

Shao, Cui-Ying; Secombes, Chris J; Porter, Andrew J

2007-01-01

The immunoglobulin isotype IgNAR (Novel Antigen Receptor) was discovered in the serum of the nurse shark (Ginglymostoma cirratum) and wobbegong shark (Orectolobus maculates) as a homodimer of two protein chains, each composed of a single variable domain (V) domain and five constant domains. The IgNAR variable domain contains an intact antigen-binding site and functions as an independent domain able to react to antigen with both high specificity and affinity. Here we describe the successful construction of a synthetic phage-displayed library based upon a single anti-lysozyme clone HEL-5A7 scaffold, which was previously selected from an immune IgNAR variable domain library. The complementarity-determining region 3 (CDR3) loop of this clone was varied in both length and composition and the derived library was used to pan against two model proteins, lysozyme and leptin. A single anti-lysozyme clone (Ly-X20) and anti-leptin clone (Lep-12E1) were selected for further study. Both clones were shown to be functionally expressed in Escherichia coli, extremely thermostable and bind to corresponding antigens specifically. The results here demonstrate that a synthetic IgNAR variable domain library based on a single framework scaffold can be used as a route to generate antigen binders quickly, easily and without the need of immunization.
Measurement of central μ-opioid receptor binding in vivo with PET and [11C]carfentanil: a test-retest study in healthy subjects

International Nuclear Information System (INIS)

Hirvonen, Jussi; Aalto, Sargo; Maksimow, Anu; Oikonen, Vesa; Naagren, Kjell; Hagelberg, Nora; Scheinin, Harry; Ingman, Kimmo; Virkkala, Jussi

2009-01-01

[ 11 C]Carfentanil has been widely used in positron emission tomography (PET) studies for measuring μ-opioid receptor binding in humans, but the reproducibility of the binding parameter estimates is unknown. Eight healthy volunteers were scanned twice during the same day with [ 11 C]carfentanil PET, and binding to receptors was assessed with both reference tissue and arterial plasma input-based models using region of interest (ROI) and voxel-based quantification. The two-tissue compartmental model distribution volume (V T ) was highly reproducible as indicated by low variability (VAR 0.93). BP ND (BP relative to the nondisplaceable tissue compartment) was also highly reproducible (VAR 0.90) both at ROI- and voxel-level, and reference tissue-based models provided stable estimates after 40 min. The reproducibility of [ 11 C]carfentanil binding parameter estimates is excellent with outcome measures based on both arterial plasma and reference tissue input, and a scanning time of 40 min appears sufficient. (orig.)
Sensitivity of extreme precipitation to temperature: the variability of scaling factors from a regional to local perspective

Science.gov (United States)

Schroeer, K.; Kirchengast, G.

2018-06-01

Potential increases in extreme rainfall induced hazards in a warming climate have motivated studies to link precipitation intensities to temperature. Increases exceeding the Clausius-Clapeyron (CC) rate of 6-7%/°C-1 are seen in short-duration, convective, high-percentile rainfall at mid latitudes, but the rates of change cease or revert at regionally variable threshold temperatures due to moisture limitations. It is unclear, however, what these findings mean in term of the actual risk of extreme precipitation on a regional to local scale. When conditioning precipitation intensities on local temperatures, key influences on the scaling relationship such as from the annual cycle and regional weather patterns need better understanding. Here we analyze these influences, using sub-hourly to daily precipitation data from a dense network of 189 stations in south-eastern Austria. We find that the temperature sensitivities in the mountainous western region are lower than in the eastern lowlands. This is due to the different weather patterns that cause extreme precipitation in these regions. Sub-hourly and hourly intensities intensify at super-CC and CC-rates, respectively, up to temperatures of about 17 °C. However, we also find that, because of the regional and seasonal variability of the precipitation intensities, a smaller scaling factor can imply a larger absolute change in intensity. Our insights underline that temperature precipitation scaling requires careful interpretation of the intent and setting of the study. When this is considered, conditional scaling factors can help to better understand which influences control the intensification of rainfall with temperature on a regional scale.
HLA-E regulatory and coding region variability and haplotypes in a Brazilian population sample.

Science.gov (United States)

Ramalho, Jaqueline; Veiga-Castelli, Luciana C; Donadi, Eduardo A; Mendes-Junior, Celso T; Castelli, Erick C

2017-11-01

far the most variable segment. Further analyses involving the binding of transcription factors and non-coding RNAs, as well as the HLA-E expression in different tissues, are necessary to evaluate whether these variable sites at regulatory segments (or even at the coding sequence) may influence the gene expression profile. Copyright © 2017 Elsevier Ltd. All rights reserved.
Climate and climate variability of the wind power resources in the Great Lakes region of the United States

Science.gov (United States)

X. Li; S. Zhong; X. Bian; W.E. Heilman

2010-01-01

The climate and climate variability of low-level winds over the Great Lakes region of the United States is examined using 30 year (1979-2008) wind records from the recently released North American Regional Reanalysis (NARR), a three-dimensional, high-spatial and temporal resolution, and dynamically consistent climate data set. The analyses focus on spatial distribution...
Global decrease of serotonin-1A receptor binding after electroconvulsive therapy in major depression measured by PET

Science.gov (United States)

Lanzenberger, R; Baldinger, P; Hahn, A; Ungersboeck, J; Mitterhauser, M; Winkler, D; Micskei, Z; Stein, P; Karanikas, G; Wadsak, W; Kasper, S; Frey, R

2013-01-01

Electroconvulsive therapy (ECT) is a potent therapy in severe treatment-refractory depression. Although commonly applied in psychiatric clinical routine since decades, the exact neurobiological mechanism regarding its efficacy remains unclear. Results from preclinical and clinical studies emphasize a crucial involvement of the serotonin-1A receptor (5-HT1A) in the mode of action of antidepressant treatment. This includes associations between treatment response and changes in 5-HT1A function and density by antidepressants. Further, alterations of the 5-HT1A receptor are consistently reported in depression. To elucidate the effect of ECT on 5-HT1A receptor binding, 12 subjects with severe treatment-resistant major depression underwent three positron emission tomography (PET) measurements using the highly selective radioligand [carbonyl-11C]WAY100635, twice before (test–retest variability) and once after 10.08±2.35 ECT sessions. Ten patients (∼83%) were responders to ECT. The voxel-wise comparison of the 5-HT1A receptor binding (BPND) before and after ECT revealed a widespread reduction in cortical and subcortical regions (P<0.05 corrected), except for the occipital cortex and the cerebellum. Strongest reductions were found in regions consistently reported to be altered in major depression and involved in emotion regulation, such as the subgenual part of the anterior cingulate cortex (−27.5%), the orbitofrontal cortex (−30.1%), the amygdala (−31.8%), the hippocampus (−30.6%) and the insula (−28.9%). No significant change was found in the raphe nuclei. There was no significant difference in receptor binding in any region comparing the first two PET scans conducted before ECT. This PET study proposes a global involvement of the postsynaptic 5-HT1A receptor binding in the effect of ECT. PMID:22751491
Using non-systematic surveys to investigate effects of regional climate variability on Australasian gannets in the Hauraki Gulf, New Zealand

Science.gov (United States)

Srinivasan, Mridula; Dassis, Mariela; Benn, Emily; Stockin, Karen A.; Martinez, Emmanuelle; Machovsky-Capuska, Gabriel E.

2015-05-01

Few studies have investigated regional and natural climate variability on seabird populations using ocean reanalysis datasets (e.g. Simple Ocean Data Assimilation (SODA)) that integrate atmospheric information to supplement ocean observations and provide improved estimates of ocean conditions. Herein we use a non-systematic dataset on Australasian gannets (Morus serrator) from 2001 to 2009 to identify potential connections between Gannet Sightings Per Unit Effort (GSPUE) and climate and oceanographic variability in a region of known importance for breeding seabirds, the Hauraki Gulf (HG), New Zealand. While no statistically significant relationships between GSPUE and global climate indices were determined, there was a significant correlation between GSPUE and regional SST anomaly for HG. Also, there appears to be a strong link between global climate indices and regional climate in the HG. Further, based on cross-correlation function coefficients and lagged multiple regression models, we identified potential leading and lagging climate variables, and climate variables but with limited predictive capacity in forecasting future GSPUE. Despite significant inter-annual variability and marginally cooler SSTs since 2001, gannet sightings appear to be increasing. We hypothesize that at present underlying physical changes in the marine ecosystem may be insufficient to affect supply of preferred gannet main prey (pilchard Sardinops spp.), which tolerate a wide thermal range. Our study showcases the potential scientific value of lengthy non-systematic data streams and when designed properly (i.e., contain abundance, flock size, and spatial data), can yield useful information in climate impact studies on seabirds and other marine fauna. Such information can be invaluable for enhancing conservation measures for protected species in fiscally constrained research environments.
Transcriptional switching by the MerR protein: Activation and repression mutants implicate distinct DNA and mercury(II) binding domains

International Nuclear Information System (INIS)

Shewchuk, L.M.; Helmann, J.D.; Ross, W.; Park, S.J.; Summers, A.O.; Walsh, C.T.

1989-01-01

Bacterial resistance to mercuric compounds is controlled by the MerR metalloregulatory protein. The MerR protein functions as both a transcriptional repressor and a mercuric ion dependent transcriptional activator. Chemical mutagenesis of the cloned merR structural gene has led to the identification of mutant proteins that are specifically deficient in transcriptional repression, activation, or both. Five mutant proteins have been overproduced, purified to homogeneity, and assayed for ability to dimerize, bind mer operator DNA, and bind mercuric ion. A mutation in the recognition helix of a proposed helix-turn-helix DNA binding motif (E22K) yields protein deficient in both activation and repression in vivo (a - r - ) and deficient in operator binding in vitro. In contrast, mutations in three of the four MerR cysteine residues are repression competent but activation deficient (a - r + ) in vivo. In vitro, the purified cysteine mutant proteins bind to the mer operator site with near wild-type affinity but are variable deficient in binding the in vivo inducer mercury(II) ion. A subset of the isolated proteins also appears compromised in their ability to form dimers at low protein concentrations. These data support a model in which DNA-bound MerR dimer binds one mercuric ion and transmits this occupancy information to a protein region involved in transcriptional activation
Representing major soil variability at regional scale by constrained Latin Hypercube Sampling of remote sensing data

NARCIS (Netherlands)

Mulder, V.L.; Bruin, de S.; Schaepman, M.E.

2013-01-01

This paper presents a sparse, remote sensing-based sampling approach making use of conditioned Latin Hypercube Sampling (cLHS) to assess variability in soil properties at regional scale. The method optimizes the sampling scheme for a defined spatial population based on selected covariates, which are
Increased topographical variability of task-related activation in perceptive and motor associative regions in adult autistics

Directory of Open Access Journals (Sweden)

Marie-Pier Poulin-Lord

2014-01-01

Conclusion: Different and possibly unique strategies are used by each autistic individual. That enhanced variability in localization of activations in the autistic group is found in regions typically more variable in non-autistics raises the possibility that autism involves an enhancement and/or an alteration of typical plasticity mechanisms. The current study also highlights the necessity to verify, in fMRI studies involving autistic people, that hypoactivation at the group level does not result from each individual successfully completing a task using a unique brain allocation, even by comparison to his own group.
Opioid binding sites in the guinea pig and rat kidney: Radioligand homogenate binding and autoradiography

Energy Technology Data Exchange (ETDEWEB)

Dissanayake, V.U.; Hughes, J.; Hunter, J.C. (Parke-Davis Research Unit, Addenbrookes Hospital Site, Cambridge (England))

1991-07-01

The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE bound with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.
Rainfall variability, climate change and regionalization in the African monsoon region

International Nuclear Information System (INIS)

Fontaine, Bernard; Roucou, Pascal; Vigaud, Nicolas; Camara, Moctar; Konare, Abdourahamane; Sanda, Seidou Ibrah; Diedhiou, Arona; Janicot, Serge

2012-01-01

This summary recalls some results at the end of the AMMA international experiment (2003-2010) in terms of variability of the African monsoon at the intra-seasonal to multi-decadal scales and of climate prospective. The results confirmed the weight of surface temperatures and marine tele-connections for inter-annual and decadal fluctuations and stressed the importance of atmospheric variability. They also described the dominant modes of intra-seasonal variability as their interactions with the surface. Several hypotheses involving memory effects related to soil water and vegetation, particularly in boreal spring and autumn have also been made. Prospective analysis from model output suggests rainfall surplus around 2050 over the Eastern-central Sahel and relative deficit to the West. Phase 2 of AMMA (2010-2020) will focus more on aspects that have a high social impact in direct collaboration with meteorological services predictability, prediction scores, operational indicators, evaluation of the part of anthropogenic forcing in the current and future variations. (authors)
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

Science.gov (United States)

Varadi, Mihaly; Zsolyomi, Fruzsina; Guharoy, Mainak; Tompa, Peter

2015-01-01

Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.
Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

Directory of Open Access Journals (Sweden)

Mihaly Varadi

Full Text Available Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.
DNA-Aptamers Binding Aminoglycoside Antibiotics

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Nadia Nikolaus

2014-02-01

Full Text Available Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.
In Vitro Whole Genome DNA Binding Analysis of the Bacterial Replication Initiator and Transcription Factor DnaA.

Directory of Open Access Journals (Sweden)

Janet L Smith

2015-05-01

Full Text Available DnaA, the replication initiation protein in bacteria, is an AAA+ ATPase that binds and hydrolyzes ATP and exists in a heterogeneous population of ATP-DnaA and ADP-DnaA. DnaA binds cooperatively to the origin of replication and several other chromosomal regions, and functions as a transcription factor at some of these regions. We determined the binding properties of Bacillus subtilis DnaA to genomic DNA in vitro at single nucleotide resolution using in vitro DNA affinity purification and deep sequencing (IDAP-Seq. We used these data to identify 269 binding regions, refine the consensus sequence of the DnaA binding site, and compare the relative affinity of binding regions for ATP-DnaA and ADP-DnaA. Most sites had a slightly higher affinity for ATP-DnaA than ADP-DnaA, but a few had a strong preference for binding ATP-DnaA. Of the 269 sites, only the eight strongest binding ones have been observed to bind DnaA in vivo, suggesting that other cellular factors or the amount of available DnaA in vivo restricts DnaA binding to these additional sites. Conversely, we found several chromosomal regions that were bound by DnaA in vivo but not in vitro, and that the nucleoid-associated protein Rok was required for binding in vivo. Our in vitro characterization of the inherent ability of DnaA to bind the genome at single nucleotide resolution provides a backdrop for interpreting data on in vivo binding and regulation of DnaA, and is an approach that should be adaptable to many other DNA binding proteins.

Variability of the extent of the Hadley circulation in the southern hemisphere: a regional perspective

Science.gov (United States)

Nguyen, H.; Hendon, H. H.; Lim, E.-P.; Boschat, G.; Maloney, E.; Timbal, B.

2018-01-01

In order to understand the regional impacts of variations in the extent of the Hadley circulation in the Southern Hemisphere, regional Hadley circulations are defined in three sectors centered on the main tropical heat sources over Africa, Asia-Pacific (Maritime Continent) and the Americas. These regional circulations are defined by computing a streamfunction from the divergent component of the meridional wind. A major finding from this study is that year-to-year variability in the extent of the hemispheric Hadley circulation in the Southern Hemisphere is primarily governed by variations of the extent of the Hadley circulation in the Asia-Pacific sector, especially during austral spring and summer when there is little co-variability with the African sector, and the American sector exhibits an out of phase behavior. An expanded Hadley circulation in the Southern Hemisphere (both hemispherically and in the Asia-Pacific sector) is associated with La Niña conditions and a poleward expansion of the tropical wet zone in the Asia-Pacific sector. While La Niña also promotes expansion in the American and African sectors during austral winter, these tropical conditions tend to promote contraction in the two sectors during austral summer as a result of compensating convergence over the Americas and Africa sectors: a process driven by variations in the Walker circulation and Rossby wave trains emanating from the tropical Indian Ocean.
Improving plot- and regional-scale crop models for simulating impacts of climate variability and extremes

Science.gov (United States)

Tao, F.; Rötter, R.

2013-12-01

Many studies on global climate report that climate variability is increasing with more frequent and intense extreme events1. There are quite large uncertainties from both the plot- and regional-scale models in simulating impacts of climate variability and extremes on crop development, growth and productivity2,3. One key to reducing the uncertainties is better exploitation of experimental data to eliminate crop model deficiencies and develop better algorithms that more adequately capture the impacts of extreme events, such as high temperature and drought, on crop performance4,5. In the present study, in a first step, the inter-annual variability in wheat yield and climate from 1971 to 2012 in Finland was investigated. Using statistical approaches the impacts of climate variability and extremes on wheat growth and productivity were quantified. In a second step, a plot-scale model, WOFOST6, and a regional-scale crop model, MCWLA7, were calibrated and validated, and applied to simulate wheat growth and yield variability from 1971-2012. Next, the estimated impacts of high temperature stress, cold damage, and drought stress on crop growth and productivity based on the statistical approaches, and on crop simulation models WOFOST and MCWLA were compared. Then, the impact mechanisms of climate extremes on crop growth and productivity in the WOFOST model and MCWLA model were identified, and subsequently, the various algorithm and impact functions were fitted against the long-term crop trial data. Finally, the impact mechanisms, algorithms and functions in WOFOST model and MCWLA model were improved to better simulate the impacts of climate variability and extremes, particularly high temperature stress, cold damage and drought stress for location-specific and large area climate impact assessments. Our studies provide a good example of how to improve, in parallel, the plot- and regional-scale models for simulating impacts of climate variability and extremes, as needed for
Variability in large-scale wind power generation: Variability in large-scale wind power generation

Energy Technology Data Exchange (ETDEWEB)

Kiviluoma, Juha [VTT Technical Research Centre of Finland, Espoo Finland; Holttinen, Hannele [VTT Technical Research Centre of Finland, Espoo Finland; Weir, David [Energy Department, Norwegian Water Resources and Energy Directorate, Oslo Norway; Scharff, Richard [KTH Royal Institute of Technology, Electric Power Systems, Stockholm Sweden; Söder, Lennart [Royal Institute of Technology, Electric Power Systems, Stockholm Sweden; Menemenlis, Nickie [Institut de recherche Hydro-Québec, Montreal Canada; Cutululis, Nicolaos A. [DTU, Wind Energy, Roskilde Denmark; Danti Lopez, Irene [Electricity Research Centre, University College Dublin, Dublin Ireland; Lannoye, Eamonn [Electric Power Research Institute, Palo Alto California USA; Estanqueiro, Ana [LNEG, Laboratorio Nacional de Energia e Geologia, UESEO, Lisbon Spain; Gomez-Lazaro, Emilio [Renewable Energy Research Institute and DIEEAC/EDII-AB, Castilla-La Mancha University, Albacete Spain; Zhang, Qin [State Grid Corporation of China, Beijing China; Bai, Jianhua [State Grid Energy Research Institute Beijing, Beijing China; Wan, Yih-Huei [National Renewable Energy Laboratory, Transmission and Grid Integration Group, Golden Colorado USA; Milligan, Michael [National Renewable Energy Laboratory, Transmission and Grid Integration Group, Golden Colorado USA

2015-10-25

The paper demonstrates the characteristics of wind power variability and net load variability in multiple power systems based on real data from multiple years. Demonstrated characteristics include probability distribution for different ramp durations, seasonal and diurnal variability and low net load events. The comparison shows regions with low variability (Sweden, Spain and Germany), medium variability (Portugal, Ireland, Finland and Denmark) and regions with higher variability (Quebec, Bonneville Power Administration and Electric Reliability Council of Texas in North America; Gansu, Jilin and Liaoning in China; and Norway and offshore wind power in Denmark). For regions with low variability, the maximum 1 h wind ramps are below 10% of nominal capacity, and for regions with high variability, they may be close to 30%. Wind power variability is mainly explained by the extent of geographical spread, but also higher capacity factor causes higher variability. It was also shown how wind power ramps are autocorrelated and dependent on the operating output level. When wind power was concentrated in smaller area, there were outliers with high changes in wind output, which were not present in large areas with well-dispersed wind power.
Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement

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Gene A Morrill

2016-09-01

Full Text Available ABSTRACT: Globins contain one or more cavities that control or affect such functions as ligand movement and ligand binding. Here we report that the extended globin family [cytoglobin (Cygb; neuroglobin (Ngb; myoglobin (Mb; hemoglobin (Hb subunits Hba(α and Hbb(β] contain either a transmembrane (TM helix or pore-lining region as well as internal cavities. Protein motif/domain analyses indicate that Ngb and Hbb each contain 5 cholesterol-binding (CRAC/CARC domains and 1 caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding motifs. The Hb αβ-tetramer contains 14 cholesterol-binding domains. Computer algorithms indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions, whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba and pore-lining region (Hbb. The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues, 55 of 154 Mb residues and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to 8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities. Erythrocyte Hb αβ-tetramers are largely cytosolic but also bind to a membrane anion exchange protein, band 3, which contains a large internal cavity and 12 TM helices (5 being pore-lining regions. The Hba TM helix may be the erythrocyte membrane band 3 attachment site. Band 3 contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO movement within the large internal cavities and
Santa Ana Winds of Southern California: Their Climatology and Variability Spanning 6.5 Decades from Regional Dynamical Modelling

Science.gov (United States)

Guzman-Morales, J.; Gershunov, A.

2015-12-01

Santa Ana Winds (SAWs) are an integral feature of the regional climate of Southern California/Northern Baja California region. In spite of their tremendous episodic impacts on the health, economy and mood of the region, climate-scale behavior of SAW is poorly understood. In the present work, we identify SAWs in mesoscale dynamical downscaling of a global reanalysis product and construct an hourly SAW catalogue spanning 65 years. We describe the long-term SAW climatology at relevant time-space resolutions, i.e, we developed local and regional SAW indices and analyse their variability on hourly, daily, annual, and multi-decadal timescales. Local and regional SAW indices are validated with available anemometer observations. Characteristic behaviors are revealed, e.g. the SAW intensity-duration relationship. At interdecadal time scales, we find that seasonal SAW activity is sensitive to prominent large-scale low-frequency modes of climate variability rooted in the tropical and north Pacific ocean-atmosphere system that are also known to affect the hydroclimate of this region. Lastly, we do not find any long-term trend in SAW frequency and intensity as previously reported. Instead, we identify a significant long-term trend in SAW behavior whereby contribution of extreme SAW events to total seasonal SAW activity has been increasing at the expense of moderate events. These findings motivate further investigation on SAW evolution in future climate and its impact on wildfires.
Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding

International Nuclear Information System (INIS)

Roche, Julien; Louis, John M.; Aniana, Annie; Ghirlando, Rodolfo; Bax, Ad

2015-01-01

The envelope glycoprotein gp41 mediates the process of membrane fusion that enables entry of the HIV-1 virus into the host cell. Strong lipid affinity of the ectodomain suggests that its heptad repeat regions play an active role in destabilizing membranes by directly binding to the lipid bilayers and thereby lowering the free-energy barrier for membrane fusion. In such a model, immediately following the shedding of gp120, the N-heptad and C-heptad helices dissociate and melt into the host cell and viral membranes, respectively, pulling the destabilized membranes into juxtaposition, ready for fusion. Post-fusion, reaching the final 6-helix bundle (6HB) conformation then involves competition between intermolecular interactions needed for formation of the symmetric 6HB trimer and the membrane affinity of gp41’s ectodomain, including its membrane-proximal regions. Our solution NMR study of the structural and dynamic properties of three constructs containing the ectodomain of gp41 with and without its membrane-proximal regions suggests that these segments do not form inter-helical interactions until the very late steps of the fusion process. Interactions between the polar termini of the heptad regions, which are not associating with the lipid surface, therefore may constitute the main driving force initiating formation of the final post-fusion states. The absence of significant intermolecular ectodomain interactions in the presence of dodecyl phosphocholine highlights the importance of trimerization of gp41’s transmembrane helix to prevent complete dissociation of the trimer during the course of fusion
Complete dissociation of the HIV-1 gp41 ectodomain and membrane proximal regions upon phospholipid binding

Energy Technology Data Exchange (ETDEWEB)

Roche, Julien; Louis, John M.; Aniana, Annie [National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Chemical Physics (United States); Ghirlando, Rodolfo [National Institutes of Health, Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Bax, Ad, E-mail: bax@nih.gov [National Institute of Diabetes and Digestive and Kidney Diseases, Laboratory of Chemical Physics (United States)

2015-04-15

The envelope glycoprotein gp41 mediates the process of membrane fusion that enables entry of the HIV-1 virus into the host cell. Strong lipid affinity of the ectodomain suggests that its heptad repeat regions play an active role in destabilizing membranes by directly binding to the lipid bilayers and thereby lowering the free-energy barrier for membrane fusion. In such a model, immediately following the shedding of gp120, the N-heptad and C-heptad helices dissociate and melt into the host cell and viral membranes, respectively, pulling the destabilized membranes into juxtaposition, ready for fusion. Post-fusion, reaching the final 6-helix bundle (6HB) conformation then involves competition between intermolecular interactions needed for formation of the symmetric 6HB trimer and the membrane affinity of gp41’s ectodomain, including its membrane-proximal regions. Our solution NMR study of the structural and dynamic properties of three constructs containing the ectodomain of gp41 with and without its membrane-proximal regions suggests that these segments do not form inter-helical interactions until the very late steps of the fusion process. Interactions between the polar termini of the heptad regions, which are not associating with the lipid surface, therefore may constitute the main driving force initiating formation of the final post-fusion states. The absence of significant intermolecular ectodomain interactions in the presence of dodecyl phosphocholine highlights the importance of trimerization of gp41’s transmembrane helix to prevent complete dissociation of the trimer during the course of fusion.
Characterization of glucagon-like peptide-1 receptor-binding determinants.

Science.gov (United States)

Xiao, Q; Jeng, W; Wheeler, M B

2000-12-01

Glucagon-like peptide 1 (GLP-1) is a potent insulinotropic hormone currently under study as a therapeutic agent for type 2 diabetes. Since an understanding of the molecular mechanisms leading to high-affinity receptor (R) binding and activation may facilitate the development of more potent GLP-1R agonists, we have localized specific regions of GLP-1R required for binding. The purified N-terminal fragment (hereafter referred to as NT) of the GLP-1R produced in either insect (Sf9) or mammalian (COS-7) cells was shown to bind GLP-1. The physical interaction of NT with GLP-1 was first demonstrated by cross-linking ((125)I-GLP-1/NT complex band at approximately 28 kDa) and secondly by attachment to Ni(2+)-NTA beads. The GLP-1R NT protein attached to beads bound GLP-1, but with lower affinity (inhibitory concentration (IC(50)): 4.5 x 10(-7) M) than wild-type (WT) GLP-1R (IC(50): 5.2 x 10(-9)M). The low affinity of GLP-1R NT suggested that other receptor domains may contribute to GLP-1 binding. This was supported by studies using chimeric glucose-dependent insulinotropic polypeptide (GIP)/GLP-1 receptors. GIP(1-151)/GLP-1R, but not GIP(1-222)/GLP-1R, exhibited specific GLP-1 binding and GLP-1-induced cAMP production, suggesting that the region encompassing transmembrane (TM) domain 1 through to TM3 was required for binding. Since it was hypothesized that certain charged or polar amino acids in this region might be involved in binding, these residues (TM2-TM3) were analyzed by substitution mutagenesis. Five mutants (K197A, D198A, K202A, D215A, R227A) displayed remarkably reduced binding affinity. These studies indicate that the NT domain of the GLP-1R is able to bind GLP-1, but charged residues concentrated at the distal TM2/extracellular loop-1 (EC1) interface (K197, D198, K202) and in EC1 (D215 and R227) probably contribute to the binding determinants of the GLP-1R.
Multi-Site and Multi-Variables Statistical Downscaling Technique in the Monsoon Dominated Region of Pakistan

Science.gov (United States)

Khan, Firdos; Pilz, Jürgen

2016-04-01

South Asia is under the severe impacts of changing climate and global warming. The last two decades showed that climate change or global warming is happening and the first decade of 21st century is considered as the warmest decade over Pakistan ever in history where temperature reached 53 0C in 2010. Consequently, the spatio-temporal distribution and intensity of precipitation is badly effected and causes floods, cyclones and hurricanes in the region which further have impacts on agriculture, water, health etc. To cope with the situation, it is important to conduct impact assessment studies and take adaptation and mitigation remedies. For impact assessment studies, we need climate variables at higher resolution. Downscaling techniques are used to produce climate variables at higher resolution; these techniques are broadly divided into two types, statistical downscaling and dynamical downscaling. The target location of this study is the monsoon dominated region of Pakistan. One reason for choosing this area is because the contribution of monsoon rains in this area is more than 80 % of the total rainfall. This study evaluates a statistical downscaling technique which can be then used for downscaling climatic variables. Two statistical techniques i.e. quantile regression and copula modeling are combined in order to produce realistic results for climate variables in the area under-study. To reduce the dimension of input data and deal with multicollinearity problems, empirical orthogonal functions will be used. Advantages of this new method are: (1) it is more robust to outliers as compared to ordinary least squares estimates and other estimation methods based on central tendency and dispersion measures; (2) it preserves the dependence among variables and among sites and (3) it can be used to combine different types of distributions. This is important in our case because we are dealing with climatic variables having different distributions over different meteorological
Autoradiographic localization of GABA-regulated chloride ionophore binding site using t-[3H]butylbicycloorthobenzoate (TBOB)

International Nuclear Information System (INIS)

O'Connor, L.H.; McEwen, B.S.

1986-01-01

t-Butylbicycloorthobenzoate (TBOB) has been shown to bind with high affinity to sites on or near the chloride ionophore in rat brain membrane preparations. The present study used in vitro quantitative autoradiography to localize the regional distribution of [ 3 H]TBOB binding sites in rat forebrain. Receptors were labelled with 10 nM [ 3 H]TBOB. Nonspecific binding was determined by adding 10 μM picrotoxin to the incubation. Autoradiograms were generated using LKB Ultrofilm and then quantitated using computer-assisted spot-densitometry. The highest specific binding was found in frontal cortex layer 4, islands of Calleja, and ventral palladium. High binding was also found in many regions including anterior hypothalamic n., ventromedial hypothalamic n., dentate gyrus, stratum oriens and stratum lacunosum moleculare of hippocampus, and substantia nigra. Nonspecific binding represented 5 to 15% of total binding and was uniformly low throughout all brain regions. Thus, this selective probe for GABA-regulated chloride ionophore binding sites should provide a useful tool for characterizing this system and its relationship to convulsant and depressant drug action
The decorin sequence SYIRIADTNIT binds collagen type I

DEFF Research Database (Denmark)

Kalamajski, Sebastian; Aspberg, Anders; Oldberg, Ake

2007-01-01

Decorin belongs to the small leucine-rich repeat proteoglycan family, interacts with fibrillar collagens, and regulates the assembly, structure, and biomechanical properties of connective tissues. The decorin-collagen type I-binding region is located in leucine-rich repeats 5-6. Site......-directed mutagenesis of this 54-residue-long collagen-binding sequence identifies Arg-207 and Asp-210 in leucine-rich repeat 6 as crucial for the binding to collagen. The synthetic peptide SYIRIADTNIT, which includes Arg-207 and Asp-210, inhibits the binding of full-length recombinant decorin to collagen in vitro....... These collagen-binding amino acids are exposed on the exterior of the beta-sheet-loop structure of the leucine-rich repeat. This resembles the location of interacting residues in other leucine-rich repeat proteins....
Binding of tryptophan and iron by reptilion plasnna proteins

African Journals Online (AJOL)

transport functions. Albumin of the alligator (Alligator mississippiensis) and other reptiles binds, amongst other ions, tryptophan (McMenamy & Watson 1968) and transferrin binds iron (Barber & Sheeler 1963). Multiple transferrins are present in the plasma of many reptiles. (Dessauer et af 1962) and the albumin region of the.
AAV8 capsid variable regions at the two-fold symmetry axis contribute to high liver transduction by mediating nuclear entry and capsid uncoating

International Nuclear Information System (INIS)

Tenney, Rebeca M.; Bell, Christie L.; Wilson, James M.

2014-01-01

Adeno-associated virus serotype 8 (AAV8) is a promising vector for liver-directed gene therapy. Although efficient uncoating of viral capsids has been implicated in AAV8's robust liver transduction, much about the biology of AAV8 hepatotropism remains unclear. Our study investigated the structural basis of AAV8 liver transduction efficiency by constructing chimeric vector capsids containing sequences derived from AAV8 and AAV2 – a highly homologous yet poorly hepatotropic serotype. Engineered vectors containing capsid variable regions (VR) VII and IX from AAV8 in an AAV2 backbone mediated near AAV8-like transduction in mouse liver, with higher numbers of chimeric genomes detected in whole liver cells and isolated nuclei. Interestingly, chimeric capsids within liver nuclei also uncoated similarly to AAV8 by 6 weeks after administration, in contrast with AAV2, of which a significantly smaller proportion were uncoated. This study links specific AAV capsid regions to the transduction ability of a clinically relevant AAV serotype. - Highlights: • We construct chimeric vectors to identify determinants of AAV8 liver transduction. • An AAV2-based vector with 17 AAV8 residues exhibited high liver transduction in mice. • This vector also surpassed AAV2 in cell entry, nuclear entry and onset of expression. • Most chimeric vector particles were uncoated at 6 weeks, like AAV8 and unlike AAV2. • Chimera retained heparin binding and was antigenically distinct from AAV2 and AAV8
AAV8 capsid variable regions at the two-fold symmetry axis contribute to high liver transduction by mediating nuclear entry and capsid uncoating

Energy Technology Data Exchange (ETDEWEB)

Tenney, Rebeca M.; Bell, Christie L.; Wilson, James M., E-mail: wilsonjm@mail.med.upenn.edu

2014-04-15

Adeno-associated virus serotype 8 (AAV8) is a promising vector for liver-directed gene therapy. Although efficient uncoating of viral capsids has been implicated in AAV8's robust liver transduction, much about the biology of AAV8 hepatotropism remains unclear. Our study investigated the structural basis of AAV8 liver transduction efficiency by constructing chimeric vector capsids containing sequences derived from AAV8 and AAV2 – a highly homologous yet poorly hepatotropic serotype. Engineered vectors containing capsid variable regions (VR) VII and IX from AAV8 in an AAV2 backbone mediated near AAV8-like transduction in mouse liver, with higher numbers of chimeric genomes detected in whole liver cells and isolated nuclei. Interestingly, chimeric capsids within liver nuclei also uncoated similarly to AAV8 by 6 weeks after administration, in contrast with AAV2, of which a significantly smaller proportion were uncoated. This study links specific AAV capsid regions to the transduction ability of a clinically relevant AAV serotype. - Highlights: • We construct chimeric vectors to identify determinants of AAV8 liver transduction. • An AAV2-based vector with 17 AAV8 residues exhibited high liver transduction in mice. • This vector also surpassed AAV2 in cell entry, nuclear entry and onset of expression. • Most chimeric vector particles were uncoated at 6 weeks, like AAV8 and unlike AAV2. • Chimera retained heparin binding and was antigenically distinct from AAV2 and AAV8.
Extended HSR/CARD domain mediates AIRE binding to DNA

Energy Technology Data Exchange (ETDEWEB)

Maslovskaja, Julia, E-mail: julia.maslovskaja@ut.ee; Saare, Mario; Liiv, Ingrid; Rebane, Ana; Peterson, Pärt

2015-12-25

Autoimmune regulator (AIRE) activates the transcription of many genes in an unusual promiscuous and stochastic manner. The mechanism by which AIRE binds to the chromatin and DNA is not fully understood, and the regulatory elements that AIRE target genes possess are not delineated. In the current study, we demonstrate that AIRE activates the expression of transiently transfected luciferase reporters that lack defined promoter regions, as well as intron and poly(A) signal sequences. Our protein-DNA interaction experiments with mutated AIRE reveal that the intact homogeneously staining region/caspase recruitment domain (HSR/CARD) and amino acids R113 and K114 are key elements involved in AIRE binding to DNA. - Highlights: • Promoter and mRNA processing elements are not important for AIRE to activate gene expression from reporter plasmids. • AIRE protein fragment aa 1–138 mediates direct binding to DNA. • Integrity of the HSR/CARD domain is needed for AIRE binding to DNA.
Extended HSR/CARD domain mediates AIRE binding to DNA

International Nuclear Information System (INIS)

Maslovskaja, Julia; Saare, Mario; Liiv, Ingrid; Rebane, Ana; Peterson, Pärt

2015-01-01

Autoimmune regulator (AIRE) activates the transcription of many genes in an unusual promiscuous and stochastic manner. The mechanism by which AIRE binds to the chromatin and DNA is not fully understood, and the regulatory elements that AIRE target genes possess are not delineated. In the current study, we demonstrate that AIRE activates the expression of transiently transfected luciferase reporters that lack defined promoter regions, as well as intron and poly(A) signal sequences. Our protein-DNA interaction experiments with mutated AIRE reveal that the intact homogeneously staining region/caspase recruitment domain (HSR/CARD) and amino acids R113 and K114 are key elements involved in AIRE binding to DNA. - Highlights: • Promoter and mRNA processing elements are not important for AIRE to activate gene expression from reporter plasmids. • AIRE protein fragment aa 1–138 mediates direct binding to DNA. • Integrity of the HSR/CARD domain is needed for AIRE binding to DNA.
Naturally occurring mutations in the human 5-lipoxygenase gene promoter that modify transcription factor binding and reporter gene transcription.

Science.gov (United States)

In, K H; Asano, K; Beier, D; Grobholz, J; Finn, P W; Silverman, E K; Silverman, E S; Collins, T; Fischer, A R; Keith, T P; Serino, K; Kim, S W; De Sanctis, G T; Yandava, C; Pillari, A; Rubin, P; Kemp, J; Israel, E; Busse, W; Ledford, D; Murray, J J; Segal, A; Tinkleman, D; Drazen, J M

1997-03-01

Five lipoxygenase (5-LO) is the first committed enzyme in the metabolic pathway leading to the synthesis of the leukotrienes. We examined genomic DNA isolated from 25 normal subjects and 31 patients with asthma (6 of whom had aspirin-sensitive asthma) for mutations in the known transcription factor binding regions and the protein encoding region of the 5-LO gene. A family of mutations in the G + C-rich transcription factor binding region was identified consisting of the deletion of one, deletion of two, or addition of one zinc finger (Sp1/Egr-1) binding sites in the region 176 to 147 bp upstream from the ATG translation start site where there are normally 5 Sp1 binding motifs in tandem. Reporter gene activity directed by any of the mutant forms of the transcription factor binding region was significantly (P < 0.05) less effective than the activity driven by the wild type transcription factor binding region. Electrophoretic mobility shift assays (EMSAs) demonstrated the capacity of wild type and mutant transcription factor binding regions to bind nuclear extracts from human umbilical vein endothelial cells (HUVECs). These data are consistent with a family of mutations in the 5-LO gene that can modify reporter gene transcription possibly through differences in Sp1 and Egr-1 transactivation.
Changes of extreme precipitation and nonlinear influence of climate variables over monsoon region in China

KAUST Repository

Gao, Tao

2017-07-19

The El Niño-Southern Oscillation (ENSO), Indian Ocean Dipole (IOD), North Atlantic Oscillation (NAO), Atlantic Multidecadal Oscillation (AMO) and Pacific decadal oscillation (PDO) are well understood to be major drivers for the variability of precipitation extremes over monsoon regions in China (MRC). However, research on monsoon extremes in China and their associations with climate variables is limited. In this study, we examine the space-time variations of extreme precipitation across the MRC, and assess the time-varying influences of the climate drivers using Bayesian dynamic linear regression and their combined nonlinear effects through fitting generalized additive models. Results suggest that the central-east and south China is dominated by less frequent but more intense precipitation. Extreme rainfalls show significant positive trends, coupled with a significant decline of dry spells, indicating an increasing chance of occurrence of flood-induced disasters in the MRC during 1960–2014. Majority of the regional indices display some abrupt shifts during the 1990s. The influences of climate variables on monsoon extremes exhibit distinct interannual or interdecadal variations. IOD, ENSO and AMO have strong impacts on monsoon and extreme precipitation, especially during the 1990s, which is generally consistent with the abrupt shifts in precipitation regimes around this period. Moreover, ENSO mainly affects moderate rainfalls and dry spells, while IOD has a more significant impact on precipitation extremes. These findings could be helpful for improving the forecasting of monsoon extremes in China and the evaluations of climate models.
Cytoplasmic protein binding to highly conserved sequences in the 3' untranslated region of mouse protamine 2 mRNA, a translationally regulated transcript of male germ cells

International Nuclear Information System (INIS)

Kwon, Y.K.; Hecht, N.B.

1991-01-01

The expression of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated translationally during male germ-cell development. The 3' untranslated region (UTR) of protamine 1 mRNA has been reported to control its time of translation. To understand the mechanisms controlling translation of the protamine mRNAs, we have sought to identify cis elements of the 3' UTR of protamine 2 mRNA that are recognized by cytoplasmic factors. From gel retardation assays, two sequence elements are shown to form specific RNA-protein complexes. Protein binding sites of the two complexes were determined by RNase T1 mapping, by blocking the putative binding sites with antisense oligonucleotides, and by competition assays. The sequences of these elements, located between nucleotides + 537 and + 572 in protamine 2 mRNA, are highly conserved among postmeiotic translationally regulated nuclear proteins of the mammalian testis. Two closely linked protein binding sites were detected. UV-crosslinking studies revealed that a protein of about 18 kDa binds to one of the conserved sequences. These data demonstrate specific protein binding to a highly conserved 3' UTR of translationally regulated testicular mRNA
Role of glial cell line-derived neurotrophic factor (GDNF)-neural cell adhesion molecule (NCAM) interactions in induction of neurite outgrowth and identification of a binding site for NCAM in the heel region of GDNF

DEFF Research Database (Denmark)

Nielsen, Janne; Gotfryd, Kamil; Li, Shizhong

2009-01-01

NCAM-induced neurite outgrowth by being independent of NCAM polysialylation. Additionally, we investigated the structural basis for GDNF-NCAM interactions and find that NCAM Ig3 is necessary for GDNF binding. Furthermore, we identify within the heel region of GDNF a binding site for NCAM...

Preclinical assessment of viral vectored and protein vaccines targeting the Duffy-binding protein region II of Plasmodium vivax

Directory of Open Access Journals (Sweden)

Simone C de Cassan

2015-07-01

Full Text Available Malaria vaccine development has largely focused on Plasmodium falciparum; however a reawakening to the importance of P. vivax has spurred efforts to develop vaccines against this difficult to treat and at times severe form of relapsing malaria, which constitutes a significant proportion of human malaria cases worldwide. The almost complete dependence of P. vivax red blood cell invasion on the interaction of the P. vivax Duffy-binding protein region II (PvDBP_RII with the human Duffy antigen receptor for chemokines (DARC, makes this antigen an attractive vaccine candidate against blood-stage P. vivax. Here, we generated both preclinical and clinically-compatible adenoviral and poxviral vectored vaccine candidates expressing the Salvador I allele of PvDBP_RII – including human adenovirus serotype 5 (HAdV5, chimpanzee adenovirus serotype 63 (ChAd63 and modified vaccinia virus Ankara (MVA vectors. We report on the antibody and T cell immunogenicity of these vaccines in mice or rabbits, either used alone in a viral vectored prime-boost regime, or in ‘mixed-modality’ adenovirus prime – protein-in-adjuvant boost regimes (using a recombinant protein PvDBP_RII protein antigen formulated in Montanide®ISA720 or Abisco®100 adjuvants. Antibodies induced by these regimes were found to bind to native parasite antigen from P. vivax infected Thai patients and were capable of inhibiting the binding of PvDBP_RII to its receptor DARC using an in vitro binding inhibition assay. In recent years, recombinant ChAd63 and MVA vectors have been quickly translated into human clinical trials for numerous antigens from P. falciparum as well as a growing number of other pathogens. The vectors reported here are immunogenic in small animals, elicit antibodies against PvDBP_RII and have recently entered clinical trials which will provide the first assessment of the safety and immunogenicity of the PvDBP_RII antigen in humans.
Quantifying uncertainty due to internal variability using high-resolution regional climate model simulations

Science.gov (United States)

Gutmann, E. D.; Ikeda, K.; Deser, C.; Rasmussen, R.; Clark, M. P.; Arnold, J. R.

2015-12-01

The uncertainty in future climate predictions is as large or larger than the mean climate change signal. As such, any predictions of future climate need to incorporate and quantify the sources of this uncertainty. One of the largest sources comes from the internal, chaotic, variability within the climate system itself. This variability has been approximated using the 30 ensemble members of the Community Earth System Model (CESM) large ensemble. Here we examine the wet and dry end members of this ensemble for cool-season precipitation in the Colorado Rocky Mountains with a set of high-resolution regional climate model simulations. We have used the Weather Research and Forecasting model (WRF) to simulate the periods 1990-2000, 2025-2035, and 2070-2080 on a 4km grid. These simulations show that the broad patterns of change depicted in CESM are inherited by the high-resolution simulations; however, the differences in the height and location of the mountains in the WRF simulation, relative to the CESM simulation, means that the location and magnitude of the precipitation changes are very different. We further show that high-resolution simulations with the Intermediate Complexity Atmospheric Research model (ICAR) predict a similar spatial pattern in the change signal as WRF for these ensemble members. We then use ICAR to examine the rest of the CESM Large Ensemble as well as the uncertainty in the regional climate model due to the choice of physics parameterizations.
A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria

Directory of Open Access Journals (Sweden)

Yunpeng Yang

2017-01-01

Full Text Available Catabolite control protein A (CcpA is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR and carbon catabolite activation (CCA, two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt consensus site that is called a catabolite response element (cre within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named crevar, has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA. It was found that the length of the intervening spacer of crevar can affect CcpA binding affinity, and moreover, the core palindromic sequence of crevar is the key structure for regulation. Such a variable architecture of crevar shows potential importance for CcpA’s diverse and fine regulation. A total of 103 potential crevar sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs, and 30 sites were confirmed to be bound by CcpA. These 30 crevar sites are associated with 27 genes involved in many important pathways. Also of significance, the crevar sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria.
Assessing Regional Scale Variability in Extreme Value Statistics Under Altered Climate Scenarios

Energy Technology Data Exchange (ETDEWEB)

Brunsell, Nathaniel [Univ. of Kansas, Lawrence, KS (United States); Mechem, David [Univ. of Kansas, Lawrence, KS (United States); Ma, Chunsheng [Wichita State Univ., KS (United States)

2015-02-20

Recent studies have suggested that low-frequency modes of climate variability can significantly influence regional climate. The climatology associated with extreme events has been shown to be particularly sensitive. This has profound implications for droughts, heat waves, and food production. We propose to examine regional climate simulations conducted over the continental United States by applying a recently developed technique which combines wavelet multi–resolution analysis with information theory metrics. This research is motivated by two fundamental questions concerning the spatial and temporal structure of extreme events. These questions are 1) what temporal scales of the extreme value distributions are most sensitive to alteration by low-frequency climate forcings and 2) what is the nature of the spatial structure of variation in these timescales? The primary objective is to assess to what extent information theory metrics can be useful in characterizing the nature of extreme weather phenomena. Specifically, we hypothesize that (1) changes in the nature of extreme events will impact the temporal probability density functions and that information theory metrics will be sensitive these changes and (2) via a wavelet multi–resolution analysis, we will be able to characterize the relative contribution of different timescales on the stochastic nature of extreme events. In order to address these hypotheses, we propose a unique combination of an established regional climate modeling approach and advanced statistical techniques to assess the effects of low-frequency modes on climate extremes over North America. The behavior of climate extremes in RCM simulations for the 20th century will be compared with statistics calculated from the United States Historical Climatology Network (USHCN) and simulations from the North American Regional Climate Change Assessment Program (NARCCAP). This effort will serve to establish the baseline behavior of climate extremes, the
Identification of actin binding protein, ABP-280, as a binding partner of human Lnk adaptor protein.

Science.gov (United States)

He, X; Li, Y; Schembri-King, J; Jakes, S; Hayashi, J

2000-08-01

Human Lnk (hLnk) is an adaptor protein with multiple functional domains that regulates T cell activation signaling. In order to identify cellular Lnk binding partners, a yeast two-hybrid screening of human spleen cDNA library was carried out using human hLnk as bait. A polypeptide sequence identical to the C-terminal segment of the actin binding protein (ABP-280) was identified as a hLnk binding protein. The expressed hLnk and the FLAG tagged C-terminal 673 amino acid residues of ABP-280 or the endogenous ABP-280 in COS-7 cells could be co-immunoprecipitated using antibodies either to hLnk, FLAG or ABP-280, respectively. Furthermore, immunofluorescence confocal microscope showed that hLnk and ABP-280 co-localized at the plasma membrane and at juxtanuclear region of COS-7 cells. In Jurkat cells, the endogenous hLnk also associates with the endogenous ABP-280 indicating that the association of these two proteins is physiological. The interacting domains of both proteins were mapped using yeast two-hybrid assays. Our results indicate that hLnk binds to the residues 2006-2454 (repeats 19-23C) of ABP-280. The domain in hLnk that associates with ABP-280 was mapped to an interdomain region of 56 amino acids between pleckstrin homology and Src homology 2 domains. These results suggest that hLnk may exert its regulatory role through its association with ABP-280.
Expression of Cry1Ac toxin-binding region in Plutella xyllostella cadherin-like receptor and studying their interaction mode by molecular docking and site-directed mutagenesis.

Science.gov (United States)

Hu, Xiaodan; Zhang, Xiao; Zhong, Jianfeng; Liu, Yuan; Zhang, Cunzheng; Xie, Yajing; Lin, Manman; Xu, Chongxin; Lu, Lina; Zhu, Qing; Liu, Xianjin

2018-05-01

Cadherin-like protein has been identified as the primary Bacillus thuringiensis (Bt) Cry toxin receptor in Lepidoptera pests and plays a key role in Cry toxin insecticidal. In this study, we successfully expressed the putative Cry1Ac toxin-binding region (CR7-CR11) of Plutella xylostella cadherin-like in Escherichia coli BL21 (DE3). The expressed CR7-CR11 fragment showed binding ability to Cry1Ac toxin under denaturing (Ligand blot) and non-denaturing (ELISA) conditions. The three-dimensional structure of CR7-CR11 was constructed by homology modeling. Molecular docking results of CR7-CR11 and Cry1Ac showed that domain II and domain III of Cry1Ac were taking part in binding to CR7-CR11, while CR7-CR8 was the region of CR7-CR11 in interacting with Cry1Ac. The interaction of toxin-receptor complex was found to arise from hydrogen bond and hydrophobic interaction. Through the computer-aided alanine mutation scanning, amino acid residues of Cry1Ac (Met341, Asn442 and Ser486) and CR7-CR11 (Asp32, Arg101 and Arg127) were predicted as the hot spot residues involved in the interaction of the toxin-receptor complex. At last, we verified the importance role of these key amino acid residues by binding assay. These results will lay a foundation for further elucidating the insecticidal mechanism of Cry toxin and enhancing Cry toxin insecticidal activity by molecular modification. Copyright © 2018 Elsevier B.V. All rights reserved.
Structural analysis of peptides capable of binding to more than one Ia antigen

DEFF Research Database (Denmark)

Sette, A; Buus, S; Colon, S

1989-01-01

The Ia binding regions were analyzed for three unrelated peptide Ag (sperm whale myoglobin 106-118, influenza hemagglutinin 130-142, and lambda repressor protein 12-26) for which binding to more than one Ia molecule has previously been demonstrated. By determining the binding profile of three...... separate series of truncated synthetic peptides, it was found that in all three cases the different Ia reactivities mapped to largely overlapping regions of the peptides; although, for two of the peptides, the regions involved in binding the different Ia specificities were distinct. Moreover, subtle...... differences were found to dramatically influence some, but not other, Ia reactivities. Using a large panel of synthetic peptides it was found that a significant correlation exists between the capacity of peptides to interact with different alleles of the same molecule (i.e., IAd and IAk), but no correlation...
A sialoreceptor binding motif in the Mycoplasma synoviae adhesin VlhA.

Directory of Open Access Journals (Sweden)

Meghan May

Full Text Available Mycoplasma synoviae depends on its adhesin VlhA to mediate cytadherence to sialylated host cell receptors. Allelic variants of VlhA arise through recombination between an assemblage of promoterless vlhA pseudogenes and a single transcription promoter site, creating lineages of M. synoviae that each express a different vlhA allele. The predicted full-length VlhA sequences adjacent to the promoter of nine lineages of M. synoviae varying in avidity of cytadherence were aligned with that of the reference strain MS53 and with a 60-a.a. hemagglutinating VlhA C-terminal fragment from a Tunisian lineage of strain WVU1853(T. Seven different sequence variants of an imperfectly conserved, single-copy, 12-a.a. candidate cytadherence motif were evident amid the flanking variable residues of the 11 total sequences examined. The motif was predicted to adopt a short hairpin structure in a low-complexity region near the C-terminus of VlhA. Biotinylated synthetic oligopeptides representing four selected variants of the 12-a.a. motif, with the whole synthesized 60-a.a. fragment as a positive control, differed (P<0.01 in the extent they bound to chicken erythrocyte membranes. All bound to a greater extent (P<0.01 than scrambled or irrelevant VlhA domain negative control peptides did. Experimentally introduced branched-chain amino acid (BCAA substitutions Val3Ile and Leu7Ile did not significantly alter binding, whereas fold-destabilizing substitutions Thr4Gly and Ala9Gly tended to reduce it (P<0.05. Binding was also reduced to background levels (P<0.01 when the peptides were exposed to desialylated membranes, or were pre-saturated with free sialic acid before exposure to untreated membranes. From this evidence we conclude that the motif P-X-(BCAA-X-F-X-(BCAA-X-A-K-X-G binds sialic acid and likely mediates VlhA-dependent M. synoviae attachment to host cells. This conserved mechanism retains the potential for fine-scale rheostasis in binding avidity, which could be a
Quantitative autoradiography of [3H]ouabain binding sites in rat brain

International Nuclear Information System (INIS)

Spyropoulos, A.C.; Rainbow, T.C.

1984-01-01

In vitro quantitative autoradiography was used to localize in rat brain binding sites for [ 3 H]ouabain, an inhibitor of the Na + ,K + -ATPase. High levels of [ 3 H]ouabain sites were found in the superior and inferior colliculi, the mammillary nucleus, the interpeduncular nucleus, and in various divisions of the olfactory, auditory and somatomotor systems. The heterogeneous distribution of [ 3 H]ouabain binding closely parallels the regional brain glucose consumption as determined by the [ 14 C]deoxyglucose method. Lesion studies of the rat hippocampus using the excitotoxin, ibotenic acid, showed both a marked decrease of neuronal cell types on the injected side and a corresponding decrease in [ 3 H]ouabain binding, indicating that some of the [ 3 H]ouabain binding sites are localized to neurons. The close correlation between [ 3 H]ouabain binding and regional glucose utilization provides further evidence for a linkage between glucose utilization and the neuronal Na + ,K + -ATPase. (Auth.)
Differences between high-affinity forskolin binding sites in dopamine-riche and other regions of rat brain

International Nuclear Information System (INIS)

Poat, J.A.; Cripps, H.E.; Iversen, L.L.

1988-01-01

Forskolin labelled with [ 3 H] bound to high- and low-affinity sites in the rat brain. The high-affinity site was discretely located, with highest densities in the striatum, nucleus accumbens, olfactory tubercule, substantia nigra, hippocampus, and the molecular layers of the cerebellum. This site did not correlate well with the distribution of adenylate cyclase. The high-affinity striatal binding site may be associated with a stimulatory guanine nucleotide-binding protein. Thus, the number of sites was increased by the addition of Mg 2+ and guanylyl imidodiphosphate. Cholera toxin stereotaxically injected into rat striatum increased the number of binding sites, and no further increase was noted following the subsequent addition of guanyl nucleotide. High-affinity forskolin binding sites in non-dopamine-rich brain areas (hippocampus and cerebullum) were modulated in a qualitatively different manner by guanyl nucleotides. In these areas the number of binding sites was significantly reduced by the addition of guanyl nucleotide. These results suggest that forskolin may have a potential role in identifying different functional/structural guanine nucleotide-binding proteins
Magnetic Field Diagnostics and Spatio-Temporal Variability of the Solar Transition Region

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Peter, H.

2013-12-01

Magnetic field diagnostics of the transition region from the chromosphere to the corona faces us with the problem that one has to apply extreme-ultraviolet (EUV) spectro-polarimetry. While for the coronal diagnostics techniques already exist in the form of infrared coronagraphy above the limb and radio observations on the disk, one has to investigate EUV observations for the transition region. However, so far the success of such observations has been limited, but various current projects aim to obtain spectro-polarimetric data in the extreme UV in the near future. Therefore it is timely to study the polarimetric signals we can expect from these observations through realistic forward modeling. We employ a 3D magneto-hydrodynamic (MHD) forward model of the solar corona and synthesize the Stokes I and Stokes V profiles of C iv (1548 Å). A signal well above 0.001 in Stokes V can be expected even if one integrates for several minutes to reach the required signal-to-noise ratio, and despite the rapidly changing intensity in the model (just as in observations). This variability of the intensity is often used as an argument against transition region magnetic diagnostics, which requires exposure times of minutes. However, the magnetic field is evolving much slower than the intensity, and therefore the degree of (circular) polarization remains rather constant when one integrates in time. Our study shows that it is possible to measure the transition region magnetic field if a polarimetric accuracy on the order of 0.001 can be reached, which we can expect from planned instrumentation.
Structural basis for the ligand-binding specificity of fatty acid-binding proteins (pFABP4 and pFABP5) in gentoo penguin.

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Lee, Chang Woo; Kim, Jung Eun; Do, Hackwon; Kim, Ryeo-Ok; Lee, Sung Gu; Park, Hyun Ho; Chang, Jeong Ho; Yim, Joung Han; Park, Hyun; Kim, Il-Chan; Lee, Jun Hyuck

2015-09-11

Fatty acid-binding proteins (FABPs) are involved in transporting hydrophobic fatty acids between various aqueous compartments of the cell by directly binding ligands inside their β-barrel cavities. Here, we report the crystal structures of ligand-unbound pFABP4, linoleate-bound pFABP4, and palmitate-bound pFABP5, obtained from gentoo penguin (Pygoscelis papua), at a resolution of 2.1 Å, 2.2 Å, and 2.3 Å, respectively. The pFABP4 and pFABP5 proteins have a canonical β-barrel structure with two short α-helices that form a cap region and fatty acid ligand binding sites in the hydrophobic cavity within the β-barrel structure. Linoleate-bound pFABP4 and palmitate-bound pFABP5 possess different ligand-binding modes and a unique ligand-binding pocket due to several sequence dissimilarities (A76/L78, T30/M32, underlining indicates pFABP4 residues) between the two proteins. Structural comparison revealed significantly different conformational changes in the β3-β4 loop region (residues 57-62) as well as the flipped Phe60 residue of pFABP5 than that in pFABP4 (the corresponding residue is Phe58). A ligand-binding study using fluorophore displacement assays shows that pFABP4 has a relatively strong affinity for linoleate as compared to pFABP5. In contrast, pFABP5 exhibits higher affinity for palmitate than that for pFABP4. In conclusion, our high-resolution structures and ligand-binding studies provide useful insights into the ligand-binding preferences of pFABPs based on key protein-ligand interactions. Copyright © 2015 Elsevier Inc. All rights reserved.
A Flexible Binding Site Architecture Provides New Insights into CcpA Global Regulation in Gram-Positive Bacteria.

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Yang, Yunpeng; Zhang, Lu; Huang, He; Yang, Chen; Yang, Sheng; Gu, Yang; Jiang, Weihong

2017-01-24

Catabolite control protein A (CcpA) is the master regulator in Gram-positive bacteria that mediates carbon catabolite repression (CCR) and carbon catabolite activation (CCA), two fundamental regulatory mechanisms that enable competitive advantages in carbon catabolism. It is generally regarded that CcpA exerts its regulatory role by binding to a typical 14- to 16-nucleotide (nt) consensus site that is called a catabolite response element (cre) within the target regions. However, here we report a previously unknown noncanonical flexible architecture of the CcpA-binding site in solventogenic clostridia, providing new mechanistic insights into catabolite regulation. This novel CcpA-binding site, named cre var , has a unique architecture that consists of two inverted repeats and an intervening spacer, all of which are variable in nucleotide composition and length, except for a 6-bp core palindromic sequence (TGTAAA/TTTACA). It was found that the length of the intervening spacer of cre var can affect CcpA binding affinity, and moreover, the core palindromic sequence of cre var is the key structure for regulation. Such a variable architecture of cre var shows potential importance for CcpA's diverse and fine regulation. A total of 103 potential cre var sites were discovered in solventogenic Clostridium acetobutylicum, of which 42 sites were picked out for electrophoretic mobility shift assays (EMSAs), and 30 sites were confirmed to be bound by CcpA. These 30 cre var sites are associated with 27 genes involved in many important pathways. Also of significance, the cre var sites are found to be widespread and function in a great number of taxonomically different Gram-positive bacteria, including pathogens, suggesting their global role in Gram-positive bacteria. In Gram-positive bacteria, the global regulator CcpA controls a large number of important physiological and metabolic processes. Although a typical consensus CcpA-binding site, cre, has been identified, it remains
Binding of 3H-actinomycin D with polytene chromosomes of Drosophila melanogaster

International Nuclear Information System (INIS)

Lakhotia, S.C.

1976-01-01

Binding of 3 H-AMD (actinomycin D) in different regions of polytene nuclei of late third instar larvae of Drosophila melanogaster has been examined by EM autoradiography. It is observed that the binding capacity of 3 H-AMD is not related to the transcribing activity of a given region of nuclei, but it may be related to the DNA content. (M.G.B.)
Source, variability, and transformation of nitrate in a regional karst aquifer: Edwards aquifer, central Texas.

Science.gov (United States)

Musgrove, MaryLynn; Opsahl, Stephen P.; Mahler, Barbara J.; Herrington, Chris; Sample, Thomas; Banta, John

2016-01-01

Many karst regions are undergoing rapid population growth and expansion of urban land accompanied by increases in wastewater generation and changing patterns of nitrate (NO3−) loading to surface and groundwater. We investigate variability and sources of NO3− in a regional karst aquifer system, the Edwards aquifer of central Texas. Samples from streams recharging the aquifer, groundwater wells, and springs were collected during 2008–12 from the Barton Springs and San Antonio segments of the Edwards aquifer and analyzed for nitrogen (N) species concentrations and NO3− stable isotopes (δ15N and δ18O). These data were augmented by historical data collected from 1937 to 2007. NO3− concentrations and discharge data indicate that short-term variability (days to months) in groundwater NO3− concentrations in the Barton Springs segment is controlled by occurrence of individual storms and multi-annual wet-dry cycles, whereas the lack of short-term variability in groundwater in the San Antonio segment indicates the dominance of transport along regional flow paths. In both segments, longer-term increases (years to decades) in NO3− concentrations cannot be attributed to hydrologic conditions; rather, isotopic ratios and land-use change indicate that septic systems and land application of treated wastewater might be the source of increased loading of NO3−. These results highlight the vulnerability of karst aquifers to NO3− contamination from urban wastewater. An analysis of N-species loading in recharge and discharge for the Barton Springs segment during 2008–10 indicates an overall mass balance in total N, but recharge contains higher concentrations of organic N and lower concentrations of NO3−than does discharge, consistent with nitrification of organic N within the aquifer and consumption of dissolved oxygen. This study demonstrates that subaqueous nitrification of organic N in the aquifer, as opposed to in soils, might be a previously
Co-ordinate control of synthesis of mitochondrial and non-mitochondrial hemoproteins: a binding site for the HAP1 (CYP1) protein in the UAS region of the yeast catalase T gene (CTT1).

Science.gov (United States)

Winkler, H; Adam, G; Mattes, E; Schanz, M; Hartig, A; Ruis, H

1988-01-01

Control of expression of the Saccharomyces cerevisiae CTT1 (catalase T) gene by the HAP1 (CYP1) gene, a mediator of heme control of mitochondrial cytochromes, was studied. Expression of a CTT1-lacZ fusion in a hap1 mutant showed that the CTT1 promoter is under HAP1 control. As demonstrated by a gel retardation assay, the HAP1 protein binds to a heme control region of the CTT1 gene. This binding in vitro is stimulated by hemin. The HAP1-binding sequence was localized by using DNA fragments spanning different regions, by DNase I footprinting and by methylation interference of DNA-protein binding. The binding site was compared to the HAP1-binding sequences previously characterized in detail (UAS1CYC1, UASCYC7). There is strikingly little similarity between the three sequences, which have only four of those 23 bp in common which are protected from DNase I digestion. However, the pattern of major and minor groove contacts in the complex is quite similar in all three cases. The results obtained show that there is true co-ordinate control of expression of mitochondrial cytochromes and at least some extra-mitochondrial hemoproteins. Heme acts as a metabolic signal in this coordination, which is mediated by the HAP1 protein. Images PMID:2844525
Decomposing global crop yield variability

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Ben-Ari, Tamara; Makowski, David

2014-11-01

Recent food crises have highlighted the need to better understand the between-year variability of agricultural production. Although increasing future production seems necessary, the globalization of commodity markets suggests that the food system would also benefit from enhanced supplies stability through a reduction in the year-to-year variability. Here, we develop an analytical expression decomposing global crop yield interannual variability into three informative components that quantify how evenly are croplands distributed in the world, the proportion of cultivated areas allocated to regions of above or below average variability and the covariation between yields in distinct world regions. This decomposition is used to identify drivers of interannual yield variations for four major crops (i.e., maize, rice, soybean and wheat) over the period 1961-2012. We show that maize production is fairly spread but marked by one prominent region with high levels of crop yield interannual variability (which encompasses the North American corn belt in the USA, and Canada). In contrast, global rice yields have a small variability because, although spatially concentrated, much of the production is located in regions of below-average variability (i.e., South, Eastern and South Eastern Asia). Because of these contrasted land use allocations, an even cultivated land distribution across regions would reduce global maize yield variance, but increase the variance of global yield rice. Intermediate results are obtained for soybean and wheat for which croplands are mainly located in regions with close-to-average variability. At the scale of large world regions, we find that covariances of regional yields have a negligible contribution to global yield variance. The proposed decomposition could be applied at any spatial and time scales, including the yearly time step. By addressing global crop production stability (or lack thereof) our results contribute to the understanding of a key
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
2-[125I]iodomelatonin binding sites in hamster brain membranes: pharmacological characteristics and regional distribution

International Nuclear Information System (INIS)

Duncan, M.J.; Takahashi, J.S.; Dubocovich, M.L.

1988-01-01

Studies in a variety of seasonally breeding mammals have shown that melatonin mediates photoperiodic effects on reproduction. Relatively little is known, however, about the site(s) or mechanisms of action of this hormone for inducing reproductive effects. Although binding sites for [3H]melatonin have been reported previously in bovine, rat, and hamster brain, the pharmacological selectivity of these sites was never demonstrated. In the present study, we have characterized binding sites for a new radioligand, 2-[125I]iodomelatonin, in brains from a photoperiodic species, the Syrian hamster. 2-[125I]Iodomelatonin labels a high affinity binding site in hamster brain membranes. Specific binding of 2-[125I]iodomelatonin is rapid, stable, saturable, and reversible. Saturation studies demonstrated that 2-[125I]iodomelatonin binds to a single class of sites with an affinity constant (Kd) of 3.3 +/- 0.5 nM and a total binding capacity (Bmax) of 110.2 +/- 13.4 fmol/mg protein (n = 4). The Kd value determined from kinetic analysis (3.1 +/- 0.9 nM; n = 5) was very similar to that obtained from saturation experiments. Competition experiments showed that the relative order of potency of a variety of indoles for inhibition of 2-[125I]iodomelatonin binding site to hamster brain membranes was as follows: 6-chloromelatonin greater than or equal to 2-iodomelatonin greater than N-acetylserotonin greater than or equal to 6-methoxymelatonin greater than or equal to melatonin greater than 6-hydroxymelatonin greater than or equal to 6,7-dichloro-2-methylmelatonin greater than 5-methoxytryptophol greater than 5-methoxytryptamine greater than or equal to 5-methoxy-N,N-dimethyltryptamine greater than N-acetyltryptamine greater than serotonin greater than 5-methoxyindole (inactive)
Determining Membrane Protein-Lipid Binding Thermodynamics Using Native Mass Spectrometry.

Science.gov (United States)

Cong, Xiao; Liu, Yang; Liu, Wen; Liang, Xiaowen; Russell, David H; Laganowsky, Arthur

2016-04-06

Membrane proteins are embedded in the biological membrane where the chemically diverse lipid environment can modulate their structure and function. However, the thermodynamics governing the molecular recognition and interaction of lipids with membrane proteins is poorly understood. Here, we report a method using native mass spectrometry (MS), to determine thermodynamics of individual ligand binding events to proteins. Unlike conventional methods, native MS can resolve individual ligand binding events and, coupled with an apparatus to control the temperature, determine binding thermodynamic parameters, such as for protein-lipid interactions. We validated our approach using three soluble protein-ligand systems (maltose binding protein, lysozyme, and nitrogen regulatory protein) and obtained similar results to those using isothermal titration calorimetry and surface plasmon resonance. We also determined for the first time the thermodynamics of individual lipid binding to the ammonia channel (AmtB), an integral membrane protein from Escherichia coli. Remarkably, we observed distinct thermodynamic signatures for the binding of different lipids and entropy-enthalpy compensation for binding lipids of variable chain length. Additionally, using a mutant form of AmtB that abolishes a specific phosphatidylglycerol (PG) binding site, we observed distinct changes in the thermodynamic signatures for binding PG, implying these signatures can identify key residues involved in specific lipid binding and potentially differentiate between specific lipid binding sites.

Spatial and temporal variability of rainfall in the Tocantins-Araguaia hydrographic region

Directory of Open Access Journals (Sweden)

Glauber Epifanio Loureiro

2015-01-01

Full Text Available Current paper examines the space-time dynamics of yearly rainfall of the Tocantins-Araguaia Hydrographic Region (TAHR, foregrounded on rainfall volume from isohyet maps and interpolated by Kriging geo-statistical method. Rainfall space dynamics was undertaken by the analysis of descriptive statistics, Index of Meteorological Irregularity (IMI and Variation Coefficient. Temporal dynamics was analyzed through the distribution of total annual volume precipitation for each TAHR sub-basin by the Standardized Anomaly Index, trend and magnitude test provided by Mann-Kendall and Sen Tests. Results correlated with meteorological anomalies of the Atlantic (Dipole and Pacific (ENOS Oceans show a highly heterogeneous rainfall behavior with temporal variability. Or rather, a decrease of rainfall extensiveness during years of intense meteorological anomaly with a rainfall increase south of the High Tocantins and Araguaia sub-basins and a decrease of rainfall in the Lower Tocantins sub-basin, with El Niño features. Although the Mann-Kendall test does not show statistically a significant trend for rainfall in the TAHR region, Sen’s estimator reveals a decrease in rainfall in the High Tocantins (-1.24 km³ year-1 and Araguaia (-1.13 km³ year-1 sub-basins and a rainfall increase in the Lower Tocantins sub-basin (0.53 km³ year-1 and in the TAHR region (-1.5 km³ year-1.
Test-retest variability of high resolution positron emission tomography (PET) imaging of cortical serotonin (5HT2A) receptors in older, healthy adults

International Nuclear Information System (INIS)

Chow, Tiffany W; Mamo, David C; Uchida, Hiroyuki; Graff-Guerrero, Ariel; Houle, Sylvain; Smith, Gwenn S; Pollock, Bruce G; Mulsant, Benoit H

2009-01-01

Position emission tomography (PET) imaging using [ 18 F]-setoperone to quantify cortical 5-HT 2A receptors has the potential to inform pharmacological treatments for geriatric depression and dementia. Prior reports indicate a significant normal aging effect on serotonin 5HT 2A receptor (5HT 2A R) binding potential. The purpose of this study was to assess the test-retest variability of [ 18 F]-setoperone PET with a high resolution scanner (HRRT) for measuring 5HT 2A R availability in subjects greater than 60 years old. Methods: Six healthy subjects (age range = 65–78 years) completed two [ 18 F]-setoperone PET scans on two separate occasions 5–16 weeks apart. The average difference in the binding potential (BP ND ) as measured on the two occasions in the frontal and temporal cortical regions ranged between 2 and 12%, with the lowest intraclass correlation coefficient in anterior cingulate regions. We conclude that the test-retest variability of [ 18 F]-setoperone PET in elderly subjects is comparable to that of [ 18 F]-setoperone and other 5HT 2A R radiotracers in younger subject samples
Differential recognition of obligate anaerobic bacteria by human mannose-binding lectin.

Science.gov (United States)

Townsend, R; Read, R C; Turner, M W; Klein, N J; Jack, D L

2001-05-01

Deficiency of the innate, humoral immune component mannose-binding lectin (MBL) predisposes individuals to a variety of infections, but the importance of MBL in infection by anaerobes has not been addressed. The attachment of MBL to a wide range of anaerobic bacteria associated with human disease and colonization was surveyed. The results suggest that for the species we examined, resistance to MBL binding may be associated with organisms that are more commonly pathogenic and that MBL binding to some bacteria may be phase variable.
RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

Science.gov (United States)

Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

2010-05-01

The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.
Contributions of internal climate variability to mitigation of projected future regional sea level rise

Science.gov (United States)

Hu, A.; Bates, S. C.

2017-12-01

Observations indicate that the global mean surface temperature is rising, so does the global mean sea level. Sea level rise (SLR) can impose significant impacts on island and coastal communities, especially when SLR is compounded with storm surges. Here, via analyzing results from two sets of ensemble simulations from the Community Earth System Model version 1, we investigate how the potential SLR benefits through mitigating the future emission scenarios from business as usual to a mild-mitigation over the 21st Century would be affected by internal climate variability. Results show that there is almost no SLR benefit in the near term due to the large SLR variability due to the internal ocean dynamics. However, toward the end of the 21st century, the SLR benefit can be as much as a 26±1% reduction of the global mean SLR due to seawater thermal expansion. Regionally, the benefits from this mitigation for both near and long terms are heterogeneous. They vary from just a 11±5% SLR reduction in Melbourne, Australia to a 35±6% reduction in London. The processes contributing to these regional differences are the coupling of the wind-driven ocean circulation with the decadal scale sea surface temperature mode in the Pacific and Southern Oceans, and the changes of the thermohaline circulation and the mid-latitude air-sea coupling in the Atlantic.
FR-like EBNA1 binding repeats in the human genome

International Nuclear Information System (INIS)

D'Herouel, Aymeric Fouquier; Birgersdotter, Anna; Werner, Maria

2010-01-01

Epstein-Barr virus (EBV) is widely spread in the human population. EBV nuclear antigen 1 (EBNA1) is a transcription factor that activates viral genes and is necessary for viral replication and partitioning, which binds the EBV genome cooperatively. We identify similar EBNA1 repeat binding sites in the human genome using a nearest-neighbor positional weight matrix. Previously experimentally verified EBNA1 sites in the human genome are successfully recovered by our approach. Most importantly, 40 novel regions are identified in the human genome, constituted of tandemly repeated binding sites for EBNA1. Genes located in the vicinity of these regions are presented as possible targets for EBNA1-mediated regulation. Among these, four are discussed in more detail: IQCB1, IMPG1, IRF2BP2 and TPO. Incorporating the cooperative actions of EBNA1 is essential when identifying regulatory regions in the human genome and we believe the findings presented here are highly valuable for the understanding of EBV-induced phenotypic changes.
Comparing the potential for identification of lactobacillus spp. of 16s rDNA variable regions

International Nuclear Information System (INIS)

Riano Pachon, Diego Mauricio; Vanegas Lopez, Maria Consuelo; Gonzalez Garcia, Laura Natalia

2013-01-01

16s rDNA is used for bacterial identification because its variation rate between species allows differentiation. The gene for this ribosomal subunit has 9 variable regions and some of them give more information than others. We were interested in evaluating the potential for species identification of each region and their combinations. We extracted the V1 to V8 regions of 16s rDNA from different strains and species of Lactobacillus and analyzed them using STAP (ss-RNA Taxonomy Assigning Pipeline) and RDP (Ribosomal Database Project) multiclassifier packages. Phylogenetic trees obtained by maximum likelihood analyses were compared. Classification results show that many regions give the correct genus classification using RDP and STAP; however they are not enough to classify up to the level of species. V5V6 region presents the highest quantity of informative fragments but also present the highest rate of false negatives. V1V3 region presents the highest rate of true positives (species) using STAP and the region V5V8 in RDP (genus).The phylogenetic result shows that the reference topology could be obtained using different combination of regions as V1V3 and V1V8.The experimental validation was done using commercial strains from a probiotic tampon. Sequencing analysis show that the V1V3 region gives the same information and result as the complete 16s rDNA; the three isolated strains correspond to the strains indicated in the product. We conclude that the V1V3 region is the minimum required region to classify Lactobacillus spp. in the correct way and this region is useful in metagenomics to analyze probiotics samples.
Site-specific fab fragment biotinylation at the conserved nucleotide binding site for enhanced Ebola detection.

Science.gov (United States)

Mustafaoglu, Nur; Alves, Nathan J; Bilgicer, Basar

2015-07-01

The nucleotide binding site (NBS) is a highly conserved region between the variable light and heavy chains at the Fab domains of all antibodies, and a small molecule that we identified, indole-3-butyric acid (IBA), binds specifically to this site. Fab fragment, with its small size and simple production methods compared to intact antibody, is good candidate for use in miniaturized diagnostic devices and targeted therapeutic applications. However, commonly used modification techniques are not well suited for Fab fragments as they are often more delicate than intact antibodies. Fab fragments are of particular interest for sensor surface functionalization but immobilization results in damage to the antigen binding site and greatly reduced activity due to their truncated size that allows only a small area that can bind to surfaces without impeding antigen binding. In this study, we describe an NBS-UV photocrosslinking functionalization method (UV-NBS(Biotin) in which a Fab fragment is site-specifically biotinylated with an IBA-EG11-Biotin linker via UV energy exposure (1 J/cm(2)) without affecting its antigen binding activity. This study demonstrates successful immobilization of biotinylated Ebola detecting Fab fragment (KZ52 Fab fragment) via the UV-NBS(Biotin) method yielding 1031-fold and 2-fold better antigen detection sensitivity compared to commonly used immobilization methods: direct physical adsorption and NHS-Biotin functionalization, respectively. Utilization of the UV-NBS(Biotin) method for site-specific conjugation to Fab fragment represents a proof of concept use of Fab fragment for various diagnostic and therapeutic applications with numerous fluorescent probes, affinity molecules and peptides. © 2015 Wiley Periodicals, Inc.
Visually Relating Gene Expression and in vivo DNA Binding Data

Energy Technology Data Exchange (ETDEWEB)

Huang, Min-Yu; Mackey, Lester; Ker?,; nen, Soile V. E.; Weber, Gunther H.; Jordan, Michael I.; Knowles, David W.; Biggin, Mark D.; Hamann, Bernd

2011-09-20

Gene expression and in vivo DNA binding data provide important information for understanding gene regulatory networks: in vivo DNA binding data indicate genomic regions where transcription factors are bound, and expression data show the output resulting from this binding. Thus, there must be functional relationships between these two types of data. While visualization and data analysis tools exist for each data type alone, there is a lack of tools that can easily explore the relationship between them. We propose an approach that uses the average expression driven by multiple of ciscontrol regions to visually relate gene expression and in vivo DNA binding data. We demonstrate the utility of this tool with examples from the network controlling early Drosophila development. The results obtained support the idea that the level of occupancy of a transcription factor on DNA strongly determines the degree to which the factor regulates a target gene, and in some cases also controls whether the regulation is positive or negative.
Antarctic climate variability on regional and continental scales over the last 2000 years

Directory of Open Access Journals (Sweden)

B. Stenni

2017-11-01

Full Text Available Climate trends in the Antarctic region remain poorly characterized, owing to the brevity and scarcity of direct climate observations and the large magnitude of interannual to decadal-scale climate variability. Here, within the framework of the PAGES Antarctica2k working group, we build an enlarged database of ice core water stable isotope records from Antarctica, consisting of 112 records. We produce both unweighted and weighted isotopic (δ18O composites and temperature reconstructions since 0 CE, binned at 5- and 10-year resolution, for seven climatically distinct regions covering the Antarctic continent. Following earlier work of the Antarctica2k working group, we also produce composites and reconstructions for the broader regions of East Antarctica, West Antarctica and the whole continent. We use three methods for our temperature reconstructions: (i a temperature scaling based on the δ18O–temperature relationship output from an ECHAM5-wiso model simulation nudged to ERA-Interim atmospheric reanalyses from 1979 to 2013, and adjusted for the West Antarctic Ice Sheet region to borehole temperature data, (ii a temperature scaling of the isotopic normalized anomalies to the variance of the regional reanalysis temperature and (iii a composite-plus-scaling approach used in a previous continent-scale reconstruction of Antarctic temperature since 1 CE but applied to the new Antarctic ice core database. Our new reconstructions confirm a significant cooling trend from 0 to 1900 CE across all Antarctic regions where records extend back into the 1st millennium, with the exception of the Wilkes Land coast and Weddell Sea coast regions. Within this long-term cooling trend from 0 to 1900 CE, we find that the warmest period occurs between 300 and 1000 CE, and the coldest interval occurs from 1200 to 1900 CE. Since 1900 CE, significant warming trends are identified for the West Antarctic Ice Sheet, the Dronning Maud Land coast and the
Spatiotemporal Variability and Covariability of Temperature, Precipitation, Soil Moisture, and Vegetation in North America for Regional Climate Model Applications

Science.gov (United States)

Castro, C. L.; Beltran-Przekurat, A. B.; Pielke, R. A.

2007-05-01

Previous work has established that the dominant modes of Pacific SSTs influence the summer climate of North America through large-scale forcing, and this effect is most pronounced during the early part of the season. It is hypothesized, then, that land surface influences become more dominant in the latter part of the season as remote teleconnection influences diminish. As a first step toward investigation of this hypothesis in a regional climate model (RCM) framework, the statistically signficant spatiotemporal patterns of variability and covariability in North American precipitation (specified by the standardized precipitation index, or SPI), soil moisture, and vegetation are determined for timescales from a month to six months. To specify these respective data we use: CPC gauge- derived precipitation (1950-2000), Variable Infiltration Capacity (VIC) Model and NOAH Model NLDAS soil moisture and temperature, and the Global Inventory Modeling and Mapping Studies Normalized Difference Vegetation Index (GIMMS-NDVI). The principal statistical tool used is multiple taper frequency singular value decomposition (MTM-SVD), and this is supplemented by wavelet analysis for specific areas of interest. The significant interannual variability in all of these data occur at a timescale of about 7 to 9 years and appears to be the integrated effect of remote SST forcing from the Pacific. Considering the entire year, the spatial pattern for precipitation resembles the typical ENSO winter signature. If the summer season is considered seperately, the out of phase relationship between precipitation anomalies in the central U.S. and core monsoon region is apparent. The largest soil moisture anomalies occur in the central U.S., since precipitation in this region has a consistent relationship to Pacific SSTs for the entire year. This helps to explain the approximately 20 year periodicity in drought conditions there. Unlike soil moisture, the largest anomalies in vegetation occur in the
Source, variability, and transformation of nitrate in a regional karst aquifer: Edwards aquifer, central Texas

Energy Technology Data Exchange (ETDEWEB)

Musgrove, M., E-mail: mmusgrov@usgs.gov [U.S. Geological Survey, 1505 Ferguson Lane, Austin, TX 78754 (United States); Opsahl, S.P. [U.S. Geological Survey, 5563 DeZavala, Ste. 290, San Antonio, TX 78249 (United States); Mahler, B.J. [U.S. Geological Survey, 1505 Ferguson Lane, Austin, TX 78754 (United States); Herrington, C. [City of Austin Watershed Protection Department, Austin, TX 78704 (United States); Sample, T.L. [U.S. Geological Survey, 19241 David Memorial Dr., Ste. 180, Conroe, TX 77385 (United States); Banta, J.R. [U.S. Geological Survey, 5563 DeZavala, Ste. 290, San Antonio, TX 78249 (United States)

2016-10-15

Many karst regions are undergoing rapid population growth and expansion of urban land accompanied by increases in wastewater generation and changing patterns of nitrate (NO{sub 3}{sup −}) loading to surface and groundwater. We investigate variability and sources of NO{sub 3}{sup −} in a regional karst aquifer system, the Edwards aquifer of central Texas. Samples from streams recharging the aquifer, groundwater wells, and springs were collected during 2008–12 from the Barton Springs and San Antonio segments of the Edwards aquifer and analyzed for nitrogen (N) species concentrations and NO{sub 3}{sup −} stable isotopes (δ{sup 15}N and δ{sup 18}O). These data were augmented by historical data collected from 1937 to 2007. NO{sub 3}{sup −} concentrations and discharge data indicate that short-term variability (days to months) in groundwater NO{sub 3}{sup −} concentrations in the Barton Springs segment is controlled by occurrence of individual storms and multi-annual wet-dry cycles, whereas the lack of short-term variability in groundwater in the San Antonio segment indicates the dominance of transport along regional flow paths. In both segments, longer-term increases (years to decades) in NO{sub 3}{sup −} concentrations cannot be attributed to hydrologic conditions; rather, isotopic ratios and land-use change indicate that septic systems and land application of treated wastewater might be the source of increased loading of NO{sub 3}{sup −}. These results highlight the vulnerability of karst aquifers to NO{sub 3}{sup −} contamination from urban wastewater. An analysis of N-species loading in recharge and discharge for the Barton Springs segment during 2008–10 indicates an overall mass balance in total N, but recharge contains higher concentrations of organic N and lower concentrations of NO{sub 3}{sup −} than does discharge, consistent with nitrification of organic N within the aquifer and consumption of dissolved oxygen. This study demonstrates
Source, variability, and transformation of nitrate in a regional karst aquifer: Edwards aquifer, central Texas

International Nuclear Information System (INIS)

Musgrove, M.; Opsahl, S.P.; Mahler, B.J.; Herrington, C.; Sample, T.L.; Banta, J.R.

2016-01-01

Many karst regions are undergoing rapid population growth and expansion of urban land accompanied by increases in wastewater generation and changing patterns of nitrate (NO 3 − ) loading to surface and groundwater. We investigate variability and sources of NO 3 − in a regional karst aquifer system, the Edwards aquifer of central Texas. Samples from streams recharging the aquifer, groundwater wells, and springs were collected during 2008–12 from the Barton Springs and San Antonio segments of the Edwards aquifer and analyzed for nitrogen (N) species concentrations and NO 3 − stable isotopes (δ 15 N and δ 18 O). These data were augmented by historical data collected from 1937 to 2007. NO 3 − concentrations and discharge data indicate that short-term variability (days to months) in groundwater NO 3 − concentrations in the Barton Springs segment is controlled by occurrence of individual storms and multi-annual wet-dry cycles, whereas the lack of short-term variability in groundwater in the San Antonio segment indicates the dominance of transport along regional flow paths. In both segments, longer-term increases (years to decades) in NO 3 − concentrations cannot be attributed to hydrologic conditions; rather, isotopic ratios and land-use change indicate that septic systems and land application of treated wastewater might be the source of increased loading of NO 3 − . These results highlight the vulnerability of karst aquifers to NO 3 − contamination from urban wastewater. An analysis of N-species loading in recharge and discharge for the Barton Springs segment during 2008–10 indicates an overall mass balance in total N, but recharge contains higher concentrations of organic N and lower concentrations of NO 3 − than does discharge, consistent with nitrification of organic N within the aquifer and consumption of dissolved oxygen. This study demonstrates that subaqueous nitrification of organic N in the aquifer, as opposed to in soils, might be a
DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP.

Science.gov (United States)

Mitra, Sneha; Biswas, Anushua; Narlikar, Leelavati

2018-04-23

Genome-wide in vivo protein-DNA interactions are routinely mapped using high-throughput chromatin immunoprecipitation (ChIP). ChIP-reported regions are typically investigated for enriched sequence-motifs, which are likely to model the DNA-binding specificity of the profiled protein and/or of co-occurring proteins. However, simple enrichment analyses can miss insights into the binding-activity of the protein. Note that ChIP reports regions making direct contact with the protein as well as those binding through intermediaries. For example, consider a ChIP experiment targeting protein X, which binds DNA at its cognate sites, but simultaneously interacts with four other proteins. Each of these proteins also binds to its own specific cognate sites along distant parts of the genome, a scenario consistent with the current view of transcriptional hubs and chromatin loops. Since ChIP will pull down all X-associated regions, the final reported data will be a union of five distinct sets of regions, each containing binding sites of one of the five proteins, respectively. Characterizing all five different motifs and the corresponding sets is important to interpret the ChIP experiment and ultimately, the role of X in regulation. We present diversity which attempts exactly this: it partitions the data so that each partition can be characterized with its own de novo motif. Diversity uses a Bayesian approach to identify the optimal number of motifs and the associated partitions, which together explain the entire dataset. This is in contrast to standard motif finders, which report motifs individually enriched in the data, but do not necessarily explain all reported regions. We show that the different motifs and associated regions identified by diversity give insights into the various complexes that may be forming along the chromatin, something that has so far not been attempted from ChIP data. Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https
A peek into tropomyosin binding and unfolding on the actin filament.

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Abhishek Singh

Full Text Available BACKGROUND: Tropomyosin is a prototypical coiled coil along its length with subtle variations in structure that allow interactions with actin and other proteins. Actin binding globally stabilizes tropomyosin. Tropomyosin-actin interaction occurs periodically along the length of tropomyosin. However, it is not well understood how tropomyosin binds actin. PRINCIPAL FINDINGS: Tropomyosin's periodic binding sites make differential contributions to two components of actin binding, cooperativity and affinity, and can be classified as primary or secondary sites. We show through mutagenesis and analysis of recombinant striated muscle alpha-tropomyosins that primary actin binding sites have a destabilizing coiled-coil interface, typically alanine-rich, embedded within a non-interface recognition sequence. Introduction of an Ala cluster in place of the native, more stable interface in period 2 and/or period 3 sites (of seven increased the affinity or cooperativity of actin binding, analysed by cosedimentation and differential scanning calorimetry. Replacement of period 3 with period 5 sequence, an unstable region of known importance for cooperative actin binding, increased the cooperativity of binding. Introduction of the fluorescent probe, pyrene, near the mutation sites in periods 2 and 3 reported local instability, stabilization by actin binding, and local unfolding before or coincident with dissociation from actin (measured using light scattering, and chain dissociation (analyzed using circular dichroism. CONCLUSIONS: This, and previous work, suggests that regions of tropomyosin involved in binding actin have non-interface residues specific for interaction with actin and an unstable interface that is locally stabilized upon binding. The destabilized interface allows residues on the coiled-coil surface to obtain an optimal conformation for interaction with actin by increasing the number of local substates that the side chains can sample. We suggest
Ropizine concurrently enhances and inhibits [3H] dextromethorpan binding to different structures of the guinea pig brain: Autoradiographic evidence for multiple binding sites

International Nuclear Information System (INIS)

Canoll, P.D.; Smith, P.R.; and Musacchio, J.M.

1990-01-01

Ropizine produces a simultaneous enhancement and inhibition of [ 3 H] dextromethorphan (DM) high-affinity binding to different areas of the guinea pig brain. These results imply that there are two distinct types of high-affinity [ 3 H]DM binding sites, which are present in variable proportions in different brain structures. The ropizine-enhances [ 3 H]DM binding type was preferentially inhibited by (+)-pentazocine. This is consistent with the presumption that the (+)-pentazocine-sensitive site is identical with the common site for DM and 3-(-3-Hydroxphenyl)-N-(1-propyl)piperidine ((+)-3-PPP). The second binding type, which is inhibited by ropizine and is not so sensitive to (+)- pentazocine, has not been fully characterized. This study demonstrates that the biphasic effects to ropizine are due, at least in part, to the effects of ropizine on two different types of [ 3 H]DM binding sites. However, this study does not rule out that the common DM/(+)-3-PPP site also might be inhibited by higher concentrations of ropizine
Coupled ocean-atmosphere surface variability and its climate impacts in the tropical Atlantic region

Science.gov (United States)

Fontaine, B.; Janicot, Serge; Roucou, P.

This study examines time evolution and statistical relationships involving the two leading ocean-atmosphere coupled modes of variability in the tropical Atlantic and some climate anomalies over the tropical 120°W-60°W region using selected historical files (75-y near global SSTs and precipitation over land), more recent observed data (30-y SST and pseudo wind stress in the tropical Atlantic) and reanalyses from the US National Centers for Environmental Prediction (NCEP/NCAR) reanalysis System on the period 1968-1997: surface air temperature, sea level pressure, moist static energy content at 850 hPa, precipitable water and precipitation. The first coupled mode detected through singular value decomposition of the SST and pseudo wind-stress data over the tropical Atlantic (30°N-20°S) expresses a modulation in the thermal transequatorial gradient of SST anomalies conducted by one month leading wind-stress anomalies mainly in the tropical north Atlantic during northern winter and fall. It features a slight dipole structure in the meridional plane. Its time variability is dominated by a quasi-decadal signal well observed in the last 20-30 ys and, when projected over longer-term SST data, in the 1920s and 1930s but with shorter periods. The second coupled mode is more confined to the south-equatorial tropical Atlantic in the northern summer and explains considerably less wind-stress/SST cross-covariance. Its time series features an interannual variability dominated by shorter frequencies with increased variance in the 1960s and 1970s before 1977. Correlations between these modes and the ENSO-like Nino3 index lead to decreasing amplitude of thermal anomalies in the tropical Atlantic during warm episodes in the Pacific. This could explain the nonstationarity of meridional anomaly gradients on seasonal and interannual time scales. Overall the relationships between the oceanic component of the coupled modes and the climate anomaly patterns denote thermodynamical
Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

Science.gov (United States)

Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

2008-02-01

In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.
RNA binding and replication by the poliovirus RNA polymerase

International Nuclear Information System (INIS)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region
Expression of human FcgammaRIIIa as a GPI-linked molecule on CHO cells to enable measurement of human IgG binding.

Science.gov (United States)

Armour, Kathryn L; Smith, Cheryl S; Clark, Michael R

2010-03-31

The efficacy of a therapeutic IgG molecule may be as dependent on the optimisation of the constant region to suit its intended indication as on the selection of its variable regions. A crucial effector function to be maximised or minimised is antibody-dependent cell-mediated cytotoxicity by natural killer cells. Traditional assays of ADCC activity suffer from considerable inter-donor and intra-donor variability, which makes the measurement of antibody binding to human FcgammaRIIIa, the key receptor for ADCC, an attractive alternative method of assessment. Here, we describe the development of cell lines and assays for this purpose. The transmembrane receptor, FcgammaRIIIa, requires co-expression with signal transducing subunits to prevent its degradation, unlike the homologous receptor FcgammaRIIIb that is expressed as a GPI-anchored molecule. Therefore, to simplify the production of cell lines as reliable assay components, we expressed FcgammaRIIIa as a GPI-anchored molecule. Separate, stable CHO cell lines that express either the 158F or the higher-affinity 158V allotype of FcgammaRIIIa were isolated using fluorescence-activated cell sorting. The identities of the expressed receptors were confirmed using a panel of monoclonal antibodies that distinguish between subclasses and allotypes of FcgammaRIII and the cell lines were shown to have slightly higher levels of receptor than FcgammaRIII-positive peripheral blood mononuclear cells. Because the affinity of FcgammaRIIIa for IgG is intermediate amongst the receptors that bind IgG, we were able to use these cell lines to develop flow cytometric assays to measure the binding of both complexed and monomeric immunoglobulin. Thus, by choosing the appropriate method, weakly- or strongly-binding IgG can be efficiently compared. We have quantified the difference in the binding of wildtype IgG1 and IgG3 molecules to the two functional allotypes of the receptor and report that the FcgammaRIIIa-158V-antibody interaction is 3

Autoradiographic analysis of tritiated imipramine binding in the human brain post mortem: effects of suicide

International Nuclear Information System (INIS)

Gross-Isseroff, R.; Israeli, M.; Biegon, A.

1989-01-01

In vitro quantitative autoradiography of high-affinity tritiated imipramine binding sites was performed on brains of 12 suicide victims and 12 matched controls. Region-specific differences in imipramine binding were found between the two groups. Thus, the pyramidal and molecular layers of the cornu ammoni hippocampal fields and the hilus of the dentate gyrus exhibited 80%, 60%, and 90% increases in binding in the suicide group, respectively. The postcentral cortical gyrus, insular cortex, and claustrum had 45%, 28%, and 75% decreases in binding in the suicide group, respectively. No difference in imipramine binding was observed in prefrontal cortical regions, in the basal ganglia, and in mesencephalic nuclei. No sex and postmortem delay effects on imipramine binding were found. Imipramine binding was positively correlated with age, the effect of age being most pronounced in portions of the basal ganglia and temporal cortex
Observed Regional Climate Variability during the Last 50 Years in Reindeer Herding Cooperatives of Finnish Fell Lapland

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Élise Lépy

2017-10-01

Full Text Available In Finnish Lapland, reindeer herders’ activity is strongly dependent on the surrounding natural environment, which is directly exposed to environmental changes and climatic variations. By assessing whether there is any evidence of change in climate in Fell Lapland over the last 50 years, this paper attempts to link global climatic trends with local conditions and respond to the need of information at the local level. It aims at assessing the changes in temperature, precipitation and snow cover at a regional and local scale, as well as determining the climatic trends for the period 1960–2011. Statistical methods were used to conduct analyses of the regional homogeneity, the annual and seasonal variability, and the cold intensity. The results show that the regional climate is not homogeneous and differences exist between locations. Nevertheless, it can be concluded that, in general, a warming trend is discernible for the period 1960–2011, frost and thaw cycles slightly increase, and variations in mean temperatures are more important in the winter. Precipitation is more variable according to the site but, in general, precipitation is increasing with time, especially in the winter, and the snow cover does not seem to contain any discernible trend.
Specific labeling of the thyroxine binding site in thyroxine-binding globulin: determination of the amino acid composition of a labeled peptide fragment isolated from a proteolytic digest of the derivatized protein.

Science.gov (United States)

Tabachnick, M; Perret, V

1987-08-01

[125I] Thyroxine has been covalently bound to the thyroxine binding site in thyroxine-binding globulin by reaction with the bifunctional reagent, 1,5-difluoro-2,4-dinitrobenzene. An average of 0.47 mol of [125I] thyroxine was incorporated per mol protein; nonspecific binding amounted to 8%. A labeled peptide fragment was isolated from a proteolytic digest of the derivatized protein by HPLC and its amino acid composition was determined. Comparison with the amino acid sequence of thyroxine-binding globulin indicated partial correspondence of the labeled peptide with two possible regions in the protein. These regions also coincide with part of the barrel structure present in the closely homologous protein, alpha 1-antitrypsin.
Using a predictive model to evaluate spatiotemporal variability in streamflow permanence across the Pacific Northwest region

Science.gov (United States)

Jaeger, K. L.

2017-12-01

The U.S. Geological Survey (USGS) has developed the PRObability Of Streamflow PERmanence (PROSPER) model, a GIS-based empirical model that provides predictions of the annual probability of a stream channel having year-round flow (Streamflow permanence probability; SPP) for any unregulated and minimally-impaired stream channel in the Pacific Northwest (Washington, Oregon, Idaho, western Montana). The model provides annual predictions for 2004-2016 at a 30-m spatial resolution based on monthly or annually updated values of climatic conditions, and static physiographic variables associated with the upstream basin. Prediction locations correspond to the channel network consistent with the National Hydrography Dataset stream grid and are publicly available through the USGS StreamStats platform (https://water.usgs.gov/osw/streamstats/). In snowmelt-driven systems, the most informative predictor variable was mean upstream snow water equivalent on May 1, which highlights the influence of late spring snow cover for supporting streamflow in mountain river networks. In non-snowmelt-driven systems, the most informative variable was mean annual precipitation. Streamflow permanence probabilities varied across the study area by geography and from year-to-year. Notably lower SPP corresponded to the climatically drier subregions of the study area. Higher SPP were concentrated in coastal and higher elevation mountain regions. In addition, SPP appeared to trend with average hydroclimatic conditions, which were also geographically coherent. The year-to-year variability lends support for the growing recognition of the spatiotemporal dynamism of streamflow permanence. An analysis of three focus basins located in contrasting geographical and hydroclimatic settings demonstrates differences in the sensitivity of streamflow permanence to antecedent climate conditions as a function of geography. Consequently, results suggest that PROSPER model can be a useful tool to evaluate regions of the
Prevalence and variability of use of home mechanical ventilators, positive airway pressure and oxygen devices in the Lombardy region, Italy.

Science.gov (United States)

Vitacca, Michele; Barbano, Luca; Colombo, Daniele; Leoni, Olivia; Guffanti, Enrico

2018-01-29

Few studies have analyzed the prevalence and accessibility of home mechanical ventilation (HMV) in Italy. We aimed to investigate the prevalence and prescription variability of HMV as well as of long-term oxygen therapy (LTOT) and continuous positive airway pressure (CPAP), in the Lombardy Region. Prescribing rates of HMV (both noninvasive and tracheostomies), CPAP (auto-CPAP, CPAP/other sleep machines) and LTOT (liquid-O2, O2-gas, concentrators) in the 15 Local Healthcare districts of Lombardy were gathered from billing data for 2012 and compared. Crude rates (per 100,000 population) and rates for the different healthcare districts were calculated. In 2012, 6325 patients were on HMV (crude prescription rate: 63/100,000) with a high variation across districts (8/100,000 in Milano 1 vs 150/100,000 in Pavia). There were 14,237 patients on CPAP (crude prescription rate: 142/100,000; CPAP/other sleep machines 95.3% vs auto-CPAP 4.7%) with also high intra-regional variation (56/100,000 in Mantova vs. 260/100,000 in Pavia). There were 21,826 patients on LTOT (prescription rate: 217/100,000 rate; liquid-O2 94%, O2-gas 2.08%, O2-concentrators 3.8%), with again high intra-regional variation (100/100,000 in Bergamo vs 410/100,000 in Valle Camonica). The crude rate of HMV prescriptions in Lombardy is very high, with a high intra-regional variability in prescribing HMV, LTOT and CPAP which is partly explainable by the accessibility to specialist centers with HMV/sleep-study facilities. Analysis of administrative data and variability mapping can help identify areas of reduced access for an improved standardization of services. An audit among Health Payer and prescribers to interpret the described huge variability could be welcomed.
Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions

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Wen Bo

2012-10-01

Full Text Available Abstract Background The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as Large Organized Chromatin K (lysine modifications (LOCKs, of histone H3 lysine-9 dimethylation (H3K9me2 or other repressive histone posttranslational modifications. The microstructure of these regions has not previously been explored. Results We analyzed the genome-wide distribution of H3K9me2 in two human pluripotent stem cell lines and three differentiated cells lines. We identified > 2,500 small regions with very low H3K9me2 signals in the body of LOCKs, which were termed as euchromatin islands (EIs. EIs are 6.5-fold enriched for DNase I Hypersensitive Sites and 8-fold enriched for the binding of CTCF, the major organizer of higher-order chromatin. Furthermore, EIs are 2–6 fold enriched for differentially DNA-methylated regions associated with tissue types (T-DMRs, reprogramming (R-DMRs and cancer (C-DMRs. Gene ontology (GO analysis suggests that EI-associated genes are functionally related to organ system development, cell adhesion and cell differentiation. Conclusions We identify the existence of EIs as a finer layer of epigenomic architecture within large heterochromatin domains. Their enrichment for CTCF sites and DNAse hypersensitive sites, as well as association with DMRs, suggest that EIs play an important role in normal epigenomic architecture and its disruption in disease.
DNA-binding specificity and molecular functions of NAC transcription factors

DEFF Research Database (Denmark)

Olsen, Addie Nina; Ernst, Heidi Asschenfeldt; Lo Leggio, Leila

2005-01-01

The family of NAC (NAM/ATAF1,2/CUC2) transcription factors has been implicated in a wide range of plant processes, but knowledge on the DNA-binding properties of the family is limited. Using a reiterative selection procedure on random oligonucleotides, we have identified consensus binding sites....... Furthermore, NAC protein binding to the CaMV 35S promoter was shown to depend on sequences similar to the consensus of the selected oligonucleotides. Electrophoretic mobility shift assays demonstrated that NAC proteins bind DNA as homo- or heterodimers and that dimerization is necessary for stable DNA binding....... The ability of NAC proteins to dimerize and to bind DNAwas analysed by structure-based mutagenesis. This identified two salt bridge-forming residues essential for NAC protein dimerization. Alteration of basic residues in a loop region containing several highly conserved residues abolished DNA binding. Thus...
N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

Science.gov (United States)

Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

2009-09-15

The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.
An intermediate region in C-terminal of phosphoprotein is required ...

African Journals Online (AJOL)

In this study, the region of P that binds to NPNC was mapped. To determine the binding region, 18 N- and C-terminally truncated P mutants were synthesized by in vitro translation in rabbit reticulocytes and mixed with purified NP (NPNC). The mutants which did not bind to NP were considered as mutants and they contain ...
How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

Science.gov (United States)

Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

2015-06-09

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the
How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

Science.gov (United States)

2016-01-01

Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the
Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

Directory of Open Access Journals (Sweden)

Ji-Long Zhang

Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.
Regional brain [(11)C]carfentanil binding following tobacco smoking.

Science.gov (United States)

Domino, Edward F; Hirasawa-Fujita, Mika; Ni, Lisong; Guthrie, Sally K; Zubieta, Jon Kar

2015-06-03

To determine if overnight tobacco abstinent carriers of the AG or GG (*G) vs. the AA variant of the human mu opioid receptor (OPRM1) A118G polymorphism (rs1799971) differ in [(11)C]carfentanil binding after tobacco smoking. Twenty healthy American male smokers who abstained from tobacco overnight were genotyped and completed positron emission tomography (PET) scans with the mu opioid receptor agonist, [(11)C]carfentanil. They smoked deniconized (denic) and average nicotine (avnic) cigarettes during the PET scans. Smoking avnic cigarette decreased the binding potential (BPND) of [(11)C]carfentanil in the right medial prefrontal cortex (mPfc; 6, 56, 18), left anterior medial prefrontal cortex (amPfc; -2, 46, 44), right ventral striatum (vStr; 16, 3, -10), left insula (Ins; -42, 10, -12), right hippocampus (Hippo; 18, -6, -14) and left cerebellum (Cbl; -10, -88, -34), and increased the BPND in left amygdala (Amy; -20, 0, -22), left putamen (Put; -22, 10, -6) and left nucleus accumbens (NAcc; -10, 12, -8). In the AA allele carriers, avnic cigarette smoking significantly changed the BPND compared to after denic smoking in most brain areas listed above. However in the *G carriers the significant BPND changes were confirmed in only amPfc and vStr. Free mu opioid receptor availability was significantly less in the *G than the AA carriers in the Amy and NAcc. The present study demonstrates that BPND changes induced by avnic smoking in OPRM1 *G carriers were blunted compared to the AA carriers. Also *G smokers had less free mu opioid receptor availability in Amy and NAcc. Copyright © 2015 Elsevier Inc. All rights reserved.
B cell recognition of the conserved HIV-1 co-receptor binding site is altered by endogenous primate CD4.

Directory of Open Access Journals (Sweden)

Mattias N E Forsell

2008-10-01

Full Text Available The surface HIV-1 exterior envelope glycoprotein, gp120, binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process. The binding site is comprised of a highly conserved region on the gp120 core, as well as elements of the third variable region (V3. Antibodies against the co-receptor binding site are abundantly elicited during natural infection of humans, but the mechanism of elicitation has remained undefined. In this study, we investigate the requirements for elicitation of co-receptor binding site antibodies by inoculating rabbits, monkeys and human-CD4 transgenic (huCD4 rabbits with envelope glycoprotein (Env trimers possessing high affinity for primate CD4. A cross-species comparison of the antibody responses showed that similar HIV-1 neutralization breadth was elicited by Env trimers in monkeys relative to wild-type (WT rabbits. In contrast, antibodies against the co-receptor site on gp120 were elicited only in monkeys and huCD4 rabbits, but not in the WT rabbits. This was supported by the detection of high-titer co-receptor antibodies in all sera from a set derived from human volunteers inoculated with recombinant gp120. These findings strongly suggest that complexes between Env and (high-affinity primate CD4 formed in vivo are responsible for the elicitation of the co-receptor-site-directed antibodies. They also imply that the naïve B cell receptor repertoire does not recognize the gp120 co-receptor site in the absence of CD4 and illustrate that conformational stabilization, imparted by primary receptor interaction, can alter the immunogenicity of a type 1 viral membrane protein.
B cell recognition of the conserved HIV-1 co-receptor binding site is altered by endogenous primate CD4.

Science.gov (United States)

Forsell, Mattias N E; Dey, Barna; Mörner, Andreas; Svehla, Krisha; O'dell, Sijy; Högerkorp, Carl-Magnus; Voss, Gerald; Thorstensson, Rigmor; Shaw, George M; Mascola, John R; Karlsson Hedestam, Gunilla B; Wyatt, Richard T

2008-10-03

The surface HIV-1 exterior envelope glycoprotein, gp120, binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process. The binding site is comprised of a highly conserved region on the gp120 core, as well as elements of the third variable region (V3). Antibodies against the co-receptor binding site are abundantly elicited during natural infection of humans, but the mechanism of elicitation has remained undefined. In this study, we investigate the requirements for elicitation of co-receptor binding site antibodies by inoculating rabbits, monkeys and human-CD4 transgenic (huCD4) rabbits with envelope glycoprotein (Env) trimers possessing high affinity for primate CD4. A cross-species comparison of the antibody responses showed that similar HIV-1 neutralization breadth was elicited by Env trimers in monkeys relative to wild-type (WT) rabbits. In contrast, antibodies against the co-receptor site on gp120 were elicited only in monkeys and huCD4 rabbits, but not in the WT rabbits. This was supported by the detection of high-titer co-receptor antibodies in all sera from a set derived from human volunteers inoculated with recombinant gp120. These findings strongly suggest that complexes between Env and (high-affinity) primate CD4 formed in vivo are responsible for the elicitation of the co-receptor-site-directed antibodies. They also imply that the naïve B cell receptor repertoire does not recognize the gp120 co-receptor site in the absence of CD4 and illustrate that conformational stabilization, imparted by primary receptor interaction, can alter the immunogenicity of a type 1 viral membrane protein.
In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

Science.gov (United States)

Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

2013-01-01

We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

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Chung, Dongjun; Kuan, Pei Fen; Li, Bo; Sanalkumar, Rajendran; Liang, Kun; Bresnick, Emery H; Dewey, Colin; Keleş, Sündüz

2011-07-01

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip) as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads). This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads). Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.
Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data.

Directory of Open Access Journals (Sweden)

Dongjun Chung

2011-07-01

Full Text Available Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq is rapidly replacing chromatin immunoprecipitation combined with genome-wide tiling array analysis (ChIP-chip as the preferred approach for mapping transcription-factor binding sites and chromatin modifications. The state of the art for analyzing ChIP-seq data relies on using only reads that map uniquely to a relevant reference genome (uni-reads. This can lead to the omission of up to 30% of alignable reads. We describe a general approach for utilizing reads that map to multiple locations on the reference genome (multi-reads. Our approach is based on allocating multi-reads as fractional counts using a weighted alignment scheme. Using human STAT1 and mouse GATA1 ChIP-seq datasets, we illustrate that incorporation of multi-reads significantly increases sequencing depths, leads to detection of novel peaks that are not otherwise identifiable with uni-reads, and improves detection of peaks in mappable regions. We investigate various genome-wide characteristics of peaks detected only by utilization of multi-reads via computational experiments. Overall, peaks from multi-read analysis have similar characteristics to peaks that are identified by uni-reads except that the majority of them reside in segmental duplications. We further validate a number of GATA1 multi-read only peaks by independent quantitative real-time ChIP analysis and identify novel target genes of GATA1. These computational and experimental results establish that multi-reads can be of critical importance for studying transcription factor binding in highly repetitive regions of genomes with ChIP-seq experiments.
New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro.

Science.gov (United States)

Klaassen, Kristel; Stankovic, Biljana; Kotur, Nikola; Djordjevic, Maja; Zukic, Branka; Nikcevic, Gordana; Ugrin, Milena; Spasovski, Vesna; Srzentic, Sanja; Pavlovic, Sonja; Stojiljkovic, Maja

2017-02-01

Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.
Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data.

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Palumbo, Michael J; Newberg, Lee A

2010-07-01

The transcription of a gene from its DNA template into an mRNA molecule is the first, and most heavily regulated, step in gene expression. Especially in bacteria, regulation is typically achieved via the binding of a transcription factor (protein) or small RNA molecule to the chromosomal region upstream of a regulated gene. The protein or RNA molecule recognizes a short, approximately conserved sequence within a gene's promoter region and, by binding to it, either enhances or represses expression of the nearby gene. Since the sought-for motif (pattern) is short and accommodating to variation, computational approaches that scan for binding sites have trouble distinguishing functional sites from look-alikes. Many computational approaches are unable to find the majority of experimentally verified binding sites without also finding many false positives. Phyloscan overcomes this difficulty by exploiting two key features of functional binding sites: (i) these sites are typically more conserved evolutionarily than are non-functional DNA sequences; and (ii) these sites often occur two or more times in the promoter region of a regulated gene. The website is free and open to all users, and there is no login requirement. Address: (http://bayesweb.wadsworth.org/phyloscan/).

Surface display of the receptor-binding region of the Lactobacillus brevis S-layer protein in Lactococcus lactis provides nonadhesive lactococci with the ability to adhere to intestinal epithelial cells.

Science.gov (United States)

Avall-Jääskeläinen, Silja; Lindholm, Agneta; Palva, Airi

2003-04-01

Lactobacillus brevis is a promising lactic acid bacterium for use as a probiotic dietary adjunct and a vaccine vector. The N-terminal region of the S-layer protein (SlpA) of L. brevis ATCC 8287 was recently shown to mediate adhesion to various human cell lines in vitro. In this study, a surface display cassette was constructed on the basis of this SlpA receptor-binding domain, a proteinase spacer, and an autolysin anchor. The cassette was expressed under control of the nisA promoter in Lactococcus lactis NZ9000. Western blot assay of lactococcal cell wall extracts with anti-SlpA antibodies confirmed that the SlpA adhesion domain of the fusion protein was expressed and located within the cell wall layer. Whole-cell enzyme-linked immunosorbent assay and immunofluorescence microscopy verified that the SlpA adhesion-mediating region was accessible on the lactococcal cell surface. In vitro adhesion assays with the human intestinal epithelial cell line Intestine 407 indicated that the recombinant lactococcal cells had gained an ability to adhere to Intestine 407 cells significantly greater than that of wild-type L. lactis NZ9000. Serum inhibition assay further confirmed that adhesion of recombinant lactococci to Intestine 407 cells was indeed mediated by the N terminus-encoding part of the slpA gene. The ability of the receptor-binding region of SlpA to adhere to fibronectin was also confirmed with this lactococcal surface display system. These results show that, with the aid of the receptor-binding region of the L. brevis SlpA protein, the ability to adhere to gut epithelial cells can indeed be transferred to another, nonadhesive, lactic acid bacterium.
Use of variability modes to evaluate AR4 climate models over the Euro-Atlantic region

Energy Technology Data Exchange (ETDEWEB)

Casado, M.J.; Pastor, M.A. [Agencia Estatal de Meteorologia (AEMET), Madrid (Spain)

2012-01-15

This paper analyzes the ability of the multi-model simulations from the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) to simulate the main leading modes of variability over the Euro-Atlantic region in winter: the North-Atlantic Oscillation (NAO), the Scandinavian mode (SCAND), the East/Atlantic Oscillation (EA) and the East Atlantic/Western Russia mode (EA/WR). These modes of variability have been evaluated both spatially, by analyzing the intensity and location of their anomaly centres, as well as temporally, by focusing on the probability density functions and e-folding time scales. The choice of variability modes as a tool for climate model assessment can be justified by the fact that modes of variability determine local climatic conditions and their likely change may have important implications for future climate changes. It is found that all the models considered are able to simulate reasonably well these four variability modes, the SCAND being the mode which is best spatially simulated. From a temporal point of view the NAO and SCAND modes are the best simulated. UKMO-HadGEM1 and CGCM3.1(T63) are the models best at reproducing spatial characteristics, whereas CCSM3 and CGCM3.1(T63) are the best ones with regard to the temporal features. GISS-AOM is the model showing the worst performance, in terms of both spatial and temporal features. These results may bring new insight into the selection and use of specific models to simulate Euro-Atlantic climate, with some models being clearly more successful in simulating patterns of temporal and spatial variability than others. (orig.)
Identification of DNA-binding proteins that interact with the 5'-flanking region of the human D-amino acid oxidase gene by pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry.

Science.gov (United States)

Tran, Diem Hong; Shishido, Yuji; Chung, Seong Pil; Trinh, Huong Thi Thanh; Yorita, Kazuko; Sakai, Takashi; Fukui, Kiyoshi

2015-12-10

D-Amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids and is expected to be a promising therapeutic target of schizophrenia and glioblastoma. The study of DNA-binding proteins has yielded much information in the regulation of transcription and other biological processes. However, proteins interacting with DAO gene have not been elucidated. Our assessment of human DAO promoter activity using luciferase reporter system indicated the 5'-flanking region of this gene (-4289 bp from transcription initiation site) has a regulatory sequence for gene expression, which is regulated by multi-protein complexes interacting with this region. By using pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry, we identified six proteins binding to the 5'-flanking region of the human DAO gene (zinc finger C2HC domain-containing protein 1A; histidine-tRNA ligase, cytoplasmic; molybdenum cofactor biosynthesis protein; 60S ribosomal protein L37; calponin-1; calmodulin binding protein and heterogeneous nuclear ribonucleoprotein A2/B1). These preliminary results will contribute to the advance in the understanding of the potential factors associated with the regulatory mechanism of DAO expression. Copyright © 2015 Elsevier B.V. All rights reserved.
Delayed Gadolinium-Enhanced MRI of Cartilage (dGEMRIC): Intra- and Interobserver Variability in Standardized Drawing of Regions of Interest

International Nuclear Information System (INIS)

Tiderius, C.J.; Tjoernstrand, J.; Aakeson, P.; Soedersten, K.; Dahlberg, L.; Leander, P.

2004-01-01

Purpose: To establish the reproducibility of a standardized region of interest (ROI) drawing procedure in delayed gadolinium-enhanced magnetic resonance imaging (MRI) of cartilage (dGEMRIC). Material and Methods: A large ROI in lateral and medial femoral weight-bearing cartilage was drawn in images of 12 healthy male volunteers by 6 investigators with different skills in MRI. The procedure was done twice, with a 1-week interval. Calculated T1-values were evaluated for intra- and interobserver variability. Results: The mean interobserver variability for both compartments ranged between 1.3% and 2.3% for the 6 different investigators without correlation to their experience in MRI. Post-contrast intra-observer variability was low in both the lateral and the medial femoral cartilage, 2.6% and 1.5%, respectively. The larger variability in lateral than in medial cartilage was related to slightly longer and thinner ROIs. Conclusion: Intra-observer variability and interobserver variability are both low when a large standardized ROI is used in dGEMRIC. The experience of the investigator does not affect the variability, which further supports a clinical applicability of the method
Role of climate variability in the heatstroke death rates of Kanto region in Japan

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Akihiko, Takaya; Morioka, Yushi; Behera, Swadhin K.

2014-07-01

The death toll by heatstroke in Japan, especially in Kanto region, has sharply increased since 1994 together with large interannual variability. The surface air temperature and humidity observed during boreal summers of 1980-2010 were examined to understand the role of climate in the death toll. The extremely hot days, when the daily maximum temperature exceeds 35°C, are more strongly associated with the death toll than the conventional Wet Bulb Globe Temperature index. The extremely hot days tend to be associated with El Niño/Southern Oscillation or the Indian Ocean Dipole, suggesting a potential link with tropical climate variability to the heatstroke related deaths. Also, the influence of these climate modes on the death toll has strengthened since 1994 probably related to global warming. It is possible to develop early warning systems based on seasonal climate predictions since recent climate models show excellent predictability skills for those climate modes.
Nonspecific DNA Binding and Bending by HUαβ: Interfaces of the Three Binding Modes Characterized by Salt Dependent Thermodynamics

Science.gov (United States)

Koh, Junseock; Shkel, Irina; Saecker, Ruth M.; Record, M. Thomas

2011-01-01

Previous ITC and FRET studies demonstrated that Escherichia coli HUαβ binds nonspecifically to duplex DNA in three different binding modes: a tighter-binding 34 bp mode which interacts with DNA in large (>34 bp) gaps between bound proteins, reversibly bending it 140° and thereby increasing its flexibility, and two weaker, modestly cooperative small-site-size modes (10 bp, 6 bp) useful for filling gaps between bound proteins shorter than 34 bp. Here we use ITC to determine the thermodynamics of these binding modes as a function of salt concentration, and deduce that DNA in the 34 bp mode is bent around but not wrapped on the body of HU, in contrast to specific binding of IHF. Analyses of binding isotherms (8, 15, 34 bp DNA) and initial binding heats (34, 38, 160 bp DNA) reveal that all three modes have similar log-log salt concentration derivatives of the binding constants (Ski) even though their binding site sizes differ greatly; most probable values of Ski on 34 bp or larger DNA are − 7.5 ± 0.5. From the similarity of Ski values, we conclude that binding interfaces of all three modes involve the same region of the arms and saddle of HU. All modes are entropy-driven, as expected for nonspecific binding driven by the polyelectrolyte effect. The bent-DNA 34 bp mode is most endothermic, presumably because of the cost of HU-induced DNA bending, while the 6 bp mode is modestly exothermic at all salt concentrations examined. Structural models consistent with the observed Ski values are proposed. PMID:21513716
Characterization of Campylobacter jejuni applying flaA short variable region sequencing, multilocus sequencing and Fourier transform infrared spectroscopy

DEFF Research Database (Denmark)

Josefsen, Mathilde Hartmann; Bonnichsen, Lise; Larsson, Jonas

flaA short variable region sequencing and phenetic Fourier transform infrared (FTIR) spectroscopy was applied on a collection of 102 Campylobacter jejuni isolated from continuous sampling of organic, free range geese and chickens. FTIR has been shown to serve as a valuable tool in typing...
The Tokar Gap Jet: Regional Circulation, Diurnal Variability, and Moisture Transport Based on Numerical Simulations

KAUST Repository

Davis, Shannon R.

2015-05-14

The structure, variability, and regional connectivity of the Tokar Gap jet (TGJ) are described using WRF Model analyses and supporting atmospheric datasets from the East African–Red Sea–Arabian Peninsula (EARSAP) region during summer 2008. Sources of the TGJ’s unique quasi-diurnal nature and association with atypically high atmospheric moisture transport are traced back to larger-scale atmospheric dynamics influencing its forcing. These include seasonal shifts in the intertropical convergence zone (ITCZ), variability of the monsoon and North African wind regimes, and ties to other orographic flow patterns. Strong modulation of the TGJ by regional processes such as the desert heating cycle, wind convergence at the ITCZ surface front, and the local land–sea breeze cycle are described. Two case studies present the interplay of these influences in detail. The first of these was an “extreme” gap wind event on 12 July, in which horizontal velocities in the Tokar Gap exceeded 26 m s−1 and the flow from the jet extended the full width of the Red Sea basin. This event coincided with development of a large mesoscale convective complex (MCC) and precipitation at the entrance of the Tokar Gap as well as smaller gaps downstream along the Arabian Peninsula. More typical behavior of the TGJ during the 2008 summer is discussed using a second case study on 19 July. Downwind impact of the TGJ is evaluated using Lagrangian model trajectories and analysis of the lateral moisture fluxes (LMFs) during jet events. These results suggest means by which TGJ contributes to large LMFs and has potential bearing upon Sahelian rainfall and MCC development.
Observations of regional and local variability in the optical properties of maritime clouds

Energy Technology Data Exchange (ETDEWEB)

White, A.B. [Univ. of Colorado at Boulder/National Oceanic and Atmospheric Administration, Boulder, CO (United States); Fairall, C.W. [Environmental Technology Lab., Boulder, CO (United States)

1996-04-01

White and Fairall (1995) calculated the optical properties of the marine boundary layer (MBL) clouds observed during the Atlantic Stratocumulus Transition Experiment (ASTEX) and compared their results with the results obtained by Fairall et al. for the MBL clouds observed during the First International Satellite Climatology Program (ISSCP) Regional Experiment (FIRE). They found a factor of two difference in the optical depth versus liquid water relationship that applies to the clouds observed in each case. In the present study, we present evidence to support this difference. We also investigate the local variability exhibited in the ASTEX optical properties using measurements of the boundary layer aerosol concentration.
Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

Directory of Open Access Journals (Sweden)

Alberto Muñoz

2016-10-01

Full Text Available Ecological Niche Models (ENMs are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models. Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species and taxonomy (amphibians and reptiles. Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural
Local-scale models reveal ecological niche variability in amphibian and reptile communities from two contrasting biogeographic regions

Science.gov (United States)

Santos, Xavier; Felicísimo, Ángel M.

2016-01-01

Ecological Niche Models (ENMs) are widely used to describe how environmental factors influence species distribution. Modelling at a local scale, compared to a large scale within a high environmental gradient, can improve our understanding of ecological species niches. The main goal of this study is to assess and compare the contribution of environmental variables to amphibian and reptile ENMs in two Spanish national parks located in contrasting biogeographic regions, i.e., the Mediterranean and the Atlantic area. The ENMs were built with maximum entropy modelling using 11 environmental variables in each territory. The contributions of these variables to the models were analysed and classified using various statistical procedures (Mann–Whitney U tests, Principal Components Analysis and General Linear Models). Distance to the hydrological network was consistently the most relevant variable for both parks and taxonomic classes. Topographic variables (i.e., slope and altitude) were the second most predictive variables, followed by climatic variables. Differences in variable contribution were observed between parks and taxonomic classes. Variables related to water availability had the larger contribution to the models in the Mediterranean park, while topography variables were decisive in the Atlantic park. Specific response curves to environmental variables were in accordance with the biogeographic affinity of species (Mediterranean and non-Mediterranean species) and taxonomy (amphibians and reptiles). Interestingly, these results were observed for species located in both parks, particularly those situated at their range limits. Our findings show that ecological niche models built at local scale reveal differences in habitat preferences within a wide environmental gradient. Therefore, modelling at local scales rather than assuming large-scale models could be preferable for the establishment of conservation strategies for herptile species in natural parks. PMID
Allorecognition of HLA-C mismatches by CD8+ T cells in hematopoietic stem cell transplantation is a complex interplay between mismatched peptide binding region residues, HLA-C expression and HLA-DPB1 disparities

Directory of Open Access Journals (Sweden)

Florence Bettens

2016-12-01

Full Text Available HLA-C locus mismatches are the most frequent class I disparities in unrelated hematopoietic stem cell transplantation (HSCT and have a detrimental impact on clinical outcome. Recently, a few retrospective clinical studies have reported some variability in the immunogenicity of HLA-C incompatibilities. To get better insight into presumably permissive HLA-C mismatches we have developed a one-way in vitro mixed lymphocyte reaction (MLR assay allowing to quantify activated CD56-CD137+CD8+ lymphocytes in HLA-C incompatible combinations. T cell-mediated alloresponses were correlated with genetic markers such as HLA-C mRNA expression and the number of amino acid mismatches in the α1/α2 domains (peptide binding region. Because of the high rate of HLA-DPB1 incompatibilities in HLA-A, B, C, DRB1 and DQB1 matched unrelated HSCT patient/donor pairs, the impact of HLA-DPB1 mismatching, a potential bystander of CD4+ T cell activation, was also considered. Heterogeneous alloresponses were measured in 63 HLA-C mismatched pairs with a positive assay in 52% of the combinations (2.3-18.6% activated CTLs, representing 24 different HLA-A~B~DRB1~DQB1 haplotypes. There was no correlation between measured alloresponses and mRNA expression of the mismatched HLA-C alleles. The HLA-C*03:03/03:04 mismatch did not induce any positive alloresponse in 5 MLRs. We also identified HLA-C*02:02 and HLA-C*06:02 as mismatched alleles with lower immunogenicity, and HLA-C*14:02 as a more immunogenic mismatch. A difference of at least 10 amino acid residues known to impact peptide/TCR binding and a bystander HLA-DPB1 incompatibility had a significant impact on CTL alloreactivity (p=0.021. The same HLA-C mismatch, when recognized by two different responders with the same HLA haplotypes, was recognized differently, emphasizing the role of the T-cell repertoire of responding cells. In conclusion, mismatched HLA-C alleles differing by10 or more amino acids in the peptide/TCR binding
Evidence on How a Conserved Glycine in the Hinge Region of HapR Regulates Its DNA Binding Ability: LESSONS FROM A NATURAL VARIANT.

Energy Technology Data Exchange (ETDEWEB)

M Dongre; N Singh; C Dureja; N Peddada; A Solanki; F Ashish; S Raychaudhuri

2011-12-31

HapR has been recognized as a quorum-sensing master regulator in Vibrio cholerae. Because it controls a plethora of disparate cellular events, the absence of a functional HapR affects the physiology of V. cholerae to a great extent. In the current study, we pursued an understanding of an observation of a natural protease-deficient non-O1, non-O139 variant V. cholerae strain V2. Intriguingly, a nonfunctional HapR (henceforth designated as HapRV2) harboring a substitution of glycine to aspartate at position 39 of the N-terminal hinge region has been identified. An in vitro gel shift assay clearly suggested the inability of HapRV2 to interact with various cognate promoters. Reinstatement of glycine at position 39 restores DNA binding ability of HapRV2 (HapRV2G), thereby rescuing the protease-negative phenotype of this strain. The elution profile of HapRV2 and HapRV2G proteins in size-exclusion chromatography and their circular dichroism spectra did not reflect any significant differences to explain the functional discrepancies between the two proteins. To gain insight into the structure-function relationship of these two proteins, we acquired small/wide angle x-ray scattering data from samples of the native and G39D mutant. Although Guinier analysis and indirect Fourier transformation of scattering indicated only a slight difference in the shape parameters, structure reconstruction using dummy amino acids concluded that although HapR adopts a 'Y' shape similar to its crystal structure, the G39D mutation in hinge drastically altered the DNA binding domains by bringing them in close proximity. This altered spatial orientation of the helix-turn-helix domains in this natural variant provides the first structural evidence on the functional role of the hinge region in quorum sensing-related DNA-binding regulatory proteins of Vibrio spp.
Binding of collagens to an enterotoxigenic strain of Escherichia coli

International Nuclear Information System (INIS)

Visai, L.; Speziale, P.; Bozzini, S.

1990-01-01

An enterotoxigenic strain of Escherichia coli, B34289c, has been shown to bind the N-terminal region of fibronectin with high affinity. We now report that this strain also binds collagen. The binding of 125I-labeled type II collagen to bacteria was time dependent and reversible. Bacteria expressed a limited number of collagen receptors (2.2 x 10(4) per cell) and bound collagen with a Kd of 20 nM. All collagen types tested (I to V) as well as all tested cyanogen bromide-generated peptides [alpha 1(I)CB2, alpha 1(I)CB3, alpha 1(I)CB7, alpha 1(I)CB8, and alpha 2(I)CB4] were recognized by bacterial receptors, as demonstrated by the ability of these proteins to inhibit the binding of 125I-labeled collagen to bacteria. Of several unlabeled proteins tested in competition experiments, fibronectin and its N-terminal region strongly inhibited binding of the radiolabeled collagen to E. coli cells. Conversely, collagen competed with an 125I-labeled 28-kilodalton fibronectin fragment for bacterial binding. Collagen bound to bacteria could be displaced by excess amounts of either unlabeled fibronectin or its N-terminal fragment. Similarly, collagen could displace 125I-labeled N-terminal peptide of fibronectin bound to the bacterial cell surface. Bacteria grown at 41 degrees C or in the presence of glucose did not express collagen or fibronectin receptors. These results indicate the presence of specific binding sites for collagen on the surface of E. coli cells and furthermore that the collagen and fibronectin binding sites are located in close proximity, possibly on the same structure
Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein-Protein Interactions.

Science.gov (United States)

Kang, Beom Sik; Pugalendhi, GaneshKumar; Kim, Ku-Jin

2017-10-13

Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.
Binding Direction-Based Two-Dimensional Flattened Contact Area Computing Algorithm for Protein–Protein Interactions

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Beom Sik Kang

2017-10-01

Full Text Available Interactions between protein molecules are essential for the assembly, function, and regulation of proteins. The contact region between two protein molecules in a protein complex is usually complementary in shape for both molecules and the area of the contact region can be used to estimate the binding strength between two molecules. Although the area is a value calculated from the three-dimensional surface, it cannot represent the three-dimensional shape of the surface. Therefore, we propose an original concept of two-dimensional contact area which provides further information such as the ruggedness of the contact region. We present a novel algorithm for calculating the binding direction between two molecules in a protein complex, and then suggest a method to compute the two-dimensional flattened area of the contact region between two molecules based on the binding direction.
Accounting for CO2 variability over East Asia with a regional joint inversion system and its preliminary evaluation

Science.gov (United States)

Kou, Xingxia; Tian, Xiangjun; Zhang, Meigen; Peng, Zhen; Zhang, Xiaoling

2017-10-01

A regional surface carbon dioxide (CO2) flux inversion system, the Tan-Tracker-Region, was developed by incorporating an assimilation scheme into the Community Multiscale Air Quality (CMAQ) regional chemical transport model to resolve fine-scale CO2 variability over East Asia. The proper orthogonal decomposition-based ensemble four-dimensional variational data assimilation approach (POD-4DVar) is the core algorithm for the joint assimilation framework, and simultaneous assimilations of CO2 concentrations and surface CO2 fluxes are applied to help reduce the uncertainty in initial CO2 concentrations. A persistence dynamical model was developed to describe the evolution of the surface CO2 fluxes and help avoid the "signal-to-noise" problem; thus, CO2 fluxes could be estimated as a whole at the model grid scale, with better use of observation information. The performance of the regional inversion system was evaluated through a group of single-observation-based observing system simulation experiments (OSSEs). The results of the experiments suggest that a reliable performance of Tan-Tracker-Region is dependent on certain assimilation parameter choices, for example, an optimized window length of approximately 3 h, an ensemble size of approximately 100, and a covariance localization radius of approximately 320 km. This is probably due to the strong diurnal variation and spatial heterogeneity in the fine-scale CMAQ simulation, which could affect the performance of the regional inversion system. In addition, because all observations can be artificially obtained in OSSEs, the performance of Tan-Tracker-Region was further evaluated through different densities of the artificial observation network in different CO2 flux situations. The results indicate that more observation sites would be useful to systematically improve the estimation of CO2 concentration and flux in large areas over the model domain. The work presented here forms a foundation for future research in which a
Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

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Alonso Ángel

2006-03-01

Full Text Available Abstract Background Papillomaviruses (PVs infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR of the virus. It is believed that there is a core of transcription factor binding sites (TFBS common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. Results We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. Conclusion There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.
The conserved Tarp actin binding domain is important for chlamydial invasion.

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Travis J Jewett

2010-07-01

Full Text Available The translocated actin recruiting phosphoprotein (Tarp is conserved among all pathogenic chlamydial species. Previous reports identified single C. trachomatis Tarp actin binding and proline rich domains required for Tarp mediated actin nucleation. A peptide antiserum specific for the Tarp actin binding domain was generated and inhibited actin polymerization in vitro and C. trachomatis entry in vivo, indicating an essential role for Tarp in chlamydial pathogenesis. Sequence analysis of Tarp orthologs from additional chlamydial species and C. trachomatis serovars indicated multiple putative actin binding sites. In order to determine whether the identified actin binding domains are functionally conserved, GST-Tarp fusions from multiple chlamydial species were examined for their ability to bind and nucleate actin. Chlamydial Tarps harbored variable numbers of actin binding sites and promoted actin nucleation as determined by in vitro polymerization assays. Our findings indicate that Tarp mediated actin binding and nucleation is a conserved feature among diverse chlamydial species and this function plays a critical role in bacterial invasion of host cells.
Aerosol and rainfall variability over the Indian monsoon region: distributions, trends and coupling

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R. Gautam

2009-09-01

Full Text Available Aerosol solar absorption over the Indian monsoon region has a potential role of modulating the monsoon circulation and rainfall distribution as suggested by recent studies based on model simulations. Prior to the onset of the monsoon, northern India is influenced by significant dust transport that constitutes the bulk of the regional aerosol loading over the Gangetic-Himalayan region. In this paper, a multi-sensor characterization of the increasing pre-monsoon aerosol loading over northern India, in terms of their spatial, temporal and vertical distribution is presented. Aerosol transport from the northwestern arid regions into the Indo-Gangetic Plains and over the foothills of the Himalayas is found to be vertically extended to elevated altitudes (up to 5 km as observed from the space-borne lidar measurements (CALIPSO. In relation with the enhanced pre-monsoon aerosol loading and the associated solar absorption effects on tropospheric temperature anomalies, this paper investigates the monsoon rainfall variability over India in recent past decades from an observational viewpoint. It is found that the early summer monsoon rainfall over India is on the rise since 1950s, as indicated by historical rainfall data, with over 20% increase for the period 1950–2004. This large sustained increase in the early summer rainfall is led by the observed strengthening of the pre-monsoon tropospheric land-sea thermal gradient over the Indian monsoon region as indicated by microwave satellite measurements (MSU of tropospheric temperatures from 1979–2007. Combined analysis of changes in tropospheric temperatures and summer monsoon rainfall in the past three decades, suggest a future possibility of an emerging rainfall pattern of a wetter monsoon over South Asia in early summer followed by a drier period.

Characterization and DNA-binding specificities of Ralstonia TAL-like effectors

KAUST Repository

Li, Lixin

2013-07-01

Transcription activator-like effectors (TALEs) from Xanthomonas sp. have been used as customizable DNA-binding modules for genome-engineering applications. Ralstonia solanacearum TALE-like proteins (RTLs) exhibit similar structural features to TALEs, including a central DNA-binding domain composed of 35 amino acid-long repeats. Here, we characterize the RTLs and show that they localize in the plant cell nucleus, mediate DNA binding, and might function as transcriptional activators. RTLs have a unique DNA-binding architecture and are enriched in repeat variable di-residues (RVDs), which determine repeat DNA-binding specificities. We determined the DNA-binding specificities for the RVD sequences ND, HN, NP, and NT. The RVD ND mediates highly specific interactions with C nucleotide, HN interacts specifically with A and G nucleotides, and NP binds to C, A, and G nucleotides. Moreover, we developed a highly efficient repeat assembly approach for engineering RTL effectors. Taken together, our data demonstrate that RTLs are unique DNA-targeting modules that are excellent alternatives to be tailored to bind to user-selected DNA sequences for targeted genomic and epigenomic modifications. These findings will facilitate research concerning RTL molecular biology and RTL roles in the pathogenicity of Ralstonia spp. © 2013 The Author.
Structural Characterisation Reveals Mechanism of IL-13-Neutralising Monoclonal Antibody Tralokinumab as Inhibition of Binding to IL-13Rα1 and IL-13Rα2.

Science.gov (United States)

Popovic, B; Breed, J; Rees, D G; Gardener, M J; Vinall, L M K; Kemp, B; Spooner, J; Keen, J; Minter, R; Uddin, F; Colice, G; Wilkinson, T; Vaughan, T; May, R D

2017-01-20

Interleukin (IL)-13 is a pleiotropic T helper type 2 cytokine frequently associated with asthma and atopic dermatitis. IL-13-mediated signalling is initiated by binding to IL-13Rα1, which then recruits IL-4Rα to form a heterodimeric receptor complex. IL-13 also binds to IL-13Rα2, considered as either a decoy or a key mediator of fibrosis. IL-13-neutralising antibodies act by preventing IL-13 binding to IL-13Rα1, IL-4Rα and/or IL-13Rα2. Tralokinumab (CAT-354) is an IL-13-neutralising human IgG4 monoclonal antibody that has shown clinical benefit in patients with asthma. To decipher how tralokinumab inhibits the effects of IL-13, we determined the structure of tralokinumab Fab in complex with human IL-13 to 2 Å resolution. The structure analysis reveals that tralokinumab prevents IL-13 from binding to both IL-13Rα1 and IL-13Rα2. This is supported by biochemical ligand-receptor interaction assay data. The tralokinumab epitope is mainly composed of residues in helices D and A of IL-13. It is mostly light chain complementarity-determining regions that are driving paratope interactions; the variable light complementarity-determining region 2 plays a key role by providing residue contacts for a network of hydrogen bonds and a salt bridge in the core of binding. The key residues within the paratope contributing to binding were identified as Asp50, Asp51, Ser30 and Lys31. This study demonstrates that tralokinumab prevents the IL-13 pharmacodynamic effect by binding to IL-13 helices A and D, thus preventing IL-13 from interacting with IL-13Rα1 and IL-13Rα2. Copyright © 2016 AstraZeneca. Published by Elsevier Ltd.. All rights reserved.
An erythrocyte-specific DNA-binding factor recognizes a regulatory sequence common to all chicken globin genes

International Nuclear Information System (INIS)

Evans, T.; Reitman, M.; Felsenfeld, G.

1988-01-01

The authors have identified a protein present only in erythroid cells that binds to two adjacent sites within an enhancer region of the chicken β-globin locus. Mutation of the sites, so that binding by the factor can no longer be detected in vitro, leads to a loss of enhancing ability, assayed by transient expression in primary erythrocytes. Binding sites for the erythroid-specific factor (Eryf1) are found within regulatory regions for all chicken globin genes. A strong Eryf1 binding site is also present within the enhancer of at least one human globin gene, and proteins from human erythroid cells (but not HeLa cells) bind to both the chicken and the human sites
Identification of the Calmodulin-Binding Domains of Fas Death Receptor.

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Bliss J Chang

Full Text Available The extrinsic apoptotic pathway is initiated by binding of a Fas ligand to the ectodomain of the surface death receptor Fas protein. Subsequently, the intracellular death domain of Fas (FasDD and that of the Fas-associated protein (FADD interact to form the core of the death-inducing signaling complex (DISC, a crucial step for activation of caspases that induce cell death. Previous studies have shown that calmodulin (CaM is recruited into the DISC in cholangiocarcinoma cells and specifically interacts with FasDD to regulate the apoptotic/survival signaling pathway. Inhibition of CaM activity in DISC stimulates apoptosis significantly. We have recently shown that CaM forms a ternary complex with FasDD (2:1 CaM:FasDD. However, the molecular mechanism by which CaM binds to two distinct FasDD motifs is not fully understood. Here, we employed mass spectrometry, nuclear magnetic resonance (NMR, biophysical, and biochemical methods to identify the binding regions of FasDD and provide a molecular basis for the role of CaM in Fas-mediated apoptosis. Proteolytic digestion and mass spectrometry data revealed that peptides spanning residues 209-239 (Fas-Pep1 and 251-288 (Fas-Pep2 constitute the two CaM-binding regions of FasDD. To determine the molecular mechanism of interaction, we have characterized the binding of recombinant/synthetic Fas-Pep1 and Fas-Pep2 peptides with CaM. Our data show that both peptides engage the N- and C-terminal lobes of CaM simultaneously. Binding of Fas-Pep1 to CaM is entropically driven while that of Fas-Pep2 to CaM is enthalpically driven, indicating that a combination of electrostatic and hydrophobic forces contribute to the stabilization of the FasDD-CaM complex. Our data suggest that because Fas-Pep1 and Fas-Pep2 are involved in extensive intermolecular contacts with the death domain of FADD, binding of CaM to these regions may hinder its ability to bind to FADD, thus greatly inhibiting the initiation of apoptotic signaling
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

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Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang

2015-08-01

Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.
Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

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Zing Tsung-Yeh Tsai

2015-08-01

Full Text Available Transcription factor (TF binding is determined by the presence of specific sequence motifs (SM and chromatin accessibility, where the latter is influenced by both chromatin state (CS and DNA structure (DS properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.
Monoclonal antibody to the rat glucocorticoid receptor. Relationship between the immunoreactive and DNA-binding domain

International Nuclear Information System (INIS)

Eisen, L.P.; Reichman, M.E.; Thompson, E.B.; Gametchu, B.; Harrison, R.W.; Eisen, H.J.

1985-01-01

The region of the glucocorticoid receptor that reacted with a monoclonal antibody (BUGR-1) was identified. In order to identify the immunoreactive region, the rat liver glucocorticoid receptor was subjected to limited proteolysis; immunoreactive fragments were identified by Western blotting. The monoclonal antibody reacted with both the undigested Mr approximately 97,000 receptor subunit and a Mr approximately 45,000 fragment containing the steroid-binding and DNA-binding domains. Digestion by trypsin also produced two steroid-binding fragments of Mr approximately 27,000 and 31,000 which did not react with the antibody and an immunoreactive Mr approximately 16,000 fragment. This Mr approximately 16,000 fragment was shown to bind to DNA-cellulose, indicating that it contained a DNA-binding domain of the receptor. The undigested receptor must have steroid associated with it to undergo activation to a DNA-binding form. However, the Mr approximately 16,000 immunoreactive fragment binds to DNA-cellulose even if it is obtained by digestion of the steroid-free holoreceptor which does not itself bind to DNA
Continental and Marine Environmental changes in Europe induced by Global Climate variability and Regional Paleogeography Changes

OpenAIRE

Popescu , Speranta - Maria

2008-01-01

version originale; My PhD and post-doctorate researches have focused on paleoclimatic, paleogeographical and paleoenvironmental reconstruction of the Mediterranean Basin and its adjacent seas (i.e. the residual former Paratethys) since 11 Ma. During this time-interval the Mediterranean marine and continental environments were affected by significant paleogeographic changes, forced by global climate and sea-level variability, plate tectonics and regional uplift of Alps s.l. and Carpathians. Tw...
Tidal and sub-tidal sea level variability at the northern shelf of the Brazilian Northeast Region.

Science.gov (United States)

Frota, Felipe F; Truccolo, Eliane C; Schettini, Carlos A F

2016-09-01

A characterization of the sea level variability at tidal and sub-tidal frequencies at the northern shore of the Brazilian Northeast shelf for the period 2009-2011 is presented. The sea level data used was obtained from the Permanent Geodetic Tide Network from the Brazilian Institute of Geography and Statistics for the Fortaleza gauge station. Local wind data was also used to assess its effects on the low-frequency sea level variability. The variability of the sea level was investigated by classical harmonic analysis and by morphology assessment over the tidal signal. The low frequencies were obtained by low-pass filtering. The tidal range oscillated with the highest value of 3.3 m during the equinox and the lowest value of 0.7 m during the solstice. Differences between the spring and neap tides were as high as 1 m. A total of 59 tidal constituents were obtained from harmonic analysis, and the regional tide was classified as semi-diurnal pure with a form number of 0.11. An assessment of the monthly variability of the main tidal constituents (M2, S2, N2, O1, and K1) indicated that the main semi-diurnal solar S2 presented the highest variability, ranging from 0.21 to 0.41 m; it was the main element altering the form number through the years. The low frequency sea-level variability is negligible, although there is a persistent signal with an energy peak in the 10-15 day period, and it cannot be explained by the effects of local winds.
Recognition of AT-Rich DNA Binding Sites by the MogR Repressor

Energy Technology Data Exchange (ETDEWEB)

Shen, Aimee; Higgins, Darren E.; Panne, Daniel; (Harvard-Med); (EMBL)

2009-07-22

The MogR transcriptional repressor of the intracellular pathogen Listeria monocytogenes recognizes AT-rich binding sites in promoters of flagellar genes to downregulate flagellar gene expression during infection. We describe here the 1.8 A resolution crystal structure of MogR bound to the recognition sequence 5' ATTTTTTAAAAAAAT 3' present within the flaA promoter region. Our structure shows that MogR binds as a dimer. Each half-site is recognized in the major groove by a helix-turn-helix motif and in the minor groove by a loop from the symmetry-related molecule, resulting in a 'crossover' binding mode. This oversampling through minor groove interactions is important for specificity. The MogR binding site has structural features of A-tract DNA and is bent by approximately 52 degrees away from the dimer. The structure explains how MogR achieves binding specificity in the AT-rich genome of L. monocytogenes and explains the evolutionary conservation of A-tract sequence elements within promoter regions of MogR-regulated flagellar genes.
Identification of carbohydrate-binding domains in the attachment proteins of type 1 and type 3 reoviruses.

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Chappell, J D; Duong, J L; Wright, B W; Dermody, T S

2000-09-01

The reovirus attachment protein, sigma1, is responsible for strain-specific patterns of viral tropism in the murine central nervous system and receptor binding on cultured cells. The sigma1 protein consists of a fibrous tail domain proximal to the virion surface and a virion-distal globular head domain. To better understand mechanisms of reovirus attachment to cells, we conducted studies to identify the region of sigma1 that binds cell surface carbohydrate. Chimeric and truncated sigma1 proteins derived from prototype reovirus strains type 1 Lang (T1L) and type 3 Dearing (T3D) were expressed in insect cells by using a baculovirus vector. Assessment of expressed protein susceptibility to proteolytic cleavage, binding to anti-sigma1 antibodies, and oligomerization indicates that the chimeric and truncated sigma1 proteins are properly folded. To assess carbohydrate binding, recombinant sigma1 proteins were tested for the capacity to agglutinate mammalian erythrocytes and to bind sialic acid presented on glycophorin, the cell surface molecule bound by type 3 reovirus on human erythrocytes. Using a panel of two wild-type and ten chimeric and truncated sigma1 proteins, the sialic acid-binding domain of type 3 sigma1 was mapped to a region of sequence proposed to form the more amino terminal of two predicted beta-sheet structures in the tail. This unit corresponds to morphologic region T(iii) observed in computer-processed electron micrographs of sigma1 protein purified from virions. In contrast, the homologous region of T1L sigma1 sequence was not implicated in carbohydrate binding; rather, sequences in the distal portion of the tail known as the neck were required. Results of these studies demonstrate that a functional receptor-binding domain, which uses sialic acid as its ligand, is contained within morphologic region T(iii) of the type 3 sigma1 tail. Furthermore, our findings indicate that T1L and T3D sigma1 proteins contain different arrangements of receptor-binding
Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

Science.gov (United States)

Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

2012-01-01

The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821
A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.

Directory of Open Access Journals (Sweden)

Sagar Darvekar

Full Text Available Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or "reader" modules. The nuclear proteins SPBP and RAI1 are composed of several putative "reader" modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif. Interactions studies in vitro and in yeast cells suggested that despite the extraordinary long loop region in their ePHD/ADD-like chromatin binding domains, the C-terminal region of both proteins seem to adopt a cross-braced topology of zinc finger interactions similar to other structurally determined ePHD/ADD structures. Both their ePHD/ADD-like domain and their novel nucleosome binding domain are highly conserved in vertebrate evolution, and construction of a phylogenetic tree displayed two well supported clusters representing SPBP and RAI1, respectively. Their genome and domain organisation suggest that SPBP and RAI1 have occurred from a gene duplication event. The phylogenetic tree suggests that this duplication has happened early in vertebrate evolution, since only one gene was identified in insects and lancelet. Finally, experimental data confirm that the conserved novel nucleosome binding region of RAI1 has the ability to bind the nucleosome core and histones. However, an adjacent conserved AT-hook motif as identified in SPBP is not present in RAI1, and deletion of the novel nucleosome binding region of RAI1 did not significantly affect its nuclear localisation.
Late Holocene climate variability in the southwestern Mediterranean region: an integrated marine and terrestrial geochemical approach

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C. Martín-Puertas

2010-12-01

Full Text Available A combination of marine (Alboran Sea cores, ODP 976 and TTR 300 G and terrestrial (Zoñar Lake, Andalucia, Spain geochemical proxies provides a high-resolution reconstruction of climate variability and human influence in the southwestern Mediterranean region for the last 4000 years at inter-centennial resolution. Proxies respond to changes in precipitation rather than temperature alone. Our combined terrestrial and marine archive documents a succession of dry and wet periods coherent with the North Atlantic climate signal. A dry period occurred prior to 2.7 cal ka BP – synchronously to the global aridity crisis of the third-millennium BC – and during the Medieval Climate Anomaly (1.4–0.7 cal ka BP. Wetter conditions prevailed from 2.7 to 1.4 cal ka BP. Hydrological signatures during the Little Ice Age are highly variable but consistent with more humidity than the Medieval Climate Anomaly. Additionally, Pb anomalies in sediments at the end of the Bronze Age suggest anthropogenic pollution earlier than the Roman Empire development in the Iberian Peninsula. The Late Holocene climate evolution of the in the study area confirms the see-saw pattern between the eastern and western Mediterranean regions and the higher influence of the North Atlantic dynamics in the western Mediterranean.
Intra-seasonal and Inter-annual variability of Bowen Ratio over rain-shadow region of North peninsular India

Science.gov (United States)

Morwal, S. B.; Narkhedkar, S. G.; Padmakumari, B.; Maheskumar, R. S.; Deshpande, C. G.; Kulkarni, J. R.

2017-05-01

Intra-seasonal and inter-annual variability of Bowen Ratio (BR) have been studied over the rain-shadow region of north peninsular India during summer monsoon season. Daily grid point data of latent heat flux (LHF), sensible heat flux (SHF) from NCEP/NCAR Reanalysis for the period 1970-2014 have been used to compute daily area-mean BR. Daily grid point rainfall data at a resolution of 0.25° × 0.25° from APHRODITE's Water Resources for the available period 1970-2007 have been used to study the association between rainfall and BR. The study revealed that BR rapidly decreases from 4.1 to 0.29 in the month of June and then remains nearly constant at the same value (≤0.1) in the rest of the season. High values of BR in the first half of June are indicative of intense thermals and convective clouds with higher bases. Low values of BR from July to September period are indicative of weak thermals and convective clouds with lower bases. Intra-seasonal and inter-annual variability of BR is found to be inversely related to precipitation over the region. BR analysis indicates that the land surface characteristics of the study region during July-September are similar to that over oceanic regions as far as intensity of thermals and associated cloud microphysical properties are concerned. Similar variation of BR is found in El Nino and La Nina years. During June, an increasing trend is observed in SHF and BR and decreasing trend in LHF from 1976 to 2014. Increasing trend in the SHF is statistically significant.
Extracellular fibrinogen-binding protein (Efb) from staphylococcus aureus Inhibits the formation of platelet-leukocyte complexes

NARCIS (Netherlands)

Posner, M.G; Upadhyay, A.; Abubaker, A.A.; Fortunato, T.M.; Vara, D.; Canobbio, I.; Bagby, S.; Pula, G.

2016-01-01

Extracellular fibrinogen-binding protein (Efb) from Staphylococcus aureus inhibits platelet activation, although its mechanism of action has not been established. In this study, we discovered that the N-terminal region of Efb (Efb-N) promotes platelet binding of fibrinogen and that Efb-N binding to
The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization

Directory of Open Access Journals (Sweden)

Tam Michael WC

2010-03-01

Full Text Available Abstract Background Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. Results The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1 RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. Conclusions The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to
The generation and selection of single-domain, v region libraries from nurse sharks.

Science.gov (United States)

Flajnik, Martin F; Dooley, Helen

2009-01-01

The cartilaginous fish (sharks, skates, and rays) are the oldest phylogenetic group in which a human-type adaptive immune system and immunoglobulins (Igs) have been found. In addition to their conventional (heavy-light chain heterodimeric) isotypes, IgM and IgW, sharks produce the novel isotype, IgNAR, a heavy chain homodimer that does not associate with light chains. Instead, its variable (V) regions act as independent, soluble units in order to bind antigen. In this chapter, we detail our immunization protocol in order to raise a humoral IgNAR response in the nurse shark (Ginglymostoma cirratum) and the subsequent cloning of the single-domain V regions from this isotype in order to select antigen-specific binders by phage display.
Features of ozone intraannual variability in polar regions based on ozone sounding data obtained at the Resolute and Amundsen-Scott stations

Energy Technology Data Exchange (ETDEWEB)

Gruzdev, A.N.; Sitnov, S.A. (AN SSSR, Institut Fiziki Atmosfery, Moscow (USSR))

1991-04-01

Ozone sounding data obtained at the Resolute and Amundsen-Scott stations are used to analyze ozone intraannual variability in Southern and Northern polar regions. For the Arctic, in particular, features associated with winter stratospheric warmings, stratospheric-tropospheric exchange, and the isolated evolution of surface ozone are noted. Correlative connections between ozone and temperature making it possible to concretize ozone variability mechanisms are analyzed. 31 refs.
Agonist and antagonist binding to rat brain muscarinic receptors: influence of aging

International Nuclear Information System (INIS)

Gurwitz, D.; Egozi, Y.; Henis, Y.I.; Kloog, Y.; Sokolovsky, M.

1987-01-01

The objective of the present study was to determine the binding properties of muscarinic receptors in six brain regions in mature and old rats of both sexes by employing direct binding of [ 3 H]-antagonist as well as of the labeled natural neurotransmitter, [ 3 H]-acetylcholine [( 3 H]-AcCh). In addition, age-related factors were evaluated in the modulation processes involved in agonist binding. The results indicate that as the rat ages the density of the muscarinic receptors is altered differently in the various brain regions: it is decreased in the cerebral cortex, hippocampus, striatum and olfactory bulb of both male and female rats, but is increased (58%) in the brain stem of senescent males while no significant change is observed for females. The use of the highly sensitive technique measuring direct binding of [ 3 H]-AcCh facilitated the separate detection of age-related changes in the two classes (high- and low-affinity) of muscarinic agonist binding sites. In old female rats the density of high-affinity [ 3 H]-AcCh binding sites was preserved in all tissues studied, indicating that the decreases in muscarinic receptor density observed with [ 3 H]-antagonist represent a loss of low-affinity agonist binding sites. In contrast, [ 3 H]-AcCh binding is decreased in the hypothalamus and increased in the brain stem of old male rats. These data imply sexual dimorphism of the aging process in central cholinergic mechanisms

Test-retest reliability of [{sup 11}C]AZ10419369 binding to 5-HT{sub 1B} receptors in human brain

Energy Technology Data Exchange (ETDEWEB)

Nord, Magdalena; Finnema, Sjoerd J.; Schain, Martin; Halldin, Christer; Farde, Lars [Karolinska Institutet, Center for Psychiatric Research, R5:00, Karolinska University Hospital, Department of Clinical Neuroscience, Stockholm (Sweden)

2014-02-15

[{sup 11}C]AZ10419369 is a recently developed 5-HT{sub 1B} receptor radioligand that is sensitive to changes in endogenous serotonin concentrations in the primate brain. Thus, [{sup 11}C] AZ10419369 may serve as a useful tool in clinical studies of the pathophysiology and pharmacological treatment of diseases related to the serotonin system, such as depression and anxiety disorders. The aim of this study was to evaluate the test-retest reliability of [{sup 11}C]AZ10419369. Eight men were examined with PET and [{sup 11}C] AZ10419369 twice on the same day. The binding potentials (BP{sub ND}) of [{sup 11}C]AZ10419369 in selected serotonergic projection areas and in the raphe nuclei (RN) were determined using the simplified reference tissue model, and for comparison also using a wavelet-aided parametric imaging approach. The BP{sub ND} values obtained from the first and second PET scans were compared by means of descriptive statistics, difference, absolute variability and intraclass correlation coefficient. Similar BP{sub ND} values were obtained with the two methods. The absolute mean differences in BP{sub ND} between PET 1 and PET 2 were less than 3 % in all serotonergic projection regions. Absolute variabilities were low in cortical regions (5 - 7 %), low to moderate (7 - 14 %) in subcortical regions, but higher (20 %) in the RN. The BP{sub ND} of [{sup 11}C]AZ10419369 is highly reproducible in cortical regions and satisfactory in subcortical projection areas. The variability in the RN is higher. Thus larger sample sizes or larger divergences are required to assess a potential difference between subjects or between experimental conditions in this region. (orig.)
A putative carbohydrate-binding domain of the lactose-binding Cytisus sessilifolius anti-H(O) lectin has a similar amino acid sequence to that of the L-fucose-binding Ulex europaeus anti-H(O) lectin.

Science.gov (United States)

Konami, Y; Yamamoto, K; Osawa, T; Irimura, T

1995-04-01

The complete amino acid sequence of a lactose-binding Cytisus sessilifolius anti-H(O) lectin II (CSA-II) was determined using a protein sequencer. After digestion of CSA-II with endoproteinase Lys-C or Asp-N, the resulting peptides were purified by reversed-phase high performance liquid chromatography (HPLC) and then subjected to sequence analysis. Comparison of the complete amino acid sequence of CSA-II with the sequences of other leguminous seed lectins revealed regions of extensive homology. The amino acid sequence of a putative carbohydrate-binding domain of CSA-II was found to be similar to those of several anti-H(O) leguminous lectins, especially to that of the L-fucose-binding Ulex europaeus lectin I (UEA-I).
Binding of [125I] Concanavalin A to isolated Langerhans islets of rats

International Nuclear Information System (INIS)

Prey, N.

1983-01-01

Langerhans islets of rats were isolated using Lacy's collagenase technique and were incubated in vitro. The binding of iodine-labelled Concanavalin A to isolated Langerhans islets was investigated. We were unable to decide whether multiple Concanavalin A binding sites are located on the cell membrane, or whether the Concanavalin A binding sites are negatively influenced via a allosteric protein. Although the secretion mechanism induced by sulfony urea is not influenced by Concanavalin A, enhanced binding of Concanavalin A indicates that the region of identification cannot be identical for glucose and sulfonyl urea. (orig./MG) [de
Variable-density ground-water flow and paleohydrology in the Waste Isolation Pilot Plant (WIPP) region, southeastern New Mexico

International Nuclear Information System (INIS)

Davies, P.B.

1989-01-01

Variable-density groundwater flow was studied near the Waste Isolation Pilot Plant in southeastern New Mexico. An analysis of the relative magnitude of pressure-related and density-related flow-driving forces indicates that density-related gravity effects are not significant at the plant and to the west but are significant in areas to the north, northeast, and south. A regional-scale model of variable-density groundwater flow in the Culebra Dolomite member of the Rustler Formation indicates that the flow velocities are relatively rapid west of the site and extremely slow east and northeast of the site. In the transition zone between those two extremes, which includes the plant, velocities are highly variable. Sensitivity simulations indicates that the central and western parts of the region, including the plant, are fairly well isolated from the eastern and northeastern boundaries. Vertical-flux simulations indicate that as much as 25% of total inflow to the Culebra could be entering as vertical flow, with most of this flow occurring west of the plant. A simple cross-sectional model was developed to examine the flow system as it drains through time following recharge during a past glacial pluvial. This model indicates that the system as a whole drains very slowly and that it apparently could have sustained flow from purely transient drainage following recharge of the system during the Pleistocene
Vitamin D-dependent rat renal calcium-binding protein: development of a radioimmunoassay, tissue distribution, and immunologic identification

International Nuclear Information System (INIS)

Sonnenberg, J.; Pansini, A.R.; Christakos, S.

1984-01-01

A sensitive double antibody RIA has been developed for the 28,000 mol wt rat renal vitamin D-dependent calcium-binding protein. Using this assay, concentrations of calcium-binding protein (CaBP) as low as 30 ng can be measured. The assay is precise (intraassay variability, 5.0%) and reproductible (interassay variability, 8.2%). Measurements of renal CaBP by RIA showed a good correlation with measurements of CaBP by the chelex resin assay and by polyacrylamide gel analysis by densitometric tracing using a purified CaBP marker. The concentration of CaBP in the vitamin D-replete rat kidney is 7.3 +/- 1.0 (mean +/- SEM) micrograms/mg protein. In vitamin D-deficient rats the level of renal CaBP is 2.6 +/- 0.3 micrograms/mg protein. Tissue distribution of immunoreactive rat renal CaBP showed the highest concentration of CaBP in the rat cerebellum (38.3 +/- 5.1 micrograms/mg protein). Lower concentrations of immunoreactive CaBP were detected in several other rat tissues. No immunoreactive CaBP was detected in rat or human serum. In necropsy human kidney and cerebellum, high levels of immunoreactive CaBP were also detected (1.5 +/- 0.1 and 27.3 +/- 2.1 micrograms/mg protein, respectively). When extracts of rat kidney and brain and human cerebellum and kidney were assayed at several dilutions, immunodisplacement curves parallel to that of pure renal CaBP were observed, indicating immunochemical similarity. Fractionation of extracts of rat cerebellum, human kidney, and human cerebellum on Sephadex G-100 revealed immunoreactivity and calcium-binding activity in the 28,000 mol wt region similar to rat kidney
Comparison of cerebral blood flow and metabolism to flumazenil binding potential in patients with hemodynamic ischemia

International Nuclear Information System (INIS)

Yukawa, Hirotsugu; Ogasawara, Kuniaki

2003-01-01

Because benzodiazepine receptors (BZR) are abundant in the cortex, an accumulation of 11 C-flumazenil which selectively bind to BZR may be useful as markers of neuron density. The aims of this study were to clarify the relationship between neuron density and cerebral oxygen metabolism and to investigate the usefulness of 11 C-flumazenil PET for detecting misery perfusion. The subjects were 16 patients with either internal carotid or middle cerebral arterial occlusive disease who underwent PET. Regional cerebral blood flow (CBF), regional cerebral oxygen extraction fraction (OEF), regional cerebral metabolic rate for oxygen (CMRO 2 ) and regional cerebrovascular reserve capacity (CVRC) to acetazolamide were calculated. After CBF study, flumazenil binding potential was measured using the [ 11 C] flumazenil bolus injection method. Forty-eight regions of interests (ROIs) were obtained in 16 patients. Flumazenil binding potential was correlated to CMRO 2 (r=0.337, p=0.0069), but in 7 of 48 ROIs, CMRO 2 decreased, whereas flumazenil binding potential did not change. Seventeen of 29 ROIs with decreased CVRC showed high OEF and the remaining 12 showed normal OEF. Flumazenil binding potential in ROIs with normal OEF was significantly lower than in those with high OEF (p=0.0003). This study demonstrated that 11 C-flumazenil PET is useful for detecting misery perfusion in patients with hemodynamic ischemia. (author)
Modeling and analysis of PET studies with norepinephrine transporter ligands: the search for a reference region

Energy Technology Data Exchange (ETDEWEB)

Logan, Jean [Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)]. E-mail: logan@bnl.gov; Ding, Y.-S. [Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973 (United States); Lin, K.-S. [Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973 (United States); Pareto, Deborah [Medical Department, Brookhaven National Laboratory, Upton, NY 11973 (United States); Functional Imaging, Berkeley National Laboratory, Berkeley, CA 94720 (United States); Fowler, Joanna [Chemistry Department, Brookhaven National Laboratory, Upton, NY 11973 (United States); Biegon, Anat [Medical Department, Brookhaven National Laboratory, Upton, NY 11973 (United States)

2005-07-01

The development of positron emission tomography (PET) ligands for the norepinephrine transporter (NET) has been slow compared to the development of radiotracers for others systems, such as the dopamine (DAT) or the serotonin transporters (SERT). The main reason for this appears to be the high nonspecific (non-NET) binding exhibited by many of these tracers, which makes the identification of a reference region difficult. With other PET ligands the use of a reference region increases the reproducibility of the outcome measure in test/retest studies. The focus of this work is to identify a suitable reference region or means of normalizing data for the NET ligands investigated. Methods: We have analyzed the results of PET studies in the baboon brain with labeled reboxetine derivatives (S,S)-[{sup 11}C]O-methyl reboxetine (SS-MRB), (S,S)-[{sup 18}F]fluororeboxetine (SS-FRB) as well as O-[{sup 11}C]nisoxetine and N-[{sup 11}C]nisoxetine (NIS), and, for comparison, the less active (R,R) enantiomers (RR-MRB, RR-FRB) in terms of the distribution volume (DV) using measured arterial input functions. Results: (1) For a given subject, a large variation in DV for successive baseline studies was observed in regions with both high and low NET density. (2) The occipital cortex and the basal ganglia were found to be the regions with the smallest change between baseline (SS-MRB) and pretreatment with cocaine, and were therefore used as a composite reference region for calculation of a distribution volume ratio (DVR). (3) The variability [as measured by the coefficient of variation (CV)=standard deviation/mean] in the distribution volume ratio (DVR) of thalamus (to reference region) was considerably reduced over that of the DV using this composite reference region. (4) Pretreatment with nisoxetine (1.0 mg/kg 10 min prior to tracer) in one study produced (in decreasing order) reductions in thalamus, cerebellum, cingulate and frontal cortex consistent with known NET densities. (5) [{sup
Modeling and analysis of PET studies with norepinephrine transporter ligands: the search for a reference region.

Science.gov (United States)

Logan, Jean; Ding, Yu-Shin; Lin, Kuo-Shyan; Pareto, Deborah; Fowler, Joanna; Biegon, Anat

2005-07-01

The development of positron emission tomography (PET) ligands for the norepinephrine transporter (NET) has been slow compared to the development of radiotracers for others systems, such as the dopamine (DAT) or the serotonin transporters (SERT). The main reason for this appears to be the high nonspecific (non-NET) binding exhibited by many of these tracers, which makes the identification of a reference region difficult. With other PET ligands the use of a reference region increases the reproducibility of the outcome measure in test/retest studies. The focus of this work is to identify a suitable reference region or means of normalizing data for the NET ligands investigated. We have analyzed the results of PET studies in the baboon brain with labeled reboxetine derivatives (S,S)-[(11)C]O-methyl reboxetine (SS-MRB), (S,S)-[(18)F]fluororeboxetine (SS-FRB) as well as O-[(11)C]nisoxetine and N-[(11)C]nisoxetine (NIS), and, for comparison, the less active (R,R) enantiomers (RR-MRB, RR-FRB) in terms of the distribution volume (DV) using measured arterial input functions. (1) For a given subject, a large variation in DV for successive baseline studies was observed in regions with both high and low NET density. (2) The occipital cortex and the basal ganglia were found to be the regions with the smallest change between baseline (SS-MRB) and pretreatment with cocaine, and were therefore used as a composite reference region for calculation of a distribution volume ratio (DVR). (3) The variability [as measured by the coefficient of variation (CV) = standard deviation/mean] in the distribution volume ratio (DVR) of thalamus (to reference region) was considerably reduced over that of the DV using this composite reference region. (4) Pretreatment with nisoxetine (1.0 mg/kg 10 min prior to tracer) in one study produced (in decreasing order) reductions in thalamus, cerebellum, cingulate and frontal cortex consistent with known NET densities. (5) [(11)C]Nisoxetine had a higher
Modeling and analysis of PET studies with norepinephrine transporter ligands: the search for a reference region

International Nuclear Information System (INIS)

Logan, Jean; Ding, Y.-S.; Lin, K.-S.; Pareto, Deborah; Fowler, Joanna; Biegon, Anat

2005-01-01

The development of positron emission tomography (PET) ligands for the norepinephrine transporter (NET) has been slow compared to the development of radiotracers for others systems, such as the dopamine (DAT) or the serotonin transporters (SERT). The main reason for this appears to be the high nonspecific (non-NET) binding exhibited by many of these tracers, which makes the identification of a reference region difficult. With other PET ligands the use of a reference region increases the reproducibility of the outcome measure in test/retest studies. The focus of this work is to identify a suitable reference region or means of normalizing data for the NET ligands investigated. Methods: We have analyzed the results of PET studies in the baboon brain with labeled reboxetine derivatives (S,S)-[ 11 C]O-methyl reboxetine (SS-MRB), (S,S)-[ 18 F]fluororeboxetine (SS-FRB) as well as O-[ 11 C]nisoxetine and N-[ 11 C]nisoxetine (NIS), and, for comparison, the less active (R,R) enantiomers (RR-MRB, RR-FRB) in terms of the distribution volume (DV) using measured arterial input functions. Results: (1) For a given subject, a large variation in DV for successive baseline studies was observed in regions with both high and low NET density. (2) The occipital cortex and the basal ganglia were found to be the regions with the smallest change between baseline (SS-MRB) and pretreatment with cocaine, and were therefore used as a composite reference region for calculation of a distribution volume ratio (DVR). (3) The variability [as measured by the coefficient of variation (CV)=standard deviation/mean] in the distribution volume ratio (DVR) of thalamus (to reference region) was considerably reduced over that of the DV using this composite reference region. (4) Pretreatment with nisoxetine (1.0 mg/kg 10 min prior to tracer) in one study produced (in decreasing order) reductions in thalamus, cerebellum, cingulate and frontal cortex consistent with known NET densities. (5) [ 11 C]Nisoxetine had
Changes of regional climate variability in central Europe during the past 250 years

Science.gov (United States)

Böhm, R.

2012-05-01

The paper uses the data potential of very long and homogenized instrumental climate time series in the south central Europe for analyzing one feature which is very dominant in the climate change debate --whether anthropogenic climate warming causes or goes along with an increase of climate extremes. The monthly resolved data of the HISTALP data collection provide 58 single series for the three climate elements, air pressure, air temperature and precipitation, that start earlier than 1831 and extend back to 1760 in some cases. Trends and long-term low frequent climate evolution is only shortly touched in the paper. The main goal is the analysis of trends or changes of high frequent interannual and interseasonal variability. In other words, it is features like extremely hot summers, very cold winters, excessively dry or wet seasons which the study aims at. The methods used are based on detrended highpass series whose variance is analyzed in discrete 30-year windows moving over the entire instrumental period. The analysis of discrete subintervals relies on the unique number of 8 (for precipitation 7) such "normal periods". The second approach is based on the same subintervals though not in fixed but moving windows over the entire instrumental period. The first result of the study is the clear evidence that there has been no increase of variability during the past 250 years in the region. The second finding is similar but concentrates on the recent three decades which are of particular interest because they are the first 30 years with dominating anthropogenic greenhouse gas forcing. We can show that also this recent anthropogenic normal period shows no widening of the PDF (probability density function) compared to the preceding ones. The third finding is based on the moving window technique. It shows that interannual variability changes show a clear centennial oscillating structure for all three climate elements in the region. For the time being we have no explanation
Binding Isotherms and Time Courses Readily from Magnetic Resonance.

Science.gov (United States)

Xu, Jia; Van Doren, Steven R

2016-08-16

Evidence is presented that binding isotherms, simple or biphasic, can be extracted directly from noninterpreted, complex 2D NMR spectra using principal component analysis (PCA) to reveal the largest trend(s) across the series. This approach renders peak picking unnecessary for tracking population changes. In 1:1 binding, the first principal component captures the binding isotherm from NMR-detected titrations in fast, slow, and even intermediate and mixed exchange regimes, as illustrated for phospholigand associations with proteins. Although the sigmoidal shifts and line broadening of intermediate exchange distorts binding isotherms constructed conventionally, applying PCA directly to these spectra along with Pareto scaling overcomes the distortion. Applying PCA to time-domain NMR data also yields binding isotherms from titrations in fast or slow exchange. The algorithm readily extracts from magnetic resonance imaging movie time courses such as breathing and heart rate in chest imaging. Similarly, two-step binding processes detected by NMR are easily captured by principal components 1 and 2. PCA obviates the customary focus on specific peaks or regions of images. Applying it directly to a series of complex data will easily delineate binding isotherms, equilibrium shifts, and time courses of reactions or fluctuations.
Regional distribution of serotonin transporter protein in postmortem human brain

International Nuclear Information System (INIS)

Kish, Stephen J.; Furukawa, Yoshiaki; Chang Lijan; Tong Junchao; Ginovart, Nathalie; Wilson, Alan; Houle, Sylvain; Meyer, Jeffrey H.

2005-01-01

Introduction: The primary approach in assessing the status of brain serotonin neurons in human conditions such as major depression and exposure to the illicit drug ecstasy has been the use of neuroimaging procedures involving radiotracers that bind to the serotonin transporter (SERT). However, there has been no consistency in the selection of a 'SERT-free' reference region for the estimation of free and nonspecific binding, as occipital cortex, cerebellum and white matter have all been employed. Objective and Methods: To identify areas of human brain that might have very low SERT levels, we measured, by a semiquantitative Western blotting procedure, SERT protein immunoreactivity throughout the postmortem brain of seven normal adult subjects. Results: Serotonin transporter could be quantitated in all examined brain areas. However, the SERT concentration in cerebellar cortex and white matter were only at trace values, being approximately 20% of average cerebral cortex and 5% of average striatum values. Conclusion: Although none of the examined brain areas are completely free of SERT, human cerebellar cortex has low SERT binding as compared to other examined brain regions, with the exception of white matter. Since the cerebellar cortical SERT binding is not zero, this region will not be a suitable reference region for SERT radioligands with very low free and nonspecific binding. For SERT radioligands with reasonably high free and nonspecific binding, the cerebellar cortex should be a useful reference region, provided other necessary radioligand assumptions are met
Regional distribution of serotonin transporter protein in postmortem human brain

Energy Technology Data Exchange (ETDEWEB)

Kish, Stephen J. [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada)]. E-mail: Stephen_Kish@CAMH.net; Furukawa, Yoshiaki [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Chang Lijan [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Tong Junchao [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Ginovart, Nathalie [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Wilson, Alan [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Houle, Sylvain [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Meyer, Jeffrey H. [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada)

2005-02-01

Introduction: The primary approach in assessing the status of brain serotonin neurons in human conditions such as major depression and exposure to the illicit drug ecstasy has been the use of neuroimaging procedures involving radiotracers that bind to the serotonin transporter (SERT). However, there has been no consistency in the selection of a 'SERT-free' reference region for the estimation of free and nonspecific binding, as occipital cortex, cerebellum and white matter have all been employed. Objective and Methods: To identify areas of human brain that might have very low SERT levels, we measured, by a semiquantitative Western blotting procedure, SERT protein immunoreactivity throughout the postmortem brain of seven normal adult subjects. Results: Serotonin transporter could be quantitated in all examined brain areas. However, the SERT concentration in cerebellar cortex and white matter were only at trace values, being approximately 20% of average cerebral cortex and 5% of average striatum values. Conclusion: Although none of the examined brain areas are completely free of SERT, human cerebellar cortex has low SERT binding as compared to other examined brain regions, with the exception of white matter. Since the cerebellar cortical SERT binding is not zero, this region will not be a suitable reference region for SERT radioligands with very low free and nonspecific binding. For SERT radioligands with reasonably high free and nonspecific binding, the cerebellar cortex should be a useful reference region, provided other necessary radioligand assumptions are met.
A novel large deletion of the ICR1 region including H19 and putative enhancer elements.

Science.gov (United States)

Fryssira, Helen; Amenta, Stella; Kanber, Deniz; Sofocleous, Christalena; Lykopoulou, Evangelia; Kanaka-Gantenbein, Christina; Cerrato, Flavia; Lüdecke, Hermann-Josef; Bens, Susanne; Riccio, Andrea; Buiting, Karin

2015-05-06

Beckwith-Wiedemann syndrome (BWS) is a rare pediatric overgrowth disorder with a variable clinical phenotype caused by deregulation affecting imprinted genes in the chromosomal region 11p15. Alterations of the imprinting control region 1 (ICR1) at the IGF2/H19 locus resulting in biallelic expression of IGF2 and biallelic silencing of H19 account for approximately 10% of patients with BWS. The majority of these patients have epimutations of the ICR1 without detectable DNA sequence changes. Only a few patients were found to have deletions. Most of these deletions are small affecting different parts of the ICR1 differentially methylated region (ICR1-DMR) removing target sequences for CTCF. Only a very few deletions reported so far include the H19 gene in addition to the CTCF binding sites. None of these deletions include IGF2. A male patient was born with hypotonia, facial dysmorphisms and hypoglycemia suggestive of Beckwith-Wiedemann syndrome. Using methylation-specific (MS)-MLPA (Multiplex ligation-dependent probe amplification) we have identified a maternally inherited large deletion of the ICR1 region in a patient and his mother. The deletion results in a variable clinical expression with a classical BWS in the mother and a more severe presentation of BWS in her son. By genome-wide SNP array analysis the deletion was found to span ~100 kb genomic DNA including the ICR1DMR, H19, two adjacent non-imprinted genes and two of three predicted enhancer elements downstream to H19. Methylation analysis by deep bisulfite next generation sequencing revealed hypermethylation of the maternal allele at the IGF2 locus in both, mother and child, although IGF2 is not affected by the deletion. We here report on a novel large familial deletion of the ICR1 region in a BWS family. Due to the deletion of the ICR1-DMR CTCF binding cannot take place and the residual enhancer elements have access to the IGF2 promoters. The aberrant methylation (hypermethylation) of the maternal IGF2
The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.

Directory of Open Access Journals (Sweden)

Antonio L C Gomes

2016-04-01

Full Text Available ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology.
Cell-type specificity of ChIP-predicted transcription factor binding sites

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Håndstad Tony

2012-08-01

Full Text Available Abstract Background Context-dependent transcription factor (TF binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identifies genome-wide TF binding sites for one particular context—the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak clustering are the strongest predictors of common peaks. Compared with strong peaks located in regions containing peaks for multiple transcription factors, weak and isolated peaks are less common between the cell types and are less associated with data that indicate regulatory activity. Conclusions Together, the results suggest that experimental noise is prevalent among weak peaks, whereas strong and clustered peaks represent high-confidence binding events that often occur in other cellular contexts. Nevertheless, 30-40% of the strongest and most clustered peaks show context-dependent regulation. We show that by combining signal intensity with additional data—ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure—we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts.
The spliceosome-associated protein Mfap1 binds to VCP in Drosophila.

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Sandra Rode

Full Text Available Posttranscriptional regulation of gene expression contributes to many developmental transitions. Previously, we found that the AAA chaperone Valosin-Containing Protein (VCP regulates ecdysone-dependent dendrite pruning of Drosophila class IV dendritic arborization (c4da neurons via an effect on RNA metabolism. In a search for RNA binding proteins associated with VCP, we identified the spliceosome-associated protein Mfap1, a component of the tri-snRNP complex. Mfap1 is a nucleolar protein in neurons and its levels are regulated by VCP. Mfap1 binds to VCP and TDP-43, a disease-associated RNA-binding protein. via distinct regions in its N- and C-terminal halfs. Similar to vcp mutations, Mfap1 overexpression causes c4da neuron dendrite pruning defects and mislocalization of TDP-43 in these cells, but genetic analyses show that Mfap1 is not a crucial VCP target during dendrite pruning. Finally, rescue experiments with a lethal mfap1 mutant show that the VCP binding region is not essential for Mfap1 function, but may act to increase its stability or activity.
Sensitivity of Sahelian Precipitation to Desert Dust under ENSO variability: a regional modeling study

Science.gov (United States)

Jordan, A.; Zaitchik, B. F.; Gnanadesikan, A.

2016-12-01

Mineral dust is estimated to comprise over half the total global aerosol burden, with a majority coming from the Sahara and Sahel region. Bounded by the Sahara Desert to the north and the Sahelian Savannah to the south, the Sahel experiences high interannual rainfall variability and a short rainy season during the boreal summer months. Observation-based data for the past three decades indicates a reduced dust emission trend, together with an increase in greening and surface roughness within the Sahel. Climate models used to study regional precipitation changes due to Saharan dust yield varied results, both in sign convention and magnitude. Inconsistency of model estimates drives future climate projections for the region that are highly varied and uncertain. We use the NASA-Unified Weather Research and Forecasting (NU-WRF) model to quantify the interaction and feedback between desert dust aerosol and Sahelian precipitation. Using nested domains at fine spatial resolution we resolve changes to mesoscale atmospheric circulation patterns due to dust, for representative phases of El Niño-Southern Oscillation (ENSO). The NU-WRF regional earth system model offers both advanced land surface data and resolvable detail of the mechanisms of the impact of Saharan dust. Results are compared to our previous work assessed over the Western Sahel using the Geophysical Fluid Dynamics Laboratory (GFDL) CM2Mc global climate model, and to other previous regional climate model studies. This prompts further research to help explain the dust-precipitation relationship and recent North African dust emission trends. This presentation will offer a quantitative analysis of differences in radiation budget, energy and moisture fluxes, and atmospheric dynamics due to desert dust aerosol over the Sahel.
[18F]haloperidol binding in baboon brain in vivo

International Nuclear Information System (INIS)

Yousef, Khalil A.; Fowler, Joanna S.; Volkow, Nora D.; Dewey, Stephen L.; Shea, Colleen; Schlyer, David J.; Gatley, S. John; Logan, Jean; Wolf, Alfred P.

1996-01-01

The binding of [ 18 F]haloperidol to dopamine D2 and to sigma recognition sites in baboon brain was examined using positron emission tomography (PET). Studies were performed at baseline and after treatment with either haloperidol (to evaluate saturability), (+)-butaclamol (which has specificity for dopamine D2 receptors) or (-)-butaclamol (which has specificity for sigma sites). Binding was widespread. Treatment with (-)-butaclamol had no effect, whereas (+)-butaclamol selectively reduced the uptake in striatum. Haloperidol increased the clearance rate from all brain regions. These results indicate that the binding profile of [ 18 F]haloperidol does not permit the selective examination of either dopamine D2 or sigma sites using PET
Efficient heterologous expression and secretion in Aspergillus oryzae of a llama variable heavy-chain antibody fragment V(HH) against EGFR.

Science.gov (United States)

Okazaki, Fumiyoshi; Aoki, Jun-ichi; Tabuchi, Soichiro; Tanaka, Tsutomu; Ogino, Chiaki; Kondo, Akihiko

2012-10-01

We have constructed a filamentous fungus Aspergillus oryzae that secretes a llama variable heavy-chain antibody fragment (V(HH)) that binds specifically to epidermal growth factor receptor (EGFR) in a culture medium. A major improvement in yield was achieved by fusing the V(HH) with a Taka-amylase A signal sequence (sTAA) and a segment of 28 amino acids from the N-terminal region of Rhizopus oryzae lipase (N28). The yields of secreted, immunologically active anti-EGFR V(HH) reached 73.8 mg/1 in a Sakaguchi flask. The V(HH) fragments were released from the sTAA or N28 proteins by an indigenous A. oryzae protease during cultivation. The purified recombinant V(HH) fragment was specifically recognized and could bind to the EGFR with a high affinity.

Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

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Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.
Collaborative Proposal: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic System Model (RASM)

Energy Technology Data Exchange (ETDEWEB)

Maslowski, Wieslaw [Naval Postgraduate School, Monterey, CA (United States). Dept. of Oceanography; Cassano, John J. [Univ. of Colorado, Boulder, CO (United States); Gutowski, Jr., William J. [Iowa State Univ., Ames, IA (United States); Lipscomb, William H. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nijssen, Bart [Univ. of Washington, Seattle, WA (United States); Roberts, Andrew [Naval Postgraduate School, Monterey, CA (United States). Dept. of Oceanography; Robertson, William [Univ. of Texas, El Paso, TX (United States); Tulaczyk, Slawek [Univ. of California, Santa Cruz, CA (United States); Zeng, Xubin [Univ. of Arizona, Tucson, AZ (United States)

2011-05-15

The primary outcome of the project was the development of the Regional Arctic System Model (RASM) and evaluation of its individual model components, coupling among them and fully coupled model results. Overall, we have demonstrated that RASM produces realistic mean and seasonal surface climate as well as its interannual and decadal variability and trends.
Temporal and spatial variability of frost-free seasons in the Great Lakes region of the United States

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Lejiang Yu; Shiyuan Zhong; Xindi Bian; Warren E. Heilman; Jeffrey A. Andresen

2014-01-01

The frequency and timing of frost events and the length of the growing season are critical limiting factors in many human and natural ecosystems. This study investigates the temporal and spatial variability of the date of last spring frost (LSF), the date of first fall frost (FFF), and the length of the frost-free season (FFS) in the Great Lakes region of the United...
Collaborative Proposal: Improving Decadal Prediction of Arctic Climate Variability and Change Using a Regional Arctic System Model (RASM)

Energy Technology Data Exchange (ETDEWEB)

Maslowski, Wieslaw [Naval Postgraduate School, Monterey, CA (United States)

2016-10-17

This project aims to develop, apply and evaluate a regional Arctic System model (RASM) for enhanced decadal predictions. Its overarching goal is to advance understanding of the past and present states of arctic climate and to facilitate improvements in seasonal to decadal predictions. In particular, it will focus on variability and long-term change of energy and freshwater flows through the arctic climate system. The project will also address modes of natural climate variability as well as extreme and rapid climate change in a region of the Earth that is: (i) a key indicator of the state of global climate through polar amplification and (ii) which is undergoing environmental transitions not seen in instrumental records. RASM will readily allow the addition of other earth system components, such as ecosystem or biochemistry models, thus allowing it to facilitate studies of climate impacts (e.g., droughts and fires) and of ecosystem adaptations to these impacts. As such, RASM is expected to become a foundation for more complete Arctic System models and part of a model hierarchy important for improving climate modeling and predictions.
A Study of Precipitation Climatology and Its Variability over Europe Using an Advanced Regional Model (WRF)

KAUST Repository

Dasari, Hari Prasad

2015-03-06

In recent years long-term precipitation trends on a regional scale have been given emphasis due to the impacts of global warming on regional hydrology. In this study, regional precipitation trends are simulated over the Europe continent for a 60-year period in 1950-2010 using an advanced regional model, WRF, to study extreme precipitation events over Europe. The model runs continuously for each year during the period at a horizontal resolution of 25 km with initial/ boundary conditions derived from the National Center for Environmental Prediction (NCEP) 2.5 degree reanalysis data sets. The E-OBS 0.25 degree rainfall observation analysis is used for model validation. Results indicate that the model could reproduce the spatial annual rainfall pattern over Europe with low amounts (250 - 750 mm) in Iberian Peninsula, moderate to large amounts (750 - 1500 mm) in central, eastern and northeastern parts of Europe and extremely heavy falls (1500 - 2000 mm) in hilly areas of Alps with a slight overestimation in Alps and underestimation in other parts of Europe. The regional model integrations showed increasing errors (mean absolute errors) and decreasing correlations with increasing time scale (daily to seasonal). Rainfall is simulated relatively better in Iberian Peninsula, northwest and central parts of Europe. A large spatial variability with the highest number of wet days over eastern, central Europe and Alps (~200 days/year) and less number of wet days over Iberian Peninsula (≤150 days/year) is also found in agreement with observations. The model could simulate the spatial rainfall climate variability reasonably well with low rainfall days (1 - 10 mm/days) in almost all zones, heavy rainfall events in western, northern, southeastern hilly and coastal zones and extremely heavy rainfall events in northern coastal zones. An increasing trend of heavy rainfall in central, southern and southeastern parts, a decreasing trend in Iberian Peninsula and a steady trend in other
Altered SPECT 123I iomazenil Binding in the Cingulate Cortex of Children with Anorexia Nervosa

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Shinichiro eNagamitsu

2016-02-01

Full Text Available Several lines of evidence suggest that anxiety plays a key role in the development and maintenance of anorexia nervosa (AN in children. The purpose of this study was to examine cortical GABA(A-benzodiazepine receptor binding before and after treatment in children beginning intensive AN treatment. Brain single photon emission computed tomography (SPECT measurements using 123I iomazenil, which binds to GABA(A-benzodiazepine receptors, was performed in 26 participants with AN who were enrolled in a multimodal treatment program. Sixteen of the 26 participants underwent a repeat SPECT scan immediately before discharge at conclusion of the intensive treatment program. Eating behavior and mood disturbances were assessed using Eating Attitudes Test with 26 items (EAT-26 and the short form of the Profile of Mood States (POMS. Clinical outcome scores were evaluated after a 1-year period. We examined association between relative iomazenil binding activity in cortical regions of interest (ROIs and psychometric profiles, and determined which psychometric profiles show interaction effects with brain regions. Further, we determined if binding activity could predict clinical outcome and treatment changes. Higher EAT-26 scores were significantly associated with lower iomazenil binding activity in the anterior posterior cingulate cortex (ACC. Higher POMS subscale scores were significantly associated with lower iomazenil binding activity in the left frontal, parietal cortex, and posterior cingulate cortex (PCC. Depression-Dejection, and Confusion POMS subscale scores, and total POMS score, showed interaction effects with brain regions in iomazenil binding activity. Decreased binding in the ACC and left parietal cortex was associated with poor clinical outcomes. Relative binding increases throughout the PCC and occipital gyrus were observed after weight gain in children with AN. These findings suggest that cortical GABAergic receptor binding is altered in children
Testosterone levels in healthy men correlate negatively with serotonin 4 receptor binding

DEFF Research Database (Denmark)

Perfalk, Erik; Cunha-Bang, Sofi da; Holst, Klaus K

2017-01-01

The serotonergic system integrates sex steroid information and plays a central role in mood and stress regulation, cognition, appetite and sleep. This interplay may be critical for likelihood of developing depressive episodes, at least in a subgroup of sensitive individuals. The serotonin 4...... positron emission tomography in a group of 41 healthy men. We estimated global 5-HT4R binding using a latent variable model framework, which models shared correlation between 5-HT4R across multiple brain regions (hippocampus, amygdala, posterior and anterior cingulate, thalamus, pallidostriatum...... and neocortex). We tested whether testosterone and estradiol predict global 5-HT4R, adjusting for age. We found that testosterone, but not estradiol, correlated negatively with global 5-HT4R levels (p=0.02) suggesting that men with high levels of testosterone have higher cerebral serotonergic tonus. Our...
A protein that binds to the P1 origin core and the oriC 13mer region in a methylation-specific fashion is the product of the host seqA gene.

Science.gov (United States)

Brendler, T; Abeles, A; Austin, S

1995-08-15

The P1 plasmid replication origin P1oriR is controlled by methylation of four GATC adenine methylation sites within heptamer repeats. A comparable (13mer) region is present in the host origin, oriC. The two origins show comparable responses to methylation; negative control by recognition of hemimethylated DNA (sequestration) and a positive requirement for methylation for efficient function. We have isolated a host protein that recognizes the P1 origin region only when it is isolated from a strain proficient for adenine methylation. The substantially purified 22 kDa protein also binds to the 13mer region of oriC in a methylation-specific fashion. It proved to be the product of the seqA gene that acts in the negative control of oriC by sequestration. We conclude that the role of the SeqA protein in sequestration is to recognize the methylation state of P1oriR and oriC by direct DNA binding. Using synthetic substrates we show that SeqA binds exclusively to the hemimethylated forms of these origins forms that are the immediate products of replication in a methylation-proficient strain. We also show that the protein can recognize sequences with multiple GATC sites, irrespective of the surrounding sequence. The basis for origin specificity is primarily the persistence of hemimethylated forms that are over-represented in the natural. DNA preparations relative to controls.
Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

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Ronne Hans

2008-11-01

Full Text Available Abstract Background The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence is important for gene regulation. Results In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. Conclusion We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.
Disruption of key NADH-binding pocket residues of the Mycobacterium tuberculosis InhA affects DD-CoA binding ability.

Science.gov (United States)

Shaw, Daniel J; Robb, Kirsty; Vetter, Beatrice V; Tong, Madeline; Molle, Virginie; Hunt, Neil T; Hoskisson, Paul A

2017-07-05

Tuberculosis (TB) is a global health problem that affects over 10 million people. There is an urgent need to develop novel antimicrobial therapies to combat TB. To achieve this, a thorough understanding of key validated drug targets is required. The enoyl reductase InhA, responsible for synthesis of essential mycolic acids in the mycobacterial cell wall, is the target for the frontline anti-TB drug isoniazid. To better understand the activity of this protein a series of mutants, targeted to the NADH co-factor binding pocket were created. Residues P193 and W222 comprise a series of hydrophobic residues surrounding the cofactor binding site and mutation of both residues negatively affect InhA function. Construction of an M155A mutant of InhA results in increased affinity for NADH and DD-CoA turnover but with a reduction in V max for DD-CoA, impairing overall activity. This suggests that NADH-binding geometry of InhA likely permits long-range interactions between residues in the NADH-binding pocket to facilitate substrate turnover in the DD-CoA binding region of the protein. Understanding the precise details of substrate binding and turnover in InhA and how this may affect protein-protein interactions may facilitate the development of improved inhibitors enabling the development of novel anti-TB drugs.
Autoradiographic localization of (125I-Tyr4)bombesin-binding sites in rat brain

International Nuclear Information System (INIS)

Zarbin, M.A.; Kuhar, M.J.; O'Donohue, T.L.; Wolf, S.S.; Moody, T.W.

1985-01-01

The binding of ( 125 I-Tyr 4 )bombesin to rat brain slices was investigated. Radiolabeled (Tyr 4 )bombesin bound with high affinity (K/sub d/ . 4 nM) to a single class of sites (B/sub max/ . 130 fmol/mg of protein); the ratio of specific to nonspecific binding was 6/1. Also, pharmacology studies indicated that the C-terminal of bombesin was important for the high affinity binding activity. Autoradiographic studies indicated that the ( 125 I-Tyr4)bombesin-binding sites were discretely distributed in certain gray but not white matter regions of rat brain. Highest grain densities were present in the olfactory bulb and tubercle, nucleus accumbens, suprachiasmatic and periventricular nuclei of the hypothalamus, central medial thalamic nucleus, medial amygdaloid nucleus, hippocampus, dentate gyrus, subiculum, nucleus of the solitary tract, and substantia gelatinosa. Moderate grain densities were present in the parietal cortex, deep layers of the neocortex, rhinal cortex, caudate putamen, stria terminalis, locus ceruleus, parabrachial nucleus, and facial nucleus. Low grain densities were present in the globus pallidus, lateral thalamus, and midbrain. Negligible grain densities were present in the cerebellum, corpus callosum, and all regions treated with 1 microM unlabeled bombesin. The discrete regional distribution of binding suggests that endogenous bombesin-like peptides may function as important regulatory agents in certain brain loci
Multiresponse semiparametric regression for modelling the effect of regional socio-economic variables on the use of information technology

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Wibowo, Wahyu; Wene, Chatrien; Budiantara, I. Nyoman; Permatasari, Erma Oktania

2017-03-01

Multiresponse semiparametric regression is simultaneous equation regression model and fusion of parametric and nonparametric model. The regression model comprise several models and each model has two components, parametric and nonparametric. The used model has linear function as parametric and polynomial truncated spline as nonparametric component. The model can handle both linearity and nonlinearity relationship between response and the sets of predictor variables. The aim of this paper is to demonstrate the application of the regression model for modeling of effect of regional socio-economic on use of information technology. More specific, the response variables are percentage of households has access to internet and percentage of households has personal computer. Then, predictor variables are percentage of literacy people, percentage of electrification and percentage of economic growth. Based on identification of the relationship between response and predictor variable, economic growth is treated as nonparametric predictor and the others are parametric predictors. The result shows that the multiresponse semiparametric regression can be applied well as indicate by the high coefficient determination, 90 percent.
ESA STSE Project “Sea Surface Temperature Diurnal Variability: Regional Extend – Implications in Atmospheric Modelling”

DEFF Research Database (Denmark)

Karagali, Ioanna

of the vertical extend of diurnal signals. Drifting buoys provide measurements close to the surface but are not always available. Moored buoys are generally not able to resolve the daily SST signal, which strongly weakens with depth within the upper water column. For such reasons, the General Ocean Turbulence......, atmospheric and oceanic modelling, bio-chemical processes and oceanic CO2 studies. The diurnal variability of SST, driven by the coincident occurrence of low enough wind and solar heating, is currently not properly understood. Atmospheric, oceanic and climate models are currently not adequately resolving...... the daily SST variability, resulting in biases of the total heat budget estimates and therefore, demised model accuracies. The ESA STSE funded project SSTDV:R.EX.-IM.A.M. aimed at characterising the regional extend of diurnal SST signals and their impact in atmospheric modelling. This study will briefly...
Characterization of Novel Calmodulin Binding Domains within IQ Motifs of IQGAP1

Science.gov (United States)

Jang, Deok-Jin; Ban, Byungkwan; Lee, Jin-A

2011-01-01

IQ motif-containing GTPase-activating protein 1 (IQGAP1), which is a well-known calmodulin (CaM) binding protein, is involved in a wide range of cellular processes including cell proliferation, tumorigenesis, adhesion, and migration. Interaction of IQGAP1 with CaM is important for its cellular functions. Although each IQ domain of IQGAP1 for CaM binding has been characterized in a Ca2+-dependent or -independent manner, it was not clear which IQ motifs are physiologically relevant for CaM binding in the cells. In this study, we performed immunoprecipitation using 3xFLAGhCaM in mammalian cell lines to characterize the domains of IQGAP1 that are key for CaM binding under physiological conditions. Interestingly, using this method, we identified two novel domains, IQ(2.7-3) and IQ(3.5-4.4), within IQGAP1 that were involved in Ca2+-independent or -dependent CaM binding, respectively. Mutant analysis clearly showed that the hydrophobic regions within IQ(2.7-3) were mainly involved in apoCaM binding, while the basic amino acids and hydrophobic region of IQ(3.5-4.4) were required for Ca2+/CaM binding. Finally, we showed that IQ(2.7-3) was the main apoCaM binding domain and both IQ(2.7-3) and IQ(3.5-4.4) were required for Ca2+/CaM binding within IQ(1- 2-3-4). Thus, we identified and characterized novel direct CaM binding motifs essential for IQGAP1. This finding indicates that IQGAP1 plays a dynamic role via direct interactions with CaM in a Ca2+-dependent or -independent manner. PMID:22080369
Exploring the composition of protein-ligand binding sites on a large scale.

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Nickolay A Khazanov

Full Text Available The residue composition of a ligand binding site determines the interactions available for diffusion-mediated ligand binding, and understanding general composition of these sites is of great importance if we are to gain insight into the functional diversity of the proteome. Many structure-based drug design methods utilize such heuristic information for improving prediction or characterization of ligand-binding sites in proteins of unknown function. The Binding MOAD database if one of the largest curated sets of protein-ligand complexes, and provides a source of diverse, high-quality data for establishing general trends of residue composition from currently available protein structures. We present an analysis of 3,295 non-redundant proteins with 9,114 non-redundant binding sites to identify residues over-represented in binding regions versus the rest of the protein surface. The Binding MOAD database delineates biologically-relevant "valid" ligands from "invalid" small-molecule ligands bound to the protein. Invalids are present in the crystallization medium and serve no known biological function. Contacts are found to differ between these classes of ligands, indicating that residue composition of biologically relevant binding sites is distinct not only from the rest of the protein surface, but also from surface regions capable of opportunistic binding of non-functional small molecules. To confirm these trends, we perform a rigorous analysis of the variation of residue propensity with respect to the size of the dataset and the content bias inherent in structure sets obtained from a large protein structure database. The optimal size of the dataset for establishing general trends of residue propensities, as well as strategies for assessing the significance of such trends, are suggested for future studies of binding-site composition.
Variability among the Most Rapidly Evolving Plastid Genomic Regions is Lineage-Specific: Implications of Pairwise Genome Comparisons in Pyrus (Rosaceae) and Other Angiosperms for Marker Choice

Science.gov (United States)

Ter-Voskanyan, Hasmik; Allgaier, Martin; Borsch, Thomas

2014-01-01

Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae)—a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC–trnV, trnR–atpA, ndhF–rpl32, psbM–trnD, and trnQ–rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters). Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid), Olea (asterids) and Cymbidium (monocots) showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF–rpl32 and trnK–rps16) were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations
Variability among the most rapidly evolving plastid genomic regions is lineage-specific: implications of pairwise genome comparisons in Pyrus (Rosaceae and other angiosperms for marker choice.

Directory of Open Access Journals (Sweden)

Nadja Korotkova

Full Text Available Plastid genomes exhibit different levels of variability in their sequences, depending on the respective kinds of genomic regions. Genes are usually more conserved while noncoding introns and spacers evolve at a faster pace. While a set of about thirty maximum variable noncoding genomic regions has been suggested to provide universally promising phylogenetic markers throughout angiosperms, applications often require several regions to be sequenced for many individuals. Our project aims to illuminate evolutionary relationships and species-limits in the genus Pyrus (Rosaceae-a typical case with very low genetic distances between taxa. In this study, we have sequenced the plastid genome of Pyrus spinosa and aligned it to the already available P. pyrifolia sequence. The overall p-distance of the two Pyrus genomes was 0.00145. The intergenic spacers between ndhC-trnV, trnR-atpA, ndhF-rpl32, psbM-trnD, and trnQ-rps16 were the most variable regions, also comprising the highest total numbers of substitutions, indels and inversions (potentially informative characters. Our comparative analysis of further plastid genome pairs with similar low p-distances from Oenothera (representing another rosid, Olea (asterids and Cymbidium (monocots showed in each case a different ranking of genomic regions in terms of variability and potentially informative characters. Only two intergenic spacers (ndhF-rpl32 and trnK-rps16 were consistently found among the 30 top-ranked regions. We have mapped the occurrence of substitutions and microstructural mutations in the four genome pairs. High AT content in specific sequence elements seems to foster frequent mutations. We conclude that the variability among the fastest evolving plastid genomic regions is lineage-specific and thus cannot be precisely predicted across angiosperms. The often lineage-specific occurrence of stem-loop elements in the sequences of introns and spacers also governs lineage-specific mutations. Sequencing
The Negatively Charged Regions of Lactoferrin Binding Protein B, an Adaptation against Anti-Microbial Peptides

Science.gov (United States)

Morgenthau, Ari; Beddek, Amanda; Schryvers, Anthony B.

2014-01-01

Lactoferrin binding protein B (LbpB) is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein’s C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides. PMID:24465982
The negatively charged regions of lactoferrin binding protein B, an adaptation against anti-microbial peptides.

Directory of Open Access Journals (Sweden)

Ari Morgenthau

Full Text Available Lactoferrin binding protein B (LbpB is a bi-lobed membrane bound lipoprotein that is part of the lactoferrin receptor complex in a variety of Gram-negative pathogens. Despite high sequence diversity among LbpBs from various strains and species, a cluster of negatively charged amino acids is invariably present in the protein's C-terminal lobe in all species except Moraxella bovis. The function of LbpB in iron acquisition has yet to be experimentally demonstrated, whereas in vitro studies have shown that LbpB confers protection against lactoferricin, a short cationic antimicrobial peptide released from the N- terminus of lactoferrin. In this study we demonstrate that the negatively charged regions can be removed from the Neisseria meningitidis LbpB without compromising stability, and this results in the inability of LbpB to protect against the bactericidal effects of lactoferricin. The release of LbpB from the cell surface by the autotransporter NalP reduces the protection against lactoferricin in the in vitro killing assay, attributed to removal of LbpB during washing steps, but is unlikely to have a similar impact in vivo. The protective effect of the negatively charged polysaccharide capsule in the killing assay was less than the protection conferred by LbpB, suggesting that LbpB plays a major role in protection against cationic antimicrobial peptides in vivo. The selective release of LbpB by NalP has been proposed to be a mechanism for evading the adaptive immune response, by reducing the antibody binding to the cell surface, but may also provide insights into the primary function of LbpB in vivo. Although TbpB and LbpB have been shown to be major targets of the human immune response, the selective release of LbpB suggests that unlike TbpB, LbpB may not be essential for iron acquisition, but important for protection against cationic antimicrobial peptides.
The Glycosylphosphatidylinositol-Anchored Variable Region of Llama Heavy Chain-Only Antibody JM4 Efficiently Blocks both Cell-Free and T Cell-T Cell Transmission of Human Immunodeficiency Virus Type 1.

Science.gov (United States)

Liu, Lihong; Wang, Weiming; Matz, Julie; Ye, Chaobaihui; Bracq, Lucie; Delon, Jerome; Kimata, Jason T; Chen, Zhiwei; Benichou, Serge; Zhou, Paul

2016-12-01

The variable regions (VHHs) of two heavy chain-only antibodies, JM2 and JM4, from llamas that have been immunized with a trimeric gp140 bound to a CD4 mimic have been recently isolated (here referred to as VHH JM2 and VHH JM4, respectively). JM2 binds the CD4-binding site of gp120 and neutralizes HIV-1 strains from subtypes B, C, and G. JM4 binds gp120 and neutralizes HIV-1 strains from subtypes A, B, C, A/E, and G in a CD4-dependent manner. In the present study, we constructed glycosylphosphatidylinositol (GPI)-anchored VHH JM2 and JM4 along with an E4 control and transduced them into human CD4 + cell lines and primary CD4 T cells. We report that by genetically linking the VHHs with a GPI attachment signal, VHHs are targeted to the lipid rafts of the plasma membranes. Expression of GPI-VHH JM4, but not GPI-VHH E4 and JM2, on the surface of transduced TZM.bl cells potently neutralizes multiple subtypes of HIV-1 isolates, including tier 2 or 3 strains, transmitted founders, quasispecies, and soluble single domain antibody (sdAb) JM4-resistant viruses. Moreover, transduction of CEMss-CCR5 cells with GPI-VHH JM4, but not with GPI-VHH E4, confers resistance to both cell-free and T cell-T cell transmission of HIV-1 and HIV-1 envelope-mediated fusion. Finally, GPI-VHH JM4-transduced human primary CD4 T cells efficiently resist both cell-free and T cell-T cell transmission of HIV-1. Thus, we conclude that VHH JM4, when targeted to the lipid rafts of the plasma membrane, efficiently neutralizes HIV-1 infection via both cell-free and T cell-T cell transmission. Our findings should have important implications for GPI-anchored antibody-based therapy against HIV-1. Lipid rafts are specialized dynamic microdomains of the plasma membrane and have been shown to be gateways for HIV-1 budding as well as entry into T cells and macrophages. In nature, many glycosylphosphatidylinositol (GPI)-anchored proteins localize in the lipid rafts. In the present study, we developed GPI

Heparin binding domain of antithrombin III: Characterization using a synthetic peptide directed polyclonal antibody

International Nuclear Information System (INIS)

Smith, J.W.; Dey, B.; Knauer, D.J.

1990-01-01

Antithrombin III (ATIII) is a plasma-borne serine protease inhibitor that apparently forms covalent complexes with thrombin. The interaction between ATIII and thrombin is enhanced several thousandfold by the glycosaminoglycan, heparin. The authors have previously proposed that the heparin binding site of ATIII residues within a region extending from amino acid residues 114-156. Computer-assisted analysis of this region revealed the presence of a 22 amino acid domain (residues 124-145), part of which shows a strong potential for the formation of an amphipathic helix: hydrophobic on one face and highly positively charged on the other. In the presence studies, polyclonal antisera were generated against a synthetic peptide corresponding to residues 124-145 in native human ATIII. Affinity-purified IgG from these antisera, as well as monovalent Fab's derived from them, specifically blocked the binding of heparin to ATIII. Additionally, occupancy of the heparin binding site by these same monovalent and bivalent IgG's at least partially substituted for heparin, accelerating linkage formation between ATIII and thrombin. These results provide the first immunological evidence that region 124-145 is directly involved in the binding of heparin to ATIII and that an antibody-induced conformational change within this region can mediate ATIII activation
Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon.

Science.gov (United States)

Rouanet, Carine; Reverchon, Sylvie; Rodionov, Dmitry A; Nasser, William

2004-07-16

In Erwinia chrysanthemi, production of pectic enzymes is modulated by a complex network involving several regulators. One of them, PecS, which belongs to the MarR family, also controls the synthesis of various other virulence factors, such as cellulases and indigoidine. Here, the PecS consensus-binding site is defined by combining a systematic evolution of ligands by an exponential enrichment approach and mutational analyses. The consensus consists of a 23-base pair palindromic-like sequence (C(-11)G(-10)A(-9)N(-8)W(-7)T(-6)C(-5)G(-4)T(-3)A(-2))T(-1)A(0)T(1)(T(2)A(3)C(4)G(5)A(6)N(7)N(8)N(9)C(10)G(11)). Mutational experiments revealed that (i) the palindromic organization is required for the binding of PecS, (ii) the very conserved part of the consensus (-6 to 6) allows for a specific interaction with PecS, but the presence of the relatively degenerated bases located apart significantly increases PecS affinity, (iii) the four bases G, A, T, and C are required for efficient binding of PecS, and (iv) the presence of several binding sites on the same promoter increases the affinity of PecS. This consensus is detected in the regions involved in PecS binding on the previously characterized target genes. This variable consensus is in agreement with the observation that the members of the MarR family are able to bind various DNA targets as dimers by means of a winged helix DNA-binding motif. Binding of PecS on a promoter region containing the defined consensus results in a repression of gene transcription in vitro. Preliminary scanning of the E. chrysanthemi genome sequence with the consensus revealed the presence of strong PecS-binding sites in the intergenic region between fliE and fliFGHIJKLMNOPQR which encode proteins involved in the biogenesis of flagellum. Accordingly, PecS directly represses fliE expression. Thus, PecS seems to control the synthesis of virulence factors required for the key steps of plant infection.
Quantifying the effects of climate variability and human activities on runoff for Kaidu River Basin in arid region of northwest China

Science.gov (United States)

Chen, Zhongsheng; Chen, Yaning; Li, Baofu

2013-02-01

Much attention has recently been focused on the effects that climate variability and human activities have had on runoff. In this study, data from the Kaidu River Basin in the arid region of northwest China were analyzed to investigate changes in annual runoff during the period of 1960-2009. The nonparametric Mann-Kendall test and the Mann-Kendall-Sneyers test were used to identify trend and step change point in the annual runoff. It was found that the basin had a significant increasing trend in annual runoff. Step change point in annual runoff was identified in the basin, which occurred in the year around 1993 dividing the long-term runoff series into a natural period (1960-1993) and a human-induced period (1994-2009). Then, the hydrologic sensitivity analysis method was employed to evaluate the effects of climate variability and human activities on mean annual runoff for the human-induced period based on precipitation and potential evapotranspiration. In 1994-2009, climate variability was the main factor that increased runoff with contribution of 90.5 %, while the increasing percentage due to human activities only accounted for 9.5 %, showing that runoff in the Kaidu River Basin is more sensitive to climate variability than human activities. This study quantitatively distinguishes the effects between climate variability and human activities on runoff, which can do duty for a reference for regional water resources assessment and management.
The complementarity-determining region sequences in IgY antivenom hypervariable regions

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David Gitirana da Rocha

2017-08-01

Full Text Available The data presented in this article are related to the research article entitled "Development of IgY antibodies against anti-snake toxins endowed with highly lethal neutralizing activity" (da Rocha et al., 2017 [1]. Complementarity-determining region (CDR sequences are variable antibody (Ab sequences that respond with specificity, duration and strength to identify and bind to antigen (Ag epitopes. B lymphocytes isolated from hens immunized with Bitis arietans (Ba and anti-Crotalus durissus terrificus (Cdt venoms and expressing high specificity, affinity and toxicity neutralizing antibody titers were used as DNA sources. The VLF1, CDR1, CDR2, VLR1 and CDR3 sequences were validated by BLASTp, and values corresponding to IgY VL and VH anti-Ba or anti-Cdt venoms were identified, registered [Gallus gallus IgY Fv Light chain (GU815099/Gallus gallus IgY Fv Heavy chain (GU815098] and used for molecular modeling of IgY scFv anti-Ba. The resulting CDR1, CDR2 and CDR3 sequences were combined to construct the three - dimensional structure of the Ab paratope.
Identification of potential small molecule binding pockets on Rho family GTPases.

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Juan Manuel Ortiz-Sanchez

Full Text Available Rho GTPases are conformational switches that control a wide variety of signaling pathways critical for eukaryotic cell development and proliferation. They represent attractive targets for drug design as their aberrant function and deregulated activity is associated with many human diseases including cancer. Extensive high-resolution structures (>100 and recent mutagenesis studies have laid the foundation for the design of new structure-based chemotherapeutic strategies. Although the inhibition of Rho signaling with drug-like compounds is an active area of current research, very little attention has been devoted to directly inhibiting Rho by targeting potential allosteric non-nucleotide binding sites. By avoiding the nucleotide binding site, compounds may minimize the potential for undesirable off-target interactions with other ubiquitous GTP and ATP binding proteins. Here we describe the application of molecular dynamics simulations, principal component analysis, sequence conservation analysis, and ensemble small-molecule fragment mapping to provide an extensive mapping of potential small-molecule binding pockets on Rho family members. Characterized sites include novel pockets in the vicinity of the conformationaly responsive switch regions as well as distal sites that appear to be related to the conformations of the nucleotide binding region. Furthermore the use of accelerated molecular dynamics simulation, an advanced sampling method that extends the accessible time-scale of conventional simulations, is found to enhance the characterization of novel binding sites when conformational changes are important for the protein mechanism.
SCM, the M Protein of Streptococcus canis Binds Immunoglobulin G.

Science.gov (United States)

Bergmann, Simone; Eichhorn, Inga; Kohler, Thomas P; Hammerschmidt, Sven; Goldmann, Oliver; Rohde, Manfred; Fulde, Marcus

2017-01-01

The M protein of Streptococcus canis (SCM) is a virulence factor and serves as a surface-associated receptor with a particular affinity for mini-plasminogen, a cleavage product of the broad-spectrum serine protease plasmin. Here, we report that SCM has an additional high-affinity immunoglobulin G (IgG) binding activity. The ability of a particular S. canis isolate to bind to IgG significantly correlates with a scm -positive phenotype, suggesting a dominant role of SCM as an IgG receptor. Subsequent heterologous expression of SCM in non-IgG binding S. gordonii and Western Blot analysis with purified recombinant SCM proteins confirmed its IgG receptor function. As expected for a zoonotic agent, the SCM-IgG interaction is species-unspecific, with a particular affinity of SCM for IgGs derived from human, cats, dogs, horses, mice, and rabbits, but not from cows and goats. Similar to other streptococcal IgG-binding proteins, the interaction between SCM and IgG occurs via the conserved Fc domain and is, therefore, non-opsonic. Interestingly, the interaction between SCM and IgG-Fc on the bacterial surface specifically prevents opsonization by C1q, which might constitute another anti-phagocytic mechanism of SCM. Extensive binding analyses with a variety of different truncated SCM fragments defined a region of 52 amino acids located in the central part of the mature SCM protein which is important for IgG binding. This binding region is highly conserved among SCM proteins derived from different S. canis isolates but differs significantly from IgG-Fc receptors of S. pyogenes and S. dysgalactiae sub. equisimilis , respectively. In summary, we present an additional role of SCM in the pathogen-host interaction of S. canis . The detailed analysis of the SCM-IgG interaction should contribute to a better understanding of the complex roles of M proteins in streptococcal pathogenesis.
Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element

International Nuclear Information System (INIS)

Mao, Grace; Brody, James P.

2007-01-01

Gene expression is controlled by protein complexes binding to short specific sequences of DNA, called cis-regulatory elements. Expression of most eukaryotic genes is controlled by dozens of these elements. Comprehensive identification and monitoring of these elements is a major goal of genomics. In pursuit of this goal, we are developing a surface plasmon resonance (SPR) based assay to identify and monitor cis-regulatory elements. To test whether we could reliably monitor protein binding to a regulatory element, we immobilized a 16 bp region of Saccharomyces cerevisiae chromosome 5 onto a gold surface. This 16 bp region of DNA is known to bind several proteins and thought to control expression of the gene RNR1, which varies through the cell cycle. We synchronized yeast cell cultures, and then sampled these cultures at a regular interval. These samples were processed to purify nuclear lysate, which was then exposed to the sensor. We found that nuclear protein binds this particular element of DNA at a significantly higher rate (as compared to unsynchronized cells) during G1 phase. Other time points show levels of DNA-nuclear protein binding similar to the unsynchronized control. We also measured the apparent association complex of the binding to be 0.014 s -1 . We conclude that (1) SPR-based assays can monitor DNA-nuclear protein binding and that (2) for this particular cis-regulatory element, maximum DNA-nuclear protein binding occurs during G1 phase
Ligand deconstruction: Why some fragment binding positions are conserved and others are not

Science.gov (United States)

Kozakov, Dima; Hall, David R.; Jehle, Stefan; Luo, Lingqi; Ochiana, Stefan O.; Jones, Elizabeth V.; Pollastri, Michael; Allen, Karen N.; Whitty, Adrian; Vajda, Sandor

2015-01-01

Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots—regions of the protein where interactions with a ligand contribute substantial binding free energy—the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand. PMID:25918377
Ligand deconstruction: Why some fragment binding positions are conserved and others are not.

Science.gov (United States)

Kozakov, Dima; Hall, David R; Jehle, Stefan; Jehle, Sefan; Luo, Lingqi; Ochiana, Stefan O; Jones, Elizabeth V; Pollastri, Michael; Allen, Karen N; Whitty, Adrian; Vajda, Sandor

2015-05-19

Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots--regions of the protein where interactions with a ligand contribute substantial binding free energy--the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.
Predictions of RNA-binding ability and aggregation propensity of proteins

OpenAIRE

Agostini, Federico, 1985-

2014-01-01

RNA-binding proteins (RBPs) control the fate of a multitude of coding and non-coding transcripts. Formation of ribonucleoprotein (RNP) complexes fine-tunes regulation of post-transcriptional events and influences gene expression. Recently, it has been observed that non-canonical proteins with RNA-binding ability are enriched in structurally disordered and low-complexity regions that are generally involved in functional and dysfunctional associations. Therefore, it is possible that interaction...
Physical linkage of a human immunoglobulin heavy chain variable region gene segment to diversity and joining region elements

International Nuclear Information System (INIS)

Schroeder, H.W. Jr.; Walter, M.A.; Hofker, M.H.; Ebens, A.; Van Dijk, K.W.; Liao, L.C.; Cox, D.W.; Milner, E.C.B.; Perlmutter, R.M.

1988-01-01

Antibody genes are assembled from a series of germ-line gene segments that are juxtaposed during the maturation of B lymphocytes. Although diversification of the adult antibody repertoire results in large part from the combinatorial joining of these gene segments, a restricted set of antibody heavy chain variable (V H ), diversity (D H ), and joining (J H ) region gene segments appears preferentially in the human fetal repertoire. The authors report here that one of these early-expressed V H elements (termed V H 6) is the most 3' V H gene segment, positioned 77 kilobases on the 5' side of the J H locus and immediately adjacent to a set of previously described D H sequences. In addition to providing a physical map linking human V H , D H , and J H elements, these results support the view that the programmed development of the antibody V H repertoire is determined in part by the chromosomal position of these gene segments
Genetic, functional and molecular features of glucocorticoid receptor binding.

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Francesca Luca

Full Text Available Glucocorticoids (GCs are key mediators of stress response and are widely used as pharmacological agents to treat immune diseases, such as asthma and inflammatory bowel disease, and certain types of cancer. GCs act mainly by activating the GC receptor (GR, which interacts with other transcription factors to regulate gene expression. Here, we combined different functional genomics approaches to gain molecular insights into the mechanisms of action of GC. By profiling the transcriptional response to GC over time in 4 Yoruba (YRI and 4 Tuscans (TSI lymphoblastoid cell lines (LCLs, we suggest that the transcriptional response to GC is variable not only in time, but also in direction (positive or negative depending on the presence of specific interacting transcription factors. Accordingly, when we performed ChIP-seq for GR and NF-κB in two YRI LCLs treated with GC or with vehicle control, we observed that features of GR binding sites differ for up- and down-regulated genes. Finally, we show that eQTLs that affect expression patterns only in the presence of GC are 1.9-fold more likely to occur in GR binding sites, compared to eQTLs that affect expression only in its absence. Our results indicate that genetic variation at GR and interacting transcription factors binding sites influences variability in gene expression, and attest to the power of combining different functional genomic approaches.
Dissociating the neural correlates of intra-item and inter-item working-memory binding.

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Carinne Piekema

Full Text Available BACKGROUND: Integration of information streams into a unitary representation is an important task of our cognitive system. Within working memory, the medial temporal lobe (MTL has been conceptually linked to the maintenance of bound representations. In a previous fMRI study, we have shown that the MTL is indeed more active during working-memory maintenance of spatial associations as compared to non-spatial associations or single items. There are two explanations for this result, the mere presence of the spatial component activates the MTL, or the MTL is recruited to bind associations between neurally non-overlapping representations. METHODOLOGY/PRINCIPAL FINDINGS: The current fMRI study investigates this issue further by directly comparing intrinsic intra-item binding (object/colour, extrinsic intra-item binding (object/location, and inter-item binding (object/object. The three binding conditions resulted in differential activation of brain regions. Specifically, we show that the MTL is important for establishing extrinsic intra-item associations and inter-item associations, in line with the notion that binding of information processed in different brain regions depends on the MTL. CONCLUSIONS/SIGNIFICANCE: Our findings indicate that different forms of working-memory binding rely on specific neural structures. In addition, these results extend previous reports indicating that the MTL is implicated in working-memory maintenance, challenging the classic distinction between short-term and long-term memory systems.
RNA-binding properties and mapping of the RNA-binding domain from the movement protein of Prunus necrotic ringspot virus.

Science.gov (United States)

Herranz, M Carmen; Pallás, Vicente

2004-03-01

The movement protein (MP) of Prunus necrotic ringspot virus (PNRSV) is involved in intercellular virus transport. In this study, putative RNA-binding properties of the PNRSV MP were studied. The PNRSV MP was produced in Escherichia coli using an expression vector. Electrophoretic mobility shift assays (EMSAs) using DIG-labelled riboprobes demonstrated that PNRSV MP bound ssRNA cooperatively without sequence specificity. Two different ribonucleoprotein complexes were found to be formed depending on the molar MP : PNRSV RNA ratio. The different responses of the complexes to urea treatment strongly suggested that they have different structural properties. Deletion mutagenesis followed by Northwestern analysis allowed location of a nucleic acid binding domain to aa 56-88. This 33 aa RNA-binding motif is the smallest region delineated among members of the family Bromoviridae for which RNA-binding properties have been demonstrated. This domain is highly conserved within all phylogenetic subgroups previously described for PNRSV isolates. Interestingly, the RNA-binding domain described here and the one described for Alfamovirus are located at the N terminus of their corresponding MPs, whereas similar domains previously characterized in members of the genera Bromovirus and Cucumovirus are present at the C terminus, strongly reflecting their corresponding phylogenetic relationships. The evolutionary implications of this observation are discussed.
Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks

NARCIS (Netherlands)

Tran Thi Tuyet, H.; Zwart, M.P.; Phuong, N.T.; Jong, de M.C.M.; Vlak, J.M.

2012-01-01

White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable
Protection against syphilis correlates with specificity of antibodies to the variable regions of Treponema pallidum repeat protein K.

Science.gov (United States)

Morgan, Cecilia A; Lukehart, Sheila A; Van Voorhis, Wesley C

2003-10-01

Syphilis has been recognized as a disease since the late 1400s, yet there is no practical vaccine available. One impediment to the development of a vaccine is the lack of understanding of multiple reinfections in humans despite the development of robust immune responses during the first episode. It has been shown that the Treponema pallidum repeat protein K (TprK) differs in seven discrete variable (V) regions in isolates and that the antibody response during infection is directed to these V regions. Immunization with TprK confers significant protection against infection with the homologous strain. We hypothesize that the antigenic diversity of TprK is involved in immune evasion, which contributes to the lack of heterologous protection. Here, using the rabbit model, we show a correlation between limited heterologous protection and tprK diversity in the challenge inoculum. We demonstrate that antibody responses to the V regions of one TprK molecule show limited cross-reactivity with heterologous TprK V regions.
Interannual Variability of Regional Hadley Circulation Intensity Over Western Pacific During Boreal Winter and Its Climatic Impact Over Asia-Australia Region

Science.gov (United States)

Huang, Ruping; Chen, Shangfeng; Chen, Wen; Hu, Peng

2018-01-01

This study investigates interannual variability of boreal winter regional Hadley circulation over western Pacific (WPHC) and its climatic impacts. A WPHC intensity index (WPHCI) is defined as the vertical shear of the divergent meridional winds. It shows that WPHCI correlates well with the El Niño-Southern Oscillation (ENSO). To investigate roles of the ENSO-unrelated part of WPHCI (WPHCIres), variables that are linearly related to the Niño-3 index have been removed. It reveals that meridional sea surface temperature gradient over the western Pacific plays an essential role in modulating the WPHCIres. The climatic impacts of WPHCIres are further investigated. Below-normal (above-normal) precipitation appears over south China (North Australia) when WPHCIres is stronger. This is due to the marked convergence (divergence) anomalies at the upper troposphere, divergence (convergence) at the lower troposphere, and the accompanied downward (upward) motion over south China (North Australia), which suppresses (enhances) precipitation there. In addition, a pronounced increase in surface air temperature (SAT) appears over south and central China when WPHCIres is stronger. A temperature diagnostic analysis suggests that the increase in SAT tendency over central China is primarily due to the warm zonal temperature advection and subsidence-induced adiabatic heating. In addition, the increase in SAT tendency over south China is primarily contributed by the warm meridional temperature advection. Further analysis shows that the correlation of WPHCIres with the East Asian winter monsoon (EAWM) is weak. Thus, this study may provide additional sources besides EAWM and ENSO to improve understanding of the Asia-Australia climate variability.
The effect of chronic ethanol on glutamate binding in human and rat brain

International Nuclear Information System (INIS)

Cummins, J.T.; Sack, M.; von Hungen, K.

1990-01-01

Quantitative autoradiographic techniques demonstrate that chronic alcohol administration causes a decrease in [ 3 H]-glutamate binding to hippocampal N-methyl-D-aspartate (NMDA) receptors. A 14% decrease in [ 3 H]-glutamate binding in the hippocampal CA 1 region is seen both in the rat after five days of ethanol administration and in postmortem hippocampal tissues from alcoholics. In the rat, 24 hr ethanol withdrawal values are intermediate between control and alcohol binding levels. There was no significant effect of ethanol on [ 3 H]-glutamate binding in the cortex or caudate
Trans-acting translational regulatory RNA binding proteins.

Science.gov (United States)

Harvey, Robert F; Smith, Tom S; Mulroney, Thomas; Queiroz, Rayner M L; Pizzinga, Mariavittoria; Dezi, Veronica; Villenueva, Eneko; Ramakrishna, Manasa; Lilley, Kathryn S; Willis, Anne E

2018-05-01

The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination. Additionally, noncanonical, trans-acting regulatory RNA-binding proteins (RBPs) are necessary to provide mRNA-specific translation, and these interact with 5' and 3' untranslated regions and coding regions of mRNA to regulate ribosome recruitment and transit. Recently it has also been demonstrated that trans-acting ribosomal proteins direct the translation of specific mRNAs. Importantly, it has been shown that subsets of RBPs often work in concert, forming distinct regulatory complexes upon different cellular perturbation, creating an RBP combinatorial code, which through the translation of specific subsets of mRNAs, dictate cell fate. With the development of new methodologies, a plethora of novel RNA binding proteins have recently been identified, although the function of many of these proteins within mRNA translation is unknown. In this review we will discuss these methodologies and their shortcomings when applied to the study of translation, which need to be addressed to enable a better understanding of trans-acting translational regulatory proteins. Moreover, we discuss the protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans-acting ribosomal proteins in directing the translation of specific mRNAs. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes Translation > Translation Regulation Translation > Translation Mechanisms. © 2018 Medical Research Council and University of Cambridge. WIREs RNA published by Wiley Periodicals, Inc.
MARs Wars: heterogeneity and clustering of DNA-binding domains in the nuclear matrix

Directory of Open Access Journals (Sweden)

Ioudinkova E. S.

2009-12-01

Full Text Available Aim. CO326 is a chicken nuclear scaffold/matrix attachment region (MAR associated with the nuclear matrix in several types of chicken cells. It contains a binding site for a sequence-specific DNA-binding protein, F326. We have studied its interaction with the nuclear matrix. Methods. We have used an in vitro MAR assay with isolated matrices from chicken HD3 cells. Results. We have found that an oligonucleotide binding site for the F326 inhibits binding of the CO326 to the nuclear matrix. At the same time, the binding of heterologous MARs is enhanced. Conclusions. Taken together, these data suggest that there exist several classes of MARs and MAR-binding domains and that the MAR-binding proteins may be clustered in the nuclear matrix.

Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

KAUST Repository

Marcatili, P.

2013-05-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated. Copyright © 2013 by The American Association of Immunologists, Inc.
Igs Expressed by Chronic Lymphocytic Leukemia B Cells Show Limited Binding-Site Structure Variability

KAUST Repository

Marcatili, P.; Ghiotto, F.; Tenca, C.; Chailyan, A.; Mazzarello, A. N.; Yan, X.-J.; Colombo, M.; Albesiano, E.; Bagnara, D.; Cutrona, G.; Morabito, F.; Bruno, S.; Ferrarini, M.; Chiorazzi, N.; Tramontano, A.; Fais, F.

2013-01-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated. Copyright © 2013 by The American Association of Immunologists, Inc.
Characterizing isotopic variability of primary production and consumers in Great Plains ecosystems during protracted regional drought

Science.gov (United States)

Haveles, A. W.; Fox-Dobbs, K.; Talmadge, K. A.; Fetrow, A.; Fox, D. L.

2012-12-01

Over the last few years (2010-2012), the Great Plains of the central USA experienced protracted drought conditions, including historically severe drought during Summer, 2011. Drought severity in the region generally decreases with increasing latitude, but episodic drought is a fundamental trait of grassland ecosystems. Documenting above ground energy and nutrient flow with current drought is critical to understanding responses of grassland ecosystems in the region to predicted increased episodicity of rainfall and recurrence of drought due to anthropogenic climate change. Characterization of biogeochemical variability of modern ecosystems at the microhabitat, local landscape, and regional scales is also necessary to interpret biogeochemical records of ancient grasslands based on paleosols and fossil mammals. Here, we characterize three grassland ecosystems that span the drought gradient in the Great Plains (sites in the Texas panhandle, southwest Kansas, and northwest Nebraska). We measured δ13C and δ15N values of plants and consumers to characterize the biogeochemical variability within each ecosystem. Vegetation at each site is a mix of trees, shrubs, herbs, and cool- and warm-growing season grasses (C3 and C4, respectively). Thus, consumers have access to isotopically distinct sources of forage that vary in abundance with microhabitat (e.g., open grassland, shrub thicket, riparian woodland). Observations indicate herbivorous arthropod (grasshoppers and crickets) abundance follows drought severity, with high abundance of many species in Texas, and low abundance of few species in Nebraska. Small mammal (rodents) abundance follows the inverse pattern with 0.8%, 3.2% and 17.2% capture success in Texas, Kansas and Nebraska, respectively. The inverse abundance patterns of consumer groups may result from greater sensitivity of small mammal consumers with high metabolic needs to lower local net primary productivity and forage quality under drought conditions. As a
Influence of soil physical and chemical variables on species composition and richness of plants in the arid region of Tabuk, Saudi Arabia

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Al-Mutairi Khalid Awadh

2017-06-01

Full Text Available The present study aims to investigate the effect of soil physical and chemical variables on the species richness and the floristic composition in four sites (Alwaz, Alqan, Sharma and Zetah of Tabuk region in the Northwestern part of Arabian Peninsula. Only organic matter (OM, pH and calcium (Ca showed significant differences (P < 0.05 amongst the four studied sites. Only magnesium and sodium were selected in the forward regression model and showed to be strong drivers of species richness of plants in Tabuk region (Adj-R2 = 0.438, F2,13 = 6.85, P = 0.009. The multivariate analysis of canonical correspondence analysis (CCA was applied to reveal the effect of the physical and chemical variables on the species composition of the plants. The CCA classifies the plant species into three groups based on their preference to the environmental variables. The first group of plant species (Group 1 is characterised by positive preference to the chloride (Cl and negative relationship with OM and pH. The second group (Group 2 is positively correlated with most of the soil variables such as OM, calcium (Ca, potassium (K, bicarbonate (HCO3, electrical conductivity (EC, sulphate (SO4 and sodium (Na. The third group (Group 3 has positive relationship with carbonate (CO3 and negative relationship with EC and magnesium (Mg. The chloride, sodium, sulphate, EC and carbonate are the main environmental factors influencing the plant species composition in Tabuk region. The cluster analysis based on the Euclidian measure shows that Alqan and Zetah have closer species composition compared to Sharma.
Regional variability of nitrate fluxes in the unsaturated zone and groundwater, Wisconsin, USA

Science.gov (United States)

Green, Christopher T.; Liao, Lixia; Nolan, Bernard T.; Juckem, Paul F.; Shope, Christopher L.; Tesoriero, Anthony J.; Jurgens, Bryant

2018-01-01

Process-based modeling of regional NO3− fluxes to groundwater is critical for understanding and managing water quality, but the complexity of NO3− reactive transport processes make implementation a challenge. This study introduces a regional vertical flux method (VFM) for efficient estimation of reactive transport of NO3− in the vadose zone and groundwater. The regional VFM was applied to 443 well samples in central-eastern Wisconsin. Chemical measurements included O2, NO3−, N2 from denitrification, and atmospheric tracers of groundwater age including carbon-14, chlorofluorocarbons, tritium, and tritiogenic helium. VFM results were consistent with observed chemistry, and calibrated parameters were in-line with estimates from previous studies. Results indicated that (1) unsaturated zone travel times were a substantial portion of the transit time to wells and streams (2) since 1945 fractions of applied N leached to groundwater have increased for manure-N, possibly due to increased injection of liquid manure, and decreased for fertilizer-N, and (3) under current practices and conditions, approximately 60% of the shallow aquifer will eventually be affected by downward migration of NO3−, with denitrification protecting the remaining 40%. Recharge variability strongly affected the unsaturated zone lag times and the eventual depth of the NO3− front. Principal components regression demonstrated that VFM parameters and predictions were significantly correlated with hydrogeochemical landscape features. The diverse and sometimes conflicting aspects of N management (e.g. limiting N volatilization versus limiting N losses to groundwater) warrant continued development of large-scale holistic strategies to manage water quality and quantity.
Regional Variability of Nitrate Fluxes in the Unsaturated Zone and Groundwater, Wisconsin, USA

Science.gov (United States)

Green, Christopher T.; Liao, Lixia; Nolan, Bernard T.; Juckem, Paul F.; Shope, Christopher L.; Tesoriero, Anthony J.; Jurgens, Bryant C.

2018-01-01

Process-based modeling of regional NO3- fluxes to groundwater is critical for understanding and managing water quality, but the complexity of NO3- reactive transport processes makes implementation a challenge. This study introduces a regional vertical flux method (VFM) for efficient estimation of reactive transport of NO3- in the vadose zone and groundwater. The regional VFM was applied to 443 well samples in central-eastern Wisconsin. Chemical measurements included O2, NO3-, N2 from denitrification, and atmospheric tracers of groundwater age including carbon-14, chlorofluorocarbons, tritium, and tritiogenic helium. VFM results were consistent with observed chemistry, and calibrated parameters were in-line with estimates from previous studies. Results indicated that (1) unsaturated zone travel times were a substantial portion of the transit time to wells and streams, (2) since 1945 fractions of applied N leached to groundwater have increased for manure-N, possibly due to increased injection of liquid manure, and decreased for fertilizer-N, and (3) under current practices and conditions, approximately 60% of the shallow aquifer will eventually be affected by downward migration of NO3-, with denitrification protecting the remaining 40%. Recharge variability strongly affected the unsaturated zone lag times and the eventual depth of the NO3- front. Principal components regression demonstrated that VFM parameters and predictions were significantly correlated with hydrogeochemical landscape features. The diverse and sometimes conflicting aspects of N management (e.g., limiting N volatilization versus limiting N losses to groundwater) warrant continued development of large-scale holistic strategies to manage water quality and quantity.
Periostin shows increased evolutionary plasticity in its alternatively spliced region

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Hoersch Sebastian

2010-01-01

Full Text Available Abstract Background Periostin (POSTN is a secreted extracellular matrix protein of poorly defined function that has been related to bone and heart development as well as to cancer. In human and mouse, it is known to undergo alternative splicing in its C-terminal region, which is devoid of known protein domains. Differential expression of periostin, sometimes of specific splicing isoforms, is observed in a broad range of human cancers, including breast, pancreatic, and colon cancer. Here, we combine genomic and transcriptomic sequence data from vertebrate organisms to study the evolution of periostin and particularly of its C-terminal region. Results We found that the C-terminal part of periostin is markedly more variable among vertebrates than the rest of periostin in terms of exon count, length, and splicing pattern, which we interpret as a consequence of neofunctionalization after the split between periostin and its paralog transforming growth factor, beta-induced (TGFBI. We also defined periostin's sequential 13-amino acid repeat units - well conserved in teleost fish, but more obscure in higher vertebrates - whose secondary structure is predicted to be consecutive beta strands. We suggest that these beta strands may mediate binding interactions with other proteins through an extended beta-zipper in a manner similar to the way repeat units in bacterial cell wall proteins have been reported to bind human fibronectin. Conclusions Our results, obtained with the help of the increasingly large collection of complete vertebrate genomes, document the evolutionary plasticity of periostin's C-terminal region, and for the first time suggest a basis for its functional role.
Specific DNA binding of a potential transcriptional regulator, inosine 5'-monophosphate dehydrogenase-related protein VII, to the promoter region of a methyl coenzyme m reductase I-encoding operon retrieved from Methanothermobacter thermautotrophicus strain DeltaH.

Science.gov (United States)

Shinzato, Naoya; Enoki, Miho; Sato, Hiroaki; Nakamura, Kohei; Matsui, Toru; Kamagata, Yoichi

2008-10-01

Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus DeltaH are expressed in response to H(2) availability. In the present study, cis elements and trans-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from mrt-expressing cultures restricted them to 46- and 41-bp-long mcr and mrt upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine beta-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen.
Cortical and subcortical 5-HT2A receptor binding in neuroleptic-naive first-episode schizophrenic patients

DEFF Research Database (Denmark)

Erritzoe, David; Rasmussen, Hans; Kristiansen, Klaus Nyegaard

2008-01-01

MRIs and PET images. The cerebellum was used as a reference region. The binding potential of specific tracer binding (BP(p)) was used as the outcome measure. No significant difference was seen in cortical receptor distribution between patients and controls. An increase in 5-HT(2A) receptor binding...
Drosophila DNA-Binding Proteins in Polycomb Repression

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Maksim Erokhin

2018-01-01

Full Text Available The formation of individual gene expression patterns in different cell types is required during differentiation and development of multicellular organisms. Polycomb group (PcG proteins are key epigenetic regulators responsible for gene repression, and dysregulation of their activities leads to developmental abnormalities and diseases. PcG proteins were first identified in Drosophila, which still remains the most convenient system for studying PcG-dependent repression. In the Drosophila genome, these proteins bind to DNA regions called Polycomb response elements (PREs. A major role in the recruitment of PcG proteins to PREs is played by DNA-binding factors, several of which have been characterized in detail. However, current knowledge is insufficient for comprehensively describing the mechanism of this process. In this review, we summarize and discuss the available data on the role of DNA-binding proteins in PcG recruitment to chromatin.
Novel Drosophila receptor that binds multiple growth factors

International Nuclear Information System (INIS)

Rosner, M.R.; Thompson, K.L.; Garcia, V.; Decker, S.J.

1986-01-01

The authors have recently reported the identification of a novel growth factor receptor from Drosophila cell cultures that has dual binding specificity for both insulin and epidermal growth factor (EGF). This 100 kDa protein is also antigenically related to the cytoplasmic region of the mammalian EGF receptor-tyrosine kinase. They now report that this protein binds to mammalian nerve growth factor and human transforming growth factor alpha as well as insulin and EGF with apparent dissociation constants ranging from 10 -6 to 10 -8 M. The 100 kDa protein can be affinity-labeled with these 125 I-labeled growth factors after immunoprecipitation with anti-EGF receptor antiserum. These four growth factors appear to share a common binding site, as evidenced by their ability to block affinity labelling by 125 I-insulin. No significant binding to the 100 kDa protein was observed with platelet-derived growth factor, transforming growth factor beta, or glucagon. The 100 kDa Drosophila protein has a unique ligand-binding spectrum with no direct counterpart in mammalian cells and may represent an evolutionary precursor of the mammalian receptors for these growth factors
Regional precipitation variability in East Asia related to climate and environmental factors during 1979-2012

Science.gov (United States)

Deng, Yinyin; Gao, Tao; Gao, Huiwang; Yao, Xiaohong; Xie, Lian

2014-01-01

This paper studies the inter-annual precipitation variations in different regions of East Asia from oceans to interior areas in China during 1979 – 2012. The results computed by Empirical Orthogonal Functions (EOF) demonstrate that the annual precipitation changes are mainly related to the El Niño-Southern Oscillation, East Asian summer monsoon and aerosols. We also found that the increased Sea surface temperature (SST) could explain the precipitation changes over the Northwest Pacific in the dry season (Oct. – May) and the East China Sea and the South China Sea in the rainy season (Jun. – Sep.). The precipitation changes over the ocean unexplained by SST were likely due to the water vapor transport dominated by dynamic factors. With the increased SST, the moisture transported from oceans to interior land was likely redistributed and caused the complicated regional variability of precipitation. Moreover, the impacts of aerosols on cloud and precipitation varied with different pollution levels and different seasons. PMID:25033387
Distinctive receptor binding properties of the surface glycoprotein of a natural Feline Leukemia Virus isolate with unusual disease spectrum

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Albritton Lorraine M

2011-05-01

Full Text Available Abstract Background Feline leukemia virus (FeLV-945, a member of the FeLV-A subgroup, was previously isolated from a cohort of naturally infected cats. An unusual multicentric lymphoma of non-T-cell origin was observed in natural and experimental infection with FeLV-945. Previous studies implicated the FeLV-945 surface glycoprotein (SU as a determinant of disease outcome by an as yet unknown mechanism. The present studies demonstrate that FeLV-945 SU confers distinctive properties of binding to the cell surface receptor. Results Virions bearing the FeLV-945 Env protein were observed to bind the cell surface receptor with significantly increased efficiency, as was soluble FeLV-945 SU protein, as compared to the corresponding virions or soluble protein from a prototype FeLV-A isolate. SU proteins cloned from other cohort isolates exhibited increased binding efficiency comparable to or greater than FeLV-945 SU. Mutational analysis implicated a domain containing variable region B (VRB to be the major determinant of increased receptor binding, and identified a single residue, valine 186, to be responsible for the effect. Conclusions The FeLV-945 SU protein binds its cell surface receptor, feTHTR1, with significantly greater efficiency than does that of prototype FeLV-A (FeLV-A/61E when present on the surface of virus particles or in soluble form, demonstrating a 2-fold difference in the relative dissociation constant. The results implicate a single residue, valine 186, as the major determinant of increased binding affinity. Computational modeling suggests a molecular mechanism by which residue 186 interacts with the receptor-binding domain through residue glutamine 110 to effect increased binding affinity. Through its increased receptor binding affinity, FeLV-945 SU might function in pathogenesis by increasing the rate of virus entry and spread in vivo, or by facilitating entry into a novel target cell with a low receptor density.
Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme

Energy Technology Data Exchange (ETDEWEB)

Affholter, J.A.; Roth, R.A. (Stanford Univ. School of Medicine, CA (USA)); Cascieri, M.A.; Bayne, M.L. (Merck Sharp and Dohme Research Labs., Rahway, NJ (USA)); Brange, J. (Novo Research Institute, Bagsvaerd (Denmark)); Casaretto, M. (Deutsches Wollforschungsinstitut an der Technischen, Aachen (West Germany))

1990-08-21

Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, the authors have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor, the first set of analogues studied were hybrid molecules of insulin and IGF I. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants (B25-Asp)insulin and (B25-His)insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin. Similar decreases in affinity are observed with the C-terminal truncation mutants (B1-24-His{sup 25}-NH{sub 2})insulin and (B1-24-Leu{sup 25}-NH{sub 2})insulin, but not (B1-24-Trp{sup 25}-NH{sub 2})insulin and (B1-24-Tyr{sup 25}-NH{sub 2})insulin. The truncated analogue with the lowest affinity for IDE ((B1-24-His{sup 25}-NH{sub 2})insulin) has one of the highest affinities for the insulin receptor. Therefore, they have identified a region of the insulin molecule responsible for its high-affinity interaction with IDE. Although the same region has been implicated in the binding of insulin to its receptor, the data suggest that the structural determinants required for binding to receptor and IDE differ.
Identification of residues in the insulin molecule important for binding to insulin-degrading enzyme

International Nuclear Information System (INIS)

Affholter, J.A.; Roth, R.A.; Cascieri, M.A.; Bayne, M.L.; Brange, J.; Casaretto, M.

1990-01-01

Insulin-degrading enzyme (IDE) hydrolyzes insulin at a limited number of sites. Although the positions of these cleavages are known, the residues of insulin important in its binding to IDE have not been defined. To this end, the authors have studied the binding of a variety of insulin analogues to the protease in a solid-phase binding assay using immunoimmobilized IDE. Since IDE binds insulin with 600-fold greater affinity than it does insulin-like growth factor, the first set of analogues studied were hybrid molecules of insulin and IGF I. Removal of the eight amino acid D-chain region of IGF I (which has been predicted to interfere with binding to the 23-25 region) results in a 25-fold increase in affinity for IDE, confirming the importance of residues 23-25 in the high-affinity recognition of IDE. A similar role for the corresponding (B24-26) residues of insulin is supported by the use of site-directed mutant and semisynthetic insulin analogues. Insulin mutants [B25-Asp]insulin and [B25-His]insulin display 16- and 20-fold decreases in IDE affinity versus wild-type insulin. Similar decreases in affinity are observed with the C-terminal truncation mutants [B1-24-His 25 -NH 2 ]insulin and [B1-24-Leu 25 -NH 2 ]insulin, but not [B1-24-Trp 25 -NH 2 ]insulin and [B1-24-Tyr 25 -NH 2 ]insulin. The truncated analogue with the lowest affinity for IDE ([B1-24-His 25 -NH 2 ]insulin) has one of the highest affinities for the insulin receptor. Therefore, they have identified a region of the insulin molecule responsible for its high-affinity interaction with IDE. Although the same region has been implicated in the binding of insulin to its receptor, the data suggest that the structural determinants required for binding to receptor and IDE differ
Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance

International Nuclear Information System (INIS)

Sattonnay, G; Tétot, R

2014-01-01

Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd 2 Ti 2 O 7 and Gd 2 Zr 2 O 7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd 2 Ti 2 O 7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd 2 Zr 2 O 7 . Therefore, the defect stability in A 2 B 2 O 7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd 2 Ti 2 O 7 amorphization induced by irradiation. (paper)
Molecular immune recognition of botulinum neurotoxin B. The light chain regions that bind human blocking antibodies from toxin-treated cervical dystonia patients. Antigenic structure of the entire BoNT/B molecule.

Science.gov (United States)

Atassi, M Zouhair; Jankovic, Joseph; Steward, Lance E; Aoki, K Roger; Dolimbek, Behzod Z

2012-01-01

We recently mapped the regions on the heavy (H) chain of botulinum neurotoxin, type B (BoNT/B) recognized by blocking antibodies (Abs) from cervical dystonia (CD) patients who develop immunoresistance during toxin treatment. Since blocking could also be effected by Abs directed against regions on the light (L) chain, we have mapped here the L chain, using the same 30 CD antisera. We synthesized, purified and characterized 32 19-residue L chain peptides that overlapped successively by 5 residues (peptide L32 overlapped with peptide N1 of the H chain by 12 residues). In a given patient, Abs against the L chain seemed less intense than those against H chain. Most sera recognized a limited set of L chain peptides. The levels of Abs against a given region varied with the patient, consistent with immune responses to each epitope being under separate MHC control. The peptides most frequently recognized were: L13, by 30 of 30 antisera (100%); L22, by 23 of 30 (76.67%); L19, by 15 of 30 (50.00%); L26, by 11 of 30 (36.70%); and L14, by 12 of 30 (40.00%). The activity of L14 probably derives from its overlap with L13. The levels of Ab binding decreased in the following order: L13 (residues 169-187), L22 (295-313), L19 (253-271), and L26 (351-369). Peptides L12 (155-173), L18 (239-257), L15 (197-215), L1 (1-19) and L23 (309-327) exhibited very low Ab binding. The remaining peptides had little or no Ab-binding activity. The antigenic regions are analyzed in terms of their three-dimensional locations and the enzyme active site. With the previous localization of the antigenic regions on the BoNT/B H chain, the human Ab recognition of the entire BoNT/B molecule is presented and compared to the recognition of BoNT/A by human blocking Abs. Copyright © 2011. Published by Elsevier GmbH.
Production of a phage-displayed single chain variable fragment ...

African Journals Online (AJOL)

Abstract. Purpose: To develop specific single chain variable fragments (scFv) against ... libraries. The binding ability of the selected scFv antibody fragments against the IBDV particles was ..... Hermelink H, Koscielniak E. A human recombinant.
Finding stability regions for preserving efficiency classification of variable returns to scale technology in data envelopment analysis

Science.gov (United States)

Zamani, P.; Borzouei, M.

2016-12-01

This paper addresses issue of sensitivity of efficiency classification of variable returns to scale (VRS) technology for enhancing the credibility of data envelopment analysis (DEA) results in practical applications when an additional decision making unit (DMU) needs to be added to the set being considered. It also develops a structured approach to assisting practitioners in making an appropriate selection of variation range for inputs and outputs of additional DMU so that this DMU be efficient and the efficiency classification of VRS technology remains unchanged. This stability region is simply specified by the concept of defining hyperplanes of production possibility set of VRS technology and the corresponding halfspaces. Furthermore, this study determines a stability region for the additional DMU within which, in addition to efficiency classification, the efficiency score of a specific inefficient DMU is preserved and also using a simulation method, a region in which some specific efficient DMUs become inefficient is provided.
Cation binding at the node of Ranvier: I. Localization of binding sites during development.

Science.gov (United States)

Zagoren, J C; Raine, C S; Suzuki, K

1982-06-17

Cations are known to bind to the node of Ranvier and the paranodal regions of myelinated fibers. The integrity of these specialized structures is essential for normal conduction. Sites of cation binding can be microscopically identified by the electrondense histochemical reaction product formed by the precipitate of copper sulfate/potassium ferrocyanide. This technique was used to study the distribution of cation binding during normal development of myelinating fibers. Sciatic nerves of C57B1 mice, at 1, 3, 5, 6, 7, 8, 9, 13, 16, 18, 24 and 30 days of age, were prepared for electron microscopy following fixation in phosphate-buffered 2.5% glutaraldehyde and 1% osmic acid, microdissection and incubation in phosphate-buffered 0.1 M cupric sulfate followed by 0.1 M potassium ferrocyanide. Localization of reaction product was studied by light and electron microscopy. By light microscopy, no reaction product was observed prior to 9 days of age. At 13 days, a few nodes and paranodes exhibited reaction product. This increased in frequency and intensity up to 30 days when almost all nodes or paranodes exhibited reaction product. Ultrastructurally, diffuse reaction product was first observed at 3 days of age in the axoplasm of the node, in the paranodal extracellular space of the terminal loops, in the Schwann cell proper and in the terminal loops of Schwann cell cytoplasm. When myelinated axons fulfilled the criteria for mature nodes, reaction product was no longer observed in the Schwann cell cytoplasm, while the intensity of reaction product in the nodal axoplasm and paranodal extracellular space of the terminal loops increased. Reaction product in the latter site appeared to be interrupted by the transverse bands. These results suggest that cation binding accompanies nodal maturity and that the Schwann cell may play a role in production or storage of the cation binding substance during myelinogenesis and development.

8-anilino-1-naphthaline sulfonate binds at the hemoglobin allosteric regulatory sites: inhibitory analyses

International Nuclear Information System (INIS)

Bokut', S.B.; Parul', D.A.; Yachnik, N.N.; Milyutin, A.A.

2001-01-01

The present study focused on the localization at least one of the ANS binding sites in the major form of human hemoglobin HbA. High-resolution docking predict ANS binding to the hemoglobin central cavity. Steady-state fluorescence titration data obtained in the absence/presence of natural effector inositol hexaphosphate (IHP) allowed to conclude that IHP competitively inhibited ANS binding to HbA. Thus, we must conclude that one of the ANS binding sites is central cavity, which makes it possible to monitor changes at this region upon ligation/deligation, effector binding and changes in hemoglobin structure
Differential recognition of syk-binding sites by each of the two phosphotyrosine-binding pockets of the Vav SH2 domain.

Science.gov (United States)

Chen, Chih-Hong; Piraner, Dan; Gorenstein, Nina M; Geahlen, Robert L; Beth Post, Carol

2013-11-01

The association of spleen tyrosine kinase (Syk), a central tyrosine kinase in B cell signaling, with Vav SH2 domain is controlled by phosphorylation of two closely spaced tyrosines in Syk linker B: Y342 and Y346. Previous studies established both singly phosphorylated and doubly phosphorylated forms play a role in signaling. The structure of the doubly phosphorylated form identified a new recognition of phosphotyrosine whereby two phosphotyrosines bind simultaneously to the Vav SH2 domain, one in the canonical pTyr pocket and one in the specificity pocket on the opposite side of the central β-sheet. It is unknown if the specificity pocket can bind phosphotyrosine independent of phosphotyrosine binding the pTyr pocket. To address this gap in knowledge, we determined the structure of the complex between Vav1 SH2 and a peptide (SykLB-YpY) modeling the singly phosphorylated-Y346 form of Syk with unphosphorylated Y342. The nuclear magnetic resonance (NMR) data conclusively establish that recognition of phosphotyrosine is swapped between the two pockets; phosphorylated pY346 binds the specificity pocket of Vav1 SH2, and unphosphorylated Y342 occupies what is normally the pTyr binding pocket. Nearly identical changes in chemical shifts occurred upon binding all three forms of singly and doubly phosphorylated peptides; however, somewhat smaller shift perturbations for SykLB-YpY from residues in regions of high internal mobility suggest that internal motions are coupled to binding affinity. The differential recognition that includes this swapped binding of phosphotyrosine to the specificity pocket of Vav SH2 increases the repertoire of possible phosphotyrosine binding by SH2 domains in regulating protein-protein interactions in cellular signaling. Copyright © 2013 Wiley Periodicals, Inc.
Complement-mediated bactericidal activity of anti-factor H binding protein monoclonal antibodies against the meningococcus relies upon blocking factor H binding.

Science.gov (United States)

Giuntini, Serena; Reason, Donald C; Granoff, Dan M

2011-09-01

Binding of the complement-downregulating protein factor H (fH) to the surface of the meningococcus is important for survival of the organism in human serum. The meningococcal vaccine candidate factor H binding protein (fHbp) is an important ligand for human fH. While some fHbp-specific monoclonal antibodies (MAbs) block binding of fH to fHbp, the stoichiometry of blocking in the presence of high serum concentrations of fH and its effect on complement-mediated bactericidal activity are unknown. To investigate this question, we constructed chimeric antibodies in which the human IgG1 constant region was paired with three murine fHbp-specific binding domains designated JAR 3, JAR 5, and MAb502. By surface plasmon resonance, the association rates for binding of all three MAbs to immobilized fHbp were >50-fold higher than that for binding of fH to fHbp, and the MAb dissociation rates were >500-fold lower than that for fH. While all three MAbs elicited similar C1q-dependent C4b deposition on live bacteria (classical complement pathway), only those antibodies that inhibited binding of fH to fHbp (JAR 3 and JAR 5) had bactericidal activity with human complement. MAb502, which did not inhibit fH binding, had complement-mediated bactericidal activity only when tested with fH-depleted human complement. When an IgG1 anti-fHbp MAb binds to sparsely exposed fHbp on the bacterial surface, there appears to be insufficient complement activation for bacteriolysis unless fH binding also is inhibited. The ability of fHbp vaccines to elicit protective antibodies, therefore, is likely to be enhanced if the antibody repertoire is of high avidity and includes fH-blocking activity.
Discrete persistent-chain model for protein binding on DNA.

Science.gov (United States)

Lam, Pui-Man; Zhen, Yi

2011-04-01

We describe and solve a discrete persistent-chain model of protein binding on DNA, involving an extra σ(i) at a site i of the DNA. This variable takes the value 1 or 0, depending on whether or not the site is occupied by a protein. In addition, if the site is occupied by a protein, there is an extra energy cost ɛ. For a small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA. For higher forces, the model can be solved numerically to obtain force-extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force-extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of nonspecific binding. ©2011 American Physical Society
[{sup 18}F]haloperidol binding in baboon brain in vivo

Energy Technology Data Exchange (ETDEWEB)

Yousef, Khalil A; Fowler, Joanna S; Volkow, Nora D; Dewey, Stephen L; Shea, Colleen; Schlyer, David J; Gatley, S John; Logan, Jean; Wolf, Alfred P

1996-01-01

The binding of [{sup 18}F]haloperidol to dopamine D2 and to sigma recognition sites in baboon brain was examined using positron emission tomography (PET). Studies were performed at baseline and after treatment with either haloperidol (to evaluate saturability), (+)-butaclamol (which has specificity for dopamine D2 receptors) or (-)-butaclamol (which has specificity for sigma sites). Binding was widespread. Treatment with (-)-butaclamol had no effect, whereas (+)-butaclamol selectively reduced the uptake in striatum. Haloperidol increased the clearance rate from all brain regions. These results indicate that the binding profile of [{sup 18}F]haloperidol does not permit the selective examination of either dopamine D2 or sigma sites using PET.
Distribution of binding energies of a water molecule in the water liquid-vapor interface

Energy Technology Data Exchange (ETDEWEB)

Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV

2008-01-01

Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.
Characterization of a second ligand binding site of the insulin receptor

International Nuclear Information System (INIS)

Hao Caili; Whittaker, Linda; Whittaker, Jonathan

2006-01-01

Insulin binding to its receptor is characterized by high affinity, curvilinear Scatchard plots, and negative cooperativity. These properties may be the consequence of binding of insulin to two receptor binding sites. The N-terminal L1 domain and the C-terminus of the α subunit contain one binding site. To locate a second site, we examined the binding properties of chimeric receptors in which the L1 and L2 domains and the first Fibronectin Type III repeat of the insulin-like growth factor-I receptor were replaced by corresponding regions of the insulin receptor. Substitutions of the L2 domain and the first Fibronectin Type III repeat together with the L1 domain produced 80- and 300-fold increases in affinity for insulin. Fusion of these domains to human immunoglobulin Fc fragment produced a protein which bound insulin with a K d of 2.9 nM. These data strongly suggest that these domains contain an insulin binding site
Regional impacts of ocean color on tropical Pacific variability

OpenAIRE

W. Anderson; A. Gnanadesikan; A. Wittenberg

2009-01-01

The role of the penetration length scale of shortwave radiation into the surface ocean and its impact on tropical Pacific variability is investigated with a fully coupled ocean, atmosphere, land and ice model. Previous work has shown that removal of all ocean color results in a system that tends strongly towards an El Niño state. Results from a suite of surface chlorophyll perturbation experiments show that the mean state and variability of the tropical Pacific is highly se...
Recombinant norovirus-specific scFv inhibit virus-like particle binding to cellular ligands

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Hardy Michele E

2008-01-01

Full Text Available Abstract Background Noroviruses cause epidemic outbreaks of gastrointestinal illness in all age-groups. The rapid onset and ease of person-to-person transmission suggest that inhibitors of the initial steps of virus binding to susceptible cells have value in limiting spread and outbreak persistence. We previously generated a monoclonal antibody (mAb 54.6 that blocks binding of recombinant norovirus-like particles (VLP to Caco-2 intestinal cells and inhibits VLP-mediated hemagglutination. In this study, we engineered the antigen binding domains of mAb 54.6 into a single chain variable fragment (scFv and tested whether these scFv could function as cell binding inhibitors, similar to the parent mAb. Results The scFv54.6 construct was engineered to encode the light (VL and heavy (VH variable domains of mAb 54.6 separated by a flexible peptide linker, and this recombinant protein was expressed in Pichia pastoris. Purified scFv54.6 recognized native VLPs by immunoblot, inhibited VLP-mediated hemagglutination, and blocked VLP binding to H carbohydrate antigen expressed on the surface of a CHO cell line stably transfected to express α 1,2-fucosyltransferase. Conclusion scFv54.6 retained the functional properties of the parent mAb with respect to inhibiting norovirus particle interactions with cells. With further engineering into a form deliverable to the gut mucosa, norovirus neutralizing antibodies represent a prophylactic strategy that would be valuable in outbreak settings.
A conserved phenylalanine as a relay between the α5 helix and the GDP binding region of heterotrimeric Gi protein α subunit.

Science.gov (United States)

Kaya, Ali I; Lokits, Alyssa D; Gilbert, James A; Iverson, Tina M; Meiler, Jens; Hamm, Heidi E

2014-08-29

G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the α5 helix in the G protein α subunit plays a major role during this activation process. However, the precise signaling pathway between the α5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the α5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the β2-β3 strands and α1 helix, leading to high basal nucleotide exchange. However, mutations in β strands β5 and β6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via β2-β3/α1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the α1 and α5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal α5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the α subunit. Rather, destabilization of the backdoor region of the Gα subunit is sufficient for triggering the activation process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Molecular characterization of the haptoglobin.hemoglobin receptor CD163. Ligand binding properties of the scavenger receptor cysteine-rich domain region

DEFF Research Database (Denmark)

Madsen, Mette; Møller, Holger J; Nielsen, Marianne Jensby

2004-01-01

binding to SRCR domain 3 exhibited effective inhibition of ligand binding. Furthermore, analysis of purified native CD163 revealed that proteolytic cleavage in SRCR domain 3 inactivates ligand binding. Calcium protects against cleavage in this domain. Analysis of the calcium sensitivity of ligand binding...... to CD163 demonstrated that optimal ligand binding requires physiological plasma calcium concentrations, and an immediate ligand release occurs at the low calcium concentrations measured in acidifying endosomes. In conclusion, SRCR domain 3 of CD163 is an exposed domain and a critical determinant...... for the calcium-sensitive coupling of haptoglobin.hemoglobin complexes....
Regional variability among nonlinear chlorophyll-phosphorus relationships in lakes

Science.gov (United States)

Filstrup, Christopher T.; Wagner, Tyler; Soranno, Patricia A.; Stanley, Emily H.; Stow, Craig A.; Webster, Katherine E.; Downing, John A.

2014-01-01

The relationship between chlorophyll a (Chl a) and total phosphorus (TP) is a fundamental relationship in lakes that reflects multiple aspects of ecosystem function and is also used in the regulation and management of inland waters. The exact form of this relationship has substantial implications on its meaning and its use. We assembled a spatially extensive data set to examine whether nonlinear models are a better fit for Chl a—TP relationships than traditional log-linear models, whether there were regional differences in the form of the relationships, and, if so, which regional factors were related to these differences. We analyzed a data set from 2105 temperate lakes across 35 ecoregions by fitting and comparing two different nonlinear models and one log-linear model. The two nonlinear models fit the data better than the log-linear model. In addition, the parameters for the best-fitting model varied among regions: the maximum and lower Chl aasymptotes were positively and negatively related to percent regional pasture land use, respectively, and the rate at which chlorophyll increased with TP was negatively related to percent regional wetland cover. Lakes in regions with more pasture fields had higher maximum chlorophyll concentrations at high TP concentrations but lower minimum chlorophyll concentrations at low TP concentrations. Lakes in regions with less wetland cover showed a steeper Chl a—TP relationship than wetland-rich regions. Interpretation of Chl a—TP relationships depends on regional differences, and theory and management based on a monolithic relationship may be inaccurate.
Altered SPECT 123I-iomazenil Binding in the Cingulate Cortex of Children with Anorexia Nervosa

Science.gov (United States)

Nagamitsu, Shinichiro; Sakurai, Rieko; Matsuoka, Michiko; Chiba, Hiromi; Ozono, Shuichi; Tanigawa, Hitoshi; Yamashita, Yushiro; Kaida, Hayato; Ishibashi, Masatoshi; Kakuma, Tatsuki; Croarkin, Paul E.; Matsuishi, Toyojiro

2016-01-01

Several lines of evidence suggest that anxiety plays a key role in the development and maintenance of anorexia nervosa (AN) in children. The purpose of this study was to examine cortical GABA(A)-benzodiazepine receptor binding before and after treatment in children beginning intensive AN treatment. Brain single-photon emission computed tomography (SPECT) measurements using 123I-iomazenil, which binds to GABA(A)-benzodiazepine receptors, was performed in 26 participants with AN who were enrolled in a multimodal treatment program. Sixteen of the 26 participants underwent a repeat SPECT scan immediately before discharge at conclusion of the intensive treatment program. Eating behavior and mood disturbances were assessed using Eating Attitudes Test with 26 items (EAT-26) and the short form of the Profile of Mood States (POMS). Clinical outcome scores were evaluated after a 1-year period. We examined association between relative iomazenil-binding activity in cortical regions of interest and psychometric profiles and determined which psychometric profiles show interaction effects with brain regions. Further, we determined if binding activity could predict clinical outcome and treatment changes. Higher EAT-26 scores were significantly associated with lower iomazenil-binding activity in the anterior and posterior cingulate cortex. Higher POMS subscale scores were significantly associated with lower iomazenil-binding activity in the left frontal, parietal cortex, and posterior cingulate cortex (PCC). “Depression–Dejection” and “Confusion” POMS subscale scores, and total POMS score showed interaction effects with brain regions in iomazenil-binding activity. Decreased binding in the anterior cingulate cortex and left parietal cortex was associated with poor clinical outcomes. Relative binding increases throughout the PCC and occipital gyrus were observed after weight gain in children with AN. These findings suggest that cortical GABAergic receptor binding is altered
Impacts of Present and Future Climate Variability on Agriculture and Forestry in the Temperate Regions. Europe

International Nuclear Information System (INIS)

Maracchi, G.; Sirotenko, O.; Bindi, M.

2005-01-01

Agriculture and forestry will be particularly sensitive to changes in mean climate and climate variability in the northern and southern regions of Europe. Agriculture may be positively affected by climate change in the northern areas through the introduction of new crop species and varieties, higher crop production and expansion of suitable areas for crop cultivation. The disadvantages may be determined by an increase in need for plant protection, risk of nutrient leaching and accelerated breakdown of soil organic matter. In the southern areas the benefits of the projected climate change will be limited, while the disadvantages will be predominant. The increased water use efficiency caused by increasing CO2 will compensate for some of the negative effects of increasing water limitation and extreme weather events, but lower harvestable yields, higher yield variability and reduction in suitable areas of traditional crops are expected for these areas. Forestry in the Mediterranean region may be mainly affected by increases in drought and forest fires. In northern Europe, the increased precipitation is expected to be large enough to compensate for the increased evapotranspiration. On the other hand, however, increased precipitation, cloudiness and rain days and the reduced duration of snow cover and soil frost may negatively affect forest work and timber logging determining lower profitability of forest production and a decrease in recreational possibilities. Adaptation management strategies should be introduced, as effective tools, to reduce the negative impacts of climate change on agricultural and forestry sectors
Simplifying complex sequence information: a PCP-consensus protein binds antibodies against all four Dengue serotypes.

Science.gov (United States)

Bowen, David M; Lewis, Jessica A; Lu, Wenzhe; Schein, Catherine H

2012-09-14

Designing proteins that reflect the natural variability of a pathogen is essential for developing novel vaccines and drugs. Flaviviruses, including Dengue (DENV) and West Nile (WNV), evolve rapidly and can "escape" neutralizing monoclonal antibodies by mutation. Designing antigens that represent many distinct strains is important for DENV, where infection with a strain from one of the four serotypes may lead to severe hemorrhagic disease on subsequent infection with a strain from another serotype. Here, a DENV physicochemical property (PCP)-consensus sequence was derived from 671 unique sequences from the Flavitrack database. PCP-consensus proteins for domain 3 of the envelope protein (EdomIII) were expressed from synthetic genes in Escherichia coli. The ability of the purified consensus proteins to bind polyclonal antibodies generated in response to infection with strains from each of the four DENV serotypes was determined. The initial consensus protein bound antibodies from DENV-1-3 in ELISA and Western blot assays. This sequence was altered in 3 steps to incorporate regions of maximum variability, identified as significant changes in the PCPs, characteristic of DENV-4 strains. The final protein was recognized by antibodies against all four serotypes. Two amino acids essential for efficient binding to all DENV antibodies are part of a discontinuous epitope previously defined for a neutralizing monoclonal antibody. The PCP-consensus method can significantly reduce the number of experiments required to define a multivalent antigen, which is particularly important when dealing with pathogens that must be tested at higher biosafety levels. Copyright © 2012 Elsevier Ltd. All rights reserved.
A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors

Energy Technology Data Exchange (ETDEWEB)

Pyburn, Tasia M.; Bensing, Barbara A.; Xiong, Yan Q.; Melancon, Bruce J.; Tomasiak, Thomas M.; Ward, Nicholas J.; Yankovskaya, Victoria; Oliver, Kevin M.; Cecchini, Gary; Sulikowski, Gary A.; Tyska, Matthew J.; Sullam, Paul M.; Iverson, T.M. (VA); (UCLA); (Vanderbilt); (UCSF)

2014-10-02

GspB is a serine-rich repeat (SRR) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIb{alpha}. This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis. To address the mechanism by which GspB recognizes its carbohydrate ligand, we determined the high-resolution x-ray crystal structure of the GspB binding region (GspB{sub BR}), both alone and in complex with a disaccharide precursor to sialyl-T antigen. Analysis of the GspB{sub BR} structure revealed that it is comprised of three independently folded subdomains or modules: (1) an Ig-fold resembling a CnaA domain from prokaryotic pathogens; (2) a second Ig-fold resembling the binding region of mammalian Siglecs; (3) a subdomain of unique fold. The disaccharide was found to bind in a pocket within the Siglec subdomain, but at a site distinct from that observed in mammalian Siglecs. Confirming the biological relevance of this binding pocket, we produced three isogenic variants of S. gordonii, each containing a single point mutation of a residue lining this binding pocket. These variants have reduced binding to carbohydrates of GPIb{alpha}. Further examination of purified GspB{sub BR}-R484E showed reduced binding to sialyl-T antigen while S. gordonii harboring this mutation did not efficiently bind platelets and showed a significant reduction in virulence, as measured by an animal model of endocarditis. Analysis of other SRR proteins revealed that the predicted binding regions of these adhesins also had a modular organization, with those known to bind carbohydrate receptors having modules homologous to the Siglec and Unique subdomains of GspBBR. This suggests that the binding specificity of the SRR family of adhesins is determined by the type and organization of discrete modules within the binding domains, which may affect the tropism of organisms for different tissues.
Phase Variability of the Recent Climate in the North Atlantic Region

Science.gov (United States)

Serykh, Ilya; Anisimov, Mikhail; Byshev, Vladimir; Neiman, Victor; Romanov, Juri; Sidorova, Alexandra

2014-05-01

The atmospheric pressure and near-surface temperature differences between the Azores High and the Icelandic Low for the period of 1900-2012 within the spatial-temporal average-out (20º latitude, 20º longitude and 12 years) were considered. The secular term of phase states of the system under consideration was found to divide into three non-intersecting subsets. Each of that was put in consequence with one of three climatic scenarios related to the periods of 1905-1935 (relatively warm phase), 1940-1970 (colder phase) and 1980-2000 (warmer phase). A life time of such a scenario lasted about 20-35 years, and the transition from one scenario to another covered 4-6 years, i.e. it run comparatively quickly. The revealed non-overlapping sub-aggregates of the thermodynamic indices related to each particular climate scenario gave an idea to follow the circulation peculiarities and the interrelated temperature differences within the limits of the Northern Atlantic ocean-atmosphere regional system. The results of this analysis bear evidence that the most probable intermittent strengthening and weakening of Hadley and Ferrell circulations occurred there in coincided phase. The analogous character of the climate system behavior was also detected in some other regional atmospheric activity centers that can be considered as a witness on the global nature of the detected phase type of modern climate inter-decadal variability. Hence, we have the grounds to suppose that mentioned above the short-period inter-decadal excitations of the modern climate have a global nature and appears everywhere. Finally, the attention was paid to the fact that at the early XXI century the thermodynamic state of the Northern Atlantic regional climate system has shown a tendency to face towards the situation, similar to the cooler scenario of the 1940-1970. We used the heat content of upper 700m Atlantic Ocean layer data from NODC to calculate its anomalies for the periods of 1955-1970, 1980-2000 and
Climate Variability and Change in the Mediterranean Region

Science.gov (United States)

Lionello, Piero; Özsoy, Emin; Planton, Serge; Zanchetta, Giovanni

2017-04-01

This special issue collects new research results on the climate of the Mediterranean region. It covers traditional topics of the MedCLIVAR programme (www.medclivar.eu, Lionello et al. 2006, Lionello et al. 2012b) being devoted to papers addressing on-going and future climate changes in the Mediterranean region and their impacts on its environment.
Molecular characterization of the receptor binding structure-activity relationships of influenza B virus hemagglutinin.

Science.gov (United States)

Carbone, V; Kim, H; Huang, J X; Baker, M A; Ong, C; Cooper, M A; Li, J; Rockman, S; Velkov, T

2013-01-01

Selectivity of α2,6-linked human-like receptors by B hemagglutinin (HA) is yet to be fully understood. This study integrates binding data with structure-recognition models to examine the impact of regional-specific sequence variations within the receptor-binding pocket on selectivity and structure activity relationships (SAR). The receptor-binding selectivity of influenza B HAs corresponding to either B/Victoria/2/1987 or the B/Yamagata/16/88 lineages was examined using surface plasmon resonance, solid-phase ELISA and gel-capture assays. Our SAR data showed that the presence of asialyl sugar units is the main determinant of receptor preference of α2,6 versus α2,3 receptor binding. Changes to the type of sialyl-glycan linkage present on receptors exhibit only a minor effect upon binding affinity. Homology-based structural models revealed that structural properties within the HA pocket, such as a glyco-conjugate at Asn194 on the 190-helix, sterically interfere with binding to avian receptor analogs by blocking the exit path of the asialyl sugars. Similarly, naturally occurring substitutions in the C-terminal region of the 190-helix and near the N-terminal end of the 140-loop narrows the horizontal borders of the binding pocket, which restricts access of the avian receptor analog LSTa. This study helps bridge the gap between ligand structure and receptor recognition for influenza B HA; and provides a consensus SAR model for the binding of human and avian receptor analogs to influenza B HA.
Self-organizing map network-based precipitation regionalization for the Tibetan Plateau and regional precipitation variability

Science.gov (United States)

Wang, Nini; Yin, Jianchuan

2017-12-01

A precipitation-based regionalization for the Tibetan Plateau (TP) was investigated for regional precipitation trend analysis and frequency analysis using data from 1113 grid points covering the period 1900-2014. The results utilizing self-organizing map (SOM) network suggest that four clusters of precipitation coherent zones can be identified, including the southwestern edge, the southern edge, the southeastern region, and the north central region. Regionalization results of the SOM network satisfactorily represent the influences of the atmospheric circulation systems such as the East Asian summer monsoon, the south Asian summer monsoon, and the mid-latitude westerlies. Regionalization results also well display the direct impacts of physical geographical features of the TP such as orography, topography, and land-sea distribution. Regional-scale annual precipitation trend as well as regional differences of annual and seasonal total precipitation were investigated by precipitation index such as precipitation concentration index (PCI) and Standardized Anomaly Index (SAI). Results demonstrate significant negative long-term linear trends in southeastern TP and the north central part of the TP, indicating arid and semi-arid regions in the TP are getting drier. The empirical mode decomposition (EMD) method shows an evolution of the main cycle with 4 and 12 months for all the representative grids of four sub-regions. The cross-wavelet analysis suggests that predominant and effective period of Indian Ocean Dipole (IOD) on monthly precipitation is around ˜12 months, except for the representative grid of the northwestern region.

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