Specific-structured lipids: nutritional perspectives and production potentials

DEFF Research Database (Denmark)

Xu, Xuebing; Høy, Carl-Erik; Balchen, Steen

1997-01-01

Structured lipids are referring to any triacylglycerols containing both long chain fatty acids (mostly essential fatty acids) and medium or short chain fatty acids. In case of specific-structured lipids (SSLs), each group of fatty acids locates specifically at sn-2 or -1.3 positions of the glycerol...... backbone. Recently the nutritional perspectives of this kind of lipids attract many interests. This causes an increasing interest in the production of them by lipase-catalyzed interesterification. One of the advantages of lipase method over chemical ones is that SSLs can be produced with particular fatty...

Developing biosafety risk hypotheses for invertebrates exposed to GM plants using conceptual food webs: a case study with elevated triacylglyceride levels in ryegrass.

Science.gov (United States)

Barratt, Barbara I P; Todd, Jacqui H; Burgess, Elisabeth P J; Malone, Louise A

2010-01-01

Regulators are acutely aware of the need for meaningful risk assessments to support decisions on the safety of GM crops to non-target invertebrates in determining their suitability for field release. We describe a process for developing appropriate, testable risk hypotheses for invertebrates in agroecosystems that might be exposed to plants developed by GM and future novel technologies. An existing model (PRONTI) generates a ranked list of invertebrate species for biosafety testing by accessing a database of biological, ecological and food web information about species which occur in cropping environments and their potential interactions with a particular stressor (Eco Invertebase). Our objective in this contribution is to explore and further utilise these resources to assist in the process of problem formulation by identifying potentially significant effects of the stressor on the invertebrate community and the ecosystem services they provide. We propose that for high ranking species, a conceptual food web using information in Eco Invertebase is constructed, and using an accepted regulatory risk analysis framework, the likelihood of risk, and magnitude of impact for each link in the food web is evaluated. Using as filters only those risks evaluated as likely to extremely likely, and the magnitude of an effect being considered as moderate to massive, the most significant potential effects can be identified. A stepwise approach is suggested to develop a sequence of appropriate tests. The GM ryegrass plant used as the "stressor" in this study has been modified to increase triacylglyceride levels in foliage by 100% to increase the metabolisable energy content of forage for grazing animals. The high-ranking "test" species chosen to illustrate the concept are New Zealand native species Wiseana cervinata (Walker) (Lepidoptera: Hepialidae), Persectania aversa (Walker) (Lepidoptera: Noctuidae), and the self-introduced grey field slug, Deroceras reticulatum (Müller). �

Understanding specificity in metabolic pathways-Structural biology of human nucleotide metabolism

International Nuclear Information System (INIS)

Welin, Martin; Nordlund, Paer

2010-01-01

Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.

Antioxidation behavior of milkweed oil 4-hydroxy-3-methyoxycinnamate esters in phospholipid bilayers

Science.gov (United States)

Milkweed (Asclepia syriaca) has seed oil that is rich in polyunsaturated triacylglycerides that contain olefinic groups. The olefinic groups can be chemically oxidized to form either epoxy or polyhydroxy triacylglycerides that can be esterified with trans-4-hydroxy-3-methoxoycinnamic acid, commonly...

Purification of specific structured lipids by distillation: Effects on acyl migration

DEFF Research Database (Denmark)

Xu, Xuebing; Skands, A.; Adler-Nissen, Jens

2001-01-01

The cause and effects of acyl migration during the purification of specific structured lipids by distillation were studied in a conventional batch deodorizer with stripping steam. The mixture of specific structured lipids produced by lipase-catalyzed acidolysis between rapeseed oil and capric acid...... influenced the rate of acyl migration, and their combinations made the effect more severe. However, diacylglycerols were found to be the main reason for acyl migration. In the distillation of the specific structured lipid product mixture, distillation temperature and time were the main factors to determine...... the degree of acyl migration and the extent of separation of free fatty acids. The results indicate that more efficient separation technology should be used to improve the quality of the purified structured lipids. in order to reduce the distillation temperature, vacuum should be made as low as possible...

Porous silicon structures with high surface area/specific pore size

Science.gov (United States)

Northrup, M.A.; Yu, C.M.; Raley, N.F.

1999-03-16

Fabrication and use of porous silicon structures to increase surface area of heated reaction chambers, electrophoresis devices, and thermopneumatic sensor-actuators, chemical preconcentrates, and filtering or control flow devices. In particular, such high surface area or specific pore size porous silicon structures will be useful in significantly augmenting the adsorption, vaporization, desorption, condensation and flow of liquids and gases in applications that use such processes on a miniature scale. Examples that will benefit from a high surface area, porous silicon structure include sample preconcentrators that are designed to adsorb and subsequently desorb specific chemical species from a sample background; chemical reaction chambers with enhanced surface reaction rates; and sensor-actuator chamber devices with increased pressure for thermopneumatic actuation of integrated membranes. Examples that benefit from specific pore sized porous silicon are chemical/biological filters and thermally-activated flow devices with active or adjacent surfaces such as electrodes or heaters. 9 figs.

Perceptual learning is specific to the trained structure of information.

Science.gov (United States)

Cohen, Yamit; Daikhin, Luba; Ahissar, Merav

2013-12-01

What do we learn when we practice a simple perceptual task? Many studies have suggested that we learn to refine or better select the sensory representations of the task-relevant dimension. Here we show that learning is specific to the trained structural regularities. Specifically, when this structure is modified after training with a fixed temporal structure, performance regresses to pretraining levels, even when the trained stimuli and task are retained. This specificity raises key questions as to the importance of low-level sensory modifications in the learning process. We trained two groups of participants on a two-tone frequency discrimination task for several days. In one group, a fixed reference tone was consistently presented in the first interval (the second tone was higher or lower), and in the other group the same reference tone was consistently presented in the second interval. When following training, these temporal protocols were switched between groups, performance of both groups regressed to pretraining levels, and further training was needed to attain postlearning performance. ERP measures, taken before and after training, indicated that participants implicitly learned the temporal regularity of the protocol and formed an attentional template that matched the trained structure of information. These results are consistent with Reverse Hierarchy Theory, which posits that even the learning of simple perceptual tasks progresses in a top-down manner, hence can benefit from temporal regularities at the trial level, albeit at the potential cost that learning may be specific to these regularities.

Templated Synthesis of Single-Walled Carbon Nanotubes with Specific Structure.

Science.gov (United States)

Yang, Feng; Wang, Xiao; Li, Meihui; Liu, Xiyan; Zhao, Xiulan; Zhang, Daqi; Zhang, Yan; Yang, Juan; Li, Yan

2016-04-19

Single-walled carbon nanotubes (SWNTs) have shown great potential in various applications attributed to their unique structure-dependent properties. Therefore, the controlled preparation of chemically and structurally pristine SWNTs is a crucial issue for their advanced applications (e.g., nanoelectronics) and has been a great challenge for two decades. Epitaxial growth from well-defined seeds has been shown to be a promising strategy to control the structure of SWNTs. Segments of carbon nanotubes, including short pipes from cutting of preformed nanotubes and caps from opening of fullerenes or cyclodehydrogenation of polycyclic hydrocarbon precursors, have been used as the seeds to grow SWNTs. Single-chirality SWNTs were obtained with both presorted chirality-pure SWNT segments and end caps obtained from polycyclic hydrocarbon molecules with designed structure. The main challenges of nanocarbon-segment-seeded processes are the stability of the seeds, yield, and efficiency. Catalyst-mediated SWNT growth is believed to be more efficient. The composition and morphology of the catalyst nanoparticles have been widely reported to affect the chirality distribution of SWNTs. However, chirality-specific SWNT growth is hard to achieve by alternating catalysts. The specificity of enzyme-catalyzed reactions brings us an awareness of the essentiality of a unique catalyst structure for the chirality-selective growth of SWNTs. Only catalysts with the desired atomic arrangements in their crystal planes can act as structural templates for chirality-specific growth of SWNTs. We have developed a new family of catalysts, tungsten-based intermetallic compounds, which have high melting points and very special crystal structures, to facilitate the growth of SWNTs with designed chirality. By the use of W6Co7 catalysts, (12,6) SWNTs were directly grown with purity higher than 92%. Both high-resolution transmission electron microscopy measurements and density functional theory simulations

Structural basis for substrate specificities of cellular deoxyribonucleoside kinases

DEFF Research Database (Denmark)

Johansson, K.; Ramaswamy, S.; Ljungcrantz, C.

2001-01-01

Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside binding site and that of the human deoxyguanosine ki......; this is apparently due to the presence of Arg 118, which provides favorable hydrogen bonding interactions with the substrate. The two new structures provide an explanation for the substrate specificity of cellular deoxyribonucleoside kinases....

The effect of natural and synthetic fatty acids on membrane structure, microdomain organization, cellular functions and human health.

Science.gov (United States)

Ibarguren, Maitane; López, David J; Escribá, Pablo V

2014-06-01

This review deals with the effects of synthetic and natural fatty acids on the biophysical properties of membranes, and on their implication on cell function. Natural fatty acids are constituents of more complex lipids, like triacylglycerides or phospholipids, which are used by cells to store and obtain energy, as well as for structural purposes. Accordingly, natural and synthetic fatty acids may modify the structure of the lipid membrane, altering its microdomain organization and other physical properties, and provoking changes in cell signaling. Therefore, by modulating fatty acids it is possible to regulate the structure of the membrane, influencing the cell processes that are reliant on this structure and potentially reverting pathological cell dysfunctions that may provoke cancer, diabetes, hypertension, Alzheimer's and Parkinson's disease. The so-called Membrane Lipid Therapy offers a strategy to regulate the membrane composition through drug administration, potentially reverting pathological processes by re-adapting cell membrane structure. Certain fatty acids and their synthetic derivatives are described here that may potentially be used in such therapies, where the cell membrane itself can be considered as a target to combat disease. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2013 Elsevier B.V. All rights reserved.

Potential-specific structure at the hematite-electrolyte interface

Energy Technology Data Exchange (ETDEWEB)

McBriarty, Martin E.; Stubbs, Joanne; Eng, Peter; Rosso, Kevin M.

2018-02-21

The atomic-scale structure of interfaces between metal oxides and aqueous electrolytes controls their catalytic, geochemical, and corrosion behavior. Measurements that probe these interfaces in situ provide important details of ion and solvent arrangements, but atomically precise structural models do not exist for common oxide-electrolyte interfaces far from equilibrium. Using a novel cell, we measured the structure of the hematite (a-Fe₂O₃) (110$\\bar{2}$)-electrolyte interface under controlled electrochemical bias using synchrotron crystal truncation rod X ray scattering. At increasingly cathodic potentials, charge-compensating protonation of surface oxygen groups increases the coverage of specifically bound water while adjacent water layers displace outwardly and became disordered. Returning to open circuit potential leaves the surface in a persistent metastable protonation state. The flux of current and ions at applied potential is thus regulated by a unique interfacial electrolyte environment, suggesting that electrical double layer models should be adapted to the dynamically changing interfacial structure far from equilibrium.

The development of flow-through bio-catalyst microreactors from silica micro structured fibers for lipid transformations.

Science.gov (United States)

Anuar, Sabiqah Tuan; Villegas, Carla; Mugo, Samuel M; Curtis, Jonathan M

2011-06-01

This study demonstrates the utility of a flow-through enzyme immobilized silica microreactor for lipid transformations. A silica micro structured fiber (MSF) consisting of 168 channels of internal diameter 4-5 μm provided a large surface area for the covalent immobilization of Candida antartica lipase. The specific activity of the immobilized lipase was determined by hydrolysis of p-nitrophenyl butyrate and calculated to be 0.81 U/mg. The catalytic performance of the lipase microreactor was demonstrated by the efficient ethanolysis of canola oil. The parameters affecting the performance of the MSF microreactor, including temperature and reaction flow rate, were investigated. Characterization of the lipid products exiting the microreactor was performed by non-aqueous reversed-phased liquid chromatography (NARP-LC) with evaporative light scattering detector (ELSD) and by comprehensive two-dimensional gas chromatography (GC x GC). Under optimized conditions of 1 μL/min flow rate of 5 mg/mL trioleoylglycerol (TO) in ethanol and 50 °C reaction temperature, 2-monooleoylglycerol was the main product at > 90% reaction yield. The regioselectivity of the Candida antartica lipase immobilized MSF microreactor in the presence of ethanol was found to be comparable to that obtained under conventional conditions. The ability of these reusable flow-through microreactors to regioselectively form monoacylglycerides in high yield from triacylglycerides demonstrate their potential use in small-scale lipid transformations or analytical lipids profiling.

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

Science.gov (United States)

Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

2015-06-18

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development. Copyright © 2015 Elsevier Ltd. All rights reserved.

Site-specific electronic structure analysis by channeling EELS and first-principles calculations.

Science.gov (United States)

Tatsumi, Kazuyoshi; Muto, Shunsuke; Yamamoto, Yu; Ikeno, Hirokazu; Yoshioka, Satoru; Tanaka, Isao

2006-01-01

Site-specific electronic structures were investigated by electron energy loss spectroscopy (EELS) under electron channeling conditions. The Al-K and Mn-L(2,3) electron energy loss near-edge structure (ELNES) of, respectively, NiAl2O4 and Mn3O4 were measured. Deconvolution of the raw spectra with the instrumental resolution function restored the blunt and hidden fine features, which allowed us to interpret the experimental spectral features by comparing with theoretical spectra obtained by first-principles calculations. The present method successfully revealed the electronic structures specific to the differently coordinated cationic sites.

Phenotype- and genotype-specific structural alterations in spasmodic dysphonia.

Science.gov (United States)

Bianchi, Serena; Battistella, Giovanni; Huddleston, Hailey; Scharf, Rebecca; Fleysher, Lazar; Rumbach, Anna F; Frucht, Steven J; Blitzer, Andrew; Ozelius, Laurie J; Simonyan, Kristina

2017-04-01

Spasmodic dysphonia is a focal dystonia characterized by involuntary spasms in the laryngeal muscles that occur selectively during speaking. Although hereditary trends have been reported in up to 16% of patients, the causative etiology of spasmodic dysphonia is unclear, and the influences of various phenotypes and genotypes on disorder pathophysiology are poorly understood. In this study, we examined structural alterations in cortical gray matter and white matter integrity in relationship to different phenotypes and putative genotypes of spasmodic dysphonia to elucidate the structural component of its complex pathophysiology. Eighty-nine patients with spasmodic dysphonia underwent high-resolution magnetic resonance imaging and diffusion-weighted imaging to examine cortical thickness and white matter fractional anisotropy in adductor versus abductor forms (distinct phenotypes) and in sporadic versus familial cases (distinct genotypes). Phenotype-specific abnormalities were localized in the left sensorimotor cortex and angular gyrus and the white matter bundle of the right superior corona radiata. Genotype-specific alterations were found in the left superior temporal gyrus, supplementary motor area, and the arcuate portion of the left superior longitudinal fasciculus. Our findings suggest that phenotypic differences in spasmodic dysphonia arise at the level of the primary and associative areas of motor control, whereas genotype-related pathophysiological mechanisms may be associated with dysfunction of regions regulating phonological and sensory processing. Identification of structural alterations specific to disorder phenotype and putative genotype provides an important step toward future delineation of imaging markers and potential targets for novel therapeutic interventions for spasmodic dysphonia. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

Crystal Structure of a UDP-glucose-specific Glycosyltransferase from a Mycobacterium Species

Energy Technology Data Exchange (ETDEWEB)

Fulton, Zara; McAlister, Adrian; Wilce, Matthew C.J.; Brammananth, Rajini; Zaker-Tabrizi, Leyla; Perugini, Matthew A.; Bottomley, Stephen P.; Coppel, Ross L.; Crellin, Paul K.; Rossjohn, Jamie; Beddoe, Travis (Monash); (Melbourne)

2008-10-24

Glycosyltransferases (GTs) are a large and ubiquitous family of enzymes that specifically transfer sugar moieties to a range of substrates. Mycobacterium tuberculosis contains a large number of GTs, many of which are implicated in cell wall synthesis, yet the majority of these GTs remain poorly characterized. Here, we report the high resolution crystal structures of an essential GT (MAP2569c) from Mycobacterium avium subsp. paratuberculosis (a close homologue of Rv1208 from M. tuberculosis) in its apo- and ligand-bound forms. The structure adopted the GT-A fold and possessed the characteristic DXD motif that coordinated an Mn{sup 2+} ion. Atypical of most GTs characterized to date, MAP2569c exhibited specificity toward the donor substrate, UDP-glucose. The structure of this ligated complex revealed an induced fit binding mechanism and provided a basis for this unique specificity. Collectively, the structural features suggested that MAP2569c may adopt a 'retaining' enzymatic mechanism, which has implications for the classification of other GTs in this large superfamily.

Structural Determinants of Specific Lipid Binding to Potassium Channels

NARCIS (Netherlands)

Weingarth, M.H.|info:eu-repo/dai/nl/330985655; Prokofyev, A.; van der Cruijsen, E.A.W.|info:eu-repo/dai/nl/330826743; Nand, D.|info:eu-repo/dai/nl/337731403; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Pongs, O.; Baldus, M.|info:eu-repo/dai/nl/314410864

2013-01-01

We have investigated specific lipid binding to the pore domain of potassium channels KcsA and chimeric KcsAKv1.3 on the structural and functional level using extensive coarse-grained and atomistic molecular dynamics simulations, solid-state NMR, and single channel measurements. We show that, while

STRUCTURAL AND DESIGN SPECIFICS OF SPACE GRID SYSTEMS

Directory of Open Access Journals (Sweden)

G. M. Gasii

2017-01-01

Full Text Available The aim of the study is to identify main trends in the development of space grid structures. In order to reach the purpose it is necessary to conduct a review of the known structural concepts, nodal connections and specifics of the space grid structures and to make conclusions on feasibility improvement of the considered structural concepts that make it possible to develop new solutions without disadvantages residing in the analogues. Analysis of papers written by foreign and national scientists and devoted to theoretical, numerical and experimental studies of stress-strain state, influence of different factors on it and geometrical optimization and designing of space grid structures has been conducted in order to achieve the objectives. Space grid structures and, in particular, flat double-layer grid and most frequent nodes have been studied in the paper. The paper contains a short review of the history on development of space grid structures. It has been found that a rapid development of structural designs was caused by scientific and technical progress and, in particular, improvement of physical and mechanical properties of materials, development of calculation methods, application of software systems for simulating behavior of the structure under load, which significantly increased the calculation accuracy and reduced complexity of design. It has been also established that main parameters that have influence on effectiveness of a structural design are geometric dimensions of its modular elements, ratio of its depth to the span. The world experience on development of connection components has been studied in the paper. The paper presents general classification of nodal connections. Main advantages and disadvantages of existing space grid structures are highlighted and it allows to determine possible methods for their improvement. Theoretical research has permitted to establish that the main direction of spatial grid structures improvement

Production of specific-structured lipids by enzymatic interesterification in a pilot continuous enzyme bed reactor

DEFF Research Database (Denmark)

Xu, Xuebing; Balchen, Steen; Høy, Carl-Erik

1998-01-01

Production of specific-structured lipids (interesterified lipids with a specific structure) by enzymatic interesterification was carried out in a continuous enzyme bed pilot scale reactor. Commercial immobilized lipase (Lipozyme IM) was used and investigations of acyl migration, pressure drop...

IgE to penicillins with different specificities can be identified by a multiepitope macromolecule: Bihaptenic penicillin structures and IgE specificities.

Science.gov (United States)

Ariza, A; Barrionuevo, E; Mayorga, C; Montañez, M I; Perez-Inestrosa, E; Ruiz-Sánchez, A; Rodríguez-Guéant, R M; Fernández, T D; Guéant, J L; Torres, M J; Blanca, M

2014-04-01

Quantitation of specific IgE by immunoassay is a recommended in vitro test for the diagnosis of immediate hypersensitivity reactions to betalactams (BLs), particularly when skin test results are negative. IgE antibodies that recognize the common nuclear structure of all BLs or the specific side chain structure can be mainly distinguished by immunoassays. The aim of this study was to develop an immunoassay system to detect IgE antibodies with different specificities. Cellulose discs conjugated with benzylpenicillin (BP), amoxicillin (AX) or both drugs, with poly-l-lysine (PLL) as carrier molecule, were used as solid phases in the radioallergosorbent test (RAST). Direct and inhibition radioimmunoassay studies were made to verify the structures recognized by serum IgE antibodies from penicillin-allergic patients. Our results indicated that the addition of both haptens did not decrease the capacity to capture IgE when serum specific to either BP or AX was used, at least in terms of sensitivity. In addition, the inclusion of two haptens improved significantly the levels of IgE detection in patients who recognized both BP and AX. Therefore, the use of a solid phase with a carrier molecule conjugated with two determinants (AX and BP) is helpful to recognize IgE antibodies against either of these determinants and is useful for screening sera with different specificities. Copyright © 2014 Elsevier B.V. All rights reserved.

Hidrólise do óleo de Azadirachta indica em água subcrítica e determinação da composição dos triacilglicerídeos e ácidos graxos por cromatografia gasosa de alta resolução a alta temperatura e cromatografia gasosa de alta resolução acoplada à espectrometria de massas Hydrolysis of Azadirachta indica oil using subcritical water and determination of triacylglycerides and fat acids by HT-HRGC-FID and HRGC-MS

Directory of Open Access Journals (Sweden)

Jair Sebastião da Silva Pinto

2010-01-01

Full Text Available The development of modern analytical tools plays an important role in quality control. The main purpose of this study was to explore the use of subcritical water as a versatile analytical tool, employed simultaneously as a reagent and solvent, as well as the application of high temperature-high resolution gas chromatography (HT-HRGC to develop a procedure for the analysis of triacylglycerides and fatty acids in Azadirachta indica A. Juss. (Neem oil without the need for solvents, chemical reagents, or catalytic agents. The developed method presented satisfactory results and is in agreement with the concepts of Green Analytical Chemistry (GAC.

Antidepressant Specificity of Serotonin Transporter Suggested by Three LeuT-SSRI Structures

Energy Technology Data Exchange (ETDEWEB)

Zhou, Z.; Zhen, J; Karpowich, N; Law, C; Reith, M; Wang, D

2009-01-01

Sertraline and fluoxetine are selective serotonin re-uptake inhibitors (SSRIs) that are widely prescribed to treat depression. They exert their effects by inhibiting the presynaptic plasma membrane serotonin transporter (SERT). All SSRIs possess halogen atoms at specific positions, which are key determinants for the drugs' specificity for SERT. For the SERT protein, however, the structural basis of its specificity for SSRIs is poorly understood. Here we report the crystal structures of LeuT, a bacterial SERT homolog, in complex with sertraline, R-fluoxetine or S-fluoxetine. The SSRI halogens all bind to exactly the same pocket within LeuT. Mutation at this halogen-binding pocket (HBP) in SERT markedly reduces the transporter's affinity for SSRIs but not for tricyclic antidepressants. Conversely, when the only nonconserved HBP residue in both norepinephrine and dopamine transporters is mutated into that found in SERT, their affinities for all the three SSRIs increase uniformly. Thus, the specificity of SERT for SSRIs is dependent largely on interaction of the drug halogens with the protein's HBP.

Specific β-turns precede PPIIL structures binding to allele-specific HLA-DRβ1* PBRs in fully-protective malaria vaccine components

Science.gov (United States)

Bermudez, Adriana; Alba, Martha P.; Vanegas, Magnolia; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2018-04-01

The 3D structural analysis of 62 peptides derived from highly pathogenic Plasmodium falciparum malaria parasite proteins involved in host cell invasion led to finding a striking association between particular β-turn types located in the N-terminal peripheral flanking residue region (preceding the polyproline II left-handed structures fitting into the HLA-DRβ* allele family) and modified immune protection-inducing protein structure induced long-lasting protective immunity. This is the first time association between two different secondary structures associated with a specific immunological function has been described: full, long-lasting protective immunity.

DAFS study of site-specific local structure of Mn in manganese ferrite films

International Nuclear Information System (INIS)

Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Zuo, X.; Harris, V.G.

2006-01-01

Manganese ferrite (MnFe 2 O 4 ) is a well-known magnetic material widely used in electronics for many years. It is well established that its magnetic behavior is strongly influenced by local structural properties of Mn ions, which are distributed between crystallographically inequivalent tetrahedral and octahedral sites in the unit cell. In order to understand and be able to tune properties of these structures, it is necessary to have detailed site-specific structural information on the system. Here we report on the application of diffraction-anomalous fine structure (DAFS) spectroscopy to resolve site-specific Mn local structures in manganese ferrite films. The DAFS measurements were done at undulator beamline 4-ID-D of the Advanced Photon Source at Argonne National Laboratory. The DAFS spectra (Fig. 1) were measured at several Bragg reflections in the vicinity of the Mn absorption K-edge, having probed separately contributions from tetrahedrally and octahedrally coordinated Mn sites. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around different inequivalent Mn sites in the unit cell. The reliability of the data treatment was checked carefully, and it was showed that the site-specific structural parameters obtained with DAFS allow us to describe fluorescence EXAFS spectrum measured independently. Fig. 2 shows individual site contributions to the imaginary part of the resonant scattering amplitude obtained from the treatment of the data of Fig. 1. The analysis of the refined site-specific absorption spectra was done using EXAFS methods based on theoretical standards. We provided direct evidence for the tetrahedral Mn-O bond distance being increased relative to the corresponding Fe-O distance in bulk manganese ferrites. The first coordination shell number was found to be reduced significantly for Mn atoms at these sites. This finding is consistent with the well-known tendency of Mn

The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4.

Science.gov (United States)

Isabet, Tatiana; Montagnac, Guillaume; Regazzoni, Karine; Raynal, Bertrand; El Khadali, Fatima; England, Patrick; Franco, Michel; Chavrier, Philippe; Houdusse, Anne; Ménétrey, Julie

2009-09-16

The JNK-interacting proteins, JIP3 and JIP4, are specific effectors of the small GTP-binding protein ARF6. The interaction of ARF6-GTP with the second leucine zipper (LZII) domains of JIP3/JIP4 regulates the binding of JIPs to kinesin-1 and dynactin. Here, we report the crystal structure of ARF6-GTP bound to the JIP4-LZII at 1.9 A resolution. The complex is a heterotetramer with dyad symmetry arranged in an ARF6-(JIP4)(2)-ARF6 configuration. Comparison of the ARF6-JIP4 interface with the equivalent region of ARF1 shows the structural basis of JIP4's specificity for ARF6. Using site-directed mutagenesis and surface plasmon resonance, we further show that non-conserved residues at the switch region borders are the key structural determinants of JIP4 specificity. A structure-derived model of the association of the ARF6-JIP3/JIP4 complex with membranes shows that the JIP4-LZII coiled-coil should lie along the membrane to prevent steric hindrances, resulting in only one ARF6 molecule bound. Such a heterotrimeric complex gives insights to better understand the ARF6-mediated motor switch regulatory function.

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

Energy Technology Data Exchange (ETDEWEB)

Dessanti, Paola [Cornell University, Ithaca, NY 14853-1301 (United States); Università di Sassari, (Italy); Zhang, Yang [Cornell University, Ithaca, NY 14853-1301 (United States); Allegrini, Simone [Università di Sassari, (Italy); Tozzi, Maria Grazia [Università di Pisa, (Italy); Sgarrella, Francesco [Università di Sassari, (Italy); Ealick, Steven E., E-mail: see3@cornell.edu [Cornell University, Ithaca, NY 14853-1301 (United States)

2012-03-01

Adenosine phosphorylase from B. cereus shows a strong preference for adenosine over other 6-oxopurine nucleosides. Mutation of Asp204 to asparagine reduces the efficiency of adenosine cleavage but does not affect inosine cleavage, effectively reversing the substrate specificity. The structures of D204N complexes explain these observations. Purine nucleoside phosphorylases catalyze the phosphorolytic cleavage of the glycosidic bond of purine (2′-deoxy)nucleosides, generating the corresponding free base and (2′-deoxy)ribose 1-phosphate. Two classes of PNPs have been identified: homotrimers specific for 6-oxopurines and homohexamers that accept both 6-oxopurines and 6-aminopurines. Bacillus cereus adenosine phosphorylase (AdoP) is a hexameric PNP; however, it is highly specific for 6-aminopurines. To investigate the structural basis for the unique substrate specificity of AdoP, the active-site mutant D204N was prepared and kinetically characterized and the structures of the wild-type protein and the D204N mutant complexed with adenosine and sulfate or with inosine and sulfate were determined at high resolution (1.2–1.4 Å). AdoP interacts directly with the preferred substrate through a hydrogen-bond donation from the catalytically important residue Asp204 to N7 of the purine base. Comparison with Escherichia coli PNP revealed a more optimal orientation of Asp204 towards N7 of adenosine and a more closed active site. When inosine is bound, two water molecules are interposed between Asp204 and the N7 and O6 atoms of the nucleoside, thus allowing the enzyme to find alternative but less efficient ways to stabilize the transition state. The mutation of Asp204 to asparagine led to a significant decrease in catalytic efficiency for adenosine without affecting the efficiency of inosine cleavage.

Does Gender-Specific Differential Item Functioning Affect the Structure in Vocational Interest Inventories?

Science.gov (United States)

Beinicke, Andrea; Pässler, Katja; Hell, Benedikt

2014-01-01

The study investigates consequences of eliminating items showing gender-specific differential item functioning (DIF) on the psychometric structure of a standard RIASEC interest inventory. Holland's hexagonal model was tested for structural invariance using a confirmatory methodological approach (confirmatory factor analysis and randomization…

Structural basis for sequence-specific recognition of DNA by TAL effectors

KAUST Repository

Deng, Dong

2012-01-05

TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.

Review of sn-2 palmitate oil implications for infant health.

Science.gov (United States)

Bar-Yoseph, Fabiana; Lifshitz, Yael; Cohen, Tzafra

2013-09-01

Human milk provides the optimal balanced nutrition for the growing infant in the first months after birth. The human mammary gland has evolved with unusual pathways, resulting in a specific positioning of fatty acids at the outer sn-1 and sn-3, and center sn-2 of the triacylglyceride, which is different from the triglycerides in other human tissues and plasma. The development of structured triglycerides enables mimicking the composition as well as structure of human milk fat in infant formulas. Studies conducted two decades ago, together with very recent studies, have provided increasing evidence that this unusual positioning of 16:0 in human milk triglycerides has a significant role for infant health in different directions, such as fat and calcium absorption, bone health, intestinal flora and infant comfort. This review aims to unravel the relevance of human milk triglyceride sn-2 16:0 for intestinal health and inflammatory pathways and for other post-absorption effects. Copyright © 2013 Elsevier Ltd. All rights reserved.

MNE SPECIFIC FACTORS OF CORPORATE CAPITAL STRUCTURE: COMPARATIVE ANALYSIS IN TERMS OF FINANCIAL RESOURCES DEMAND AND SUPPLY

Directory of Open Access Journals (Sweden)

Sergiy Tsyganov

2015-11-01

Full Text Available This paper investigates corporate capital structure of multinational enterprises. Its core subject is focused on corporate capital structure defining factors that are specific for MNE rather than for domestic corporations. Substantial part of scientific literature concentrates on country specific and firm specific factors of corporate capital structure with most research devoted to domestic corporations. The main goal of our paper is to discover among plenty of corporate capital structure factors those that are specific for MNE and to develop a new approach for analyzing these factors in terms of financial resources demand and supply. There are some corporate capital structure factors that influence directly and some that have indirect influence while there is also another set of factors having both direct and indirect influence on indebtedness. Different theoretical and empirical research confirm different directions. Methodology of our study is based on analysis of two fundamental market driving forces that are demand and supply. Their influence on corporate capital structure is of a primary origin and that is why the suggested approach is to our mind theoretically significant and practically important. Demand factors imply that a corporation creates demand for financial resources and its capital structure is defined internally. Supply factors imply an external capital structure since it is created by external investors’ supply of financial resources. On empirical level, we use the primary data of corporate financial statements to analyze the leverage of MNE based in different countries and representing different industries. The key results of our study show that the main MNE specific factors of capital structure include such demand factors as multinationality level, assets tangibility and political risk. The first two are firm specific factors that can influence corporate capital structure either directly or indirectly according to

Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor

OpenAIRE

Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

2015-01-01

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits P. falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report 3 crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all 3 structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of...

Site-specific local structure of Mn in artificial manganese ferrite films

International Nuclear Information System (INIS)

Kravtsov, E.; Haskel, D.; Cady, A.; Yang, A.; Vittoria, C.; Harris, V. G.; Zuo, X.

2006-01-01

Diffraction anomalous fine structure (DAFS) spectroscopy has been applied to resolve site-specific Mn local structure in manganese ferrite films grown under nonequilibrium conditions. The DAFS spectra were measured at a number of Bragg reflections in the vicinity of the Mn absorption K edge. The DAFS data analysis done with an iterative Kramers-Kroenig algorithm made it possible to solve separately the local structure around crystallographically inequivalent Mn sites in the unit cell with nominal octahedral and tetrahedral coordination. The strong preference for Mn to be tetrahedrally coordinated in this compound is not only manifested in the relative site occupancies but also in a strong reduction in coordination number for Mn ions at nominal octahedral sites

Graded territories: Towards the design, specification and simulation of materially graded bending active structures

DEFF Research Database (Denmark)

Nicholas, Paul; Tamke, Martin; Ramsgaard Thomsen, Mette

2012-01-01

these structures, the property of bending is activated and varied through bespoke material means so as to match a desired form. Within the architectural design process, formal control depends upon design approaches for material specification and simulation that consider behavior at the level of the material...... element as well as the structure. We describe an evolving approach to material specification and simulation, and highlight the digital and material considerations that frame the process.......The ability to make materials with bespoke behavior affords new perspectives on incorporating material properties within the design process not available through natural materials. This paper reports the design and assembly of two bending-active, fibre-reinforced composite structures. Within...

[Production, specificity and structure of immunoglobulins].

Science.gov (United States)

Goujard, C; Delfraissy, J F

1991-03-21

Immunoglobulin is a key factor of the immune response resulting from B-cell activation and associated with T-cell stimulation. Because of its structure, this antibody has a dual function: it specifically recognizes the inducer antigen in the variable region and eliminates it by a constant portion which is responsible for effector properties. Surface immunoglobulin, therefore, is the B-cell antigen receptor; it differs from the T-cell receptor in that it recognizes the antigen unbound to the major istocompatibility complex; binding the antigen results in direct signal transduction first in the cytoplasm, then in the nucleus. This receptor can be secreted in the body: it is made up of circulating immunoglobulins. Human immunoglobulins are divided into 5 classes, each of them with its own response kinetics, distribution and functions. The variability of the antibody response accounts for a genetic organization involving numerous genes which may be associated with each other, or mutate, or recombine during maturation of the lymphocytes. Altogether, this system has a theoretical capacity of response to three hundred million different antigens.

Structured flowcharts for control logic specification in the Tritium Systems Test Assembly

International Nuclear Information System (INIS)

Nielson, C.W.; Claborn, G.W.

1983-01-01

The Tritium Systems Test Assembly (TSTA) contains several subsystems employing sophisticated chemical and physical processes to purify, transport, and capture the isotopes of hydrogen. The ultimate responsibility for the correct and safe operation of these subsystems lies with their designers. However, the logic is implemented in a computer system with program control. A means to insure unambiguous specification of the control logic in a form understandable to both the non-programming designers and the software staff was required. The computer programs are written in RATFOR, a language providing clear control structures and powerful symbol definition facilities. However, the actual code was considered unsatisfactory as a means of primary specification by the non-programming designers. On the other hand, simple English language descriptions of the desired behavior were not precise enough to insure correctness. Experimentation with traditional flowcharts proved that they were more difficult to follow than the RATFOR code. On the other hand, the use of structured flowcharts derived from those introduced by Nassi and Shneidermanl have proven to be very powerful. Using simple geometric forms for the basic control structures such as loops and conditional tests, and by using expansion rather than connection as the means of reducing any flowchart to a single page, a specification that is both understandable and precise has been obtained. A computer code automates the production and modification of these flowcharts. Combining these flowcharts with primitive subroutines which hide most of the details of control implementation has provided an effective medium for algorithm specification and validation. Examples of the flowcharts and the language used to specify them will be given

Individual differences in personality traits reflect structural variance in specific brain regions.

Science.gov (United States)

Gardini, Simona; Cloninger, C Robert; Venneri, Annalena

2009-06-30

Personality dimensions such as novelty seeking (NS), harm avoidance (HA), reward dependence (RD) and persistence (PER) are said to be heritable, stable across time and dependent on genetic and neurobiological factors. Recently a better understanding of the relationship between personality traits and brain structures/systems has become possible due to advances in neuroimaging techniques. This Magnetic Resonance Imaging (MRI) study investigated if individual differences in these personality traits reflected structural variance in specific brain regions. A large sample of eighty five young adult participants completed the Three-dimensional Personality Questionnaire (TPQ) and had their brain imaged with MRI. A voxel-based correlation analysis was carried out between individuals' personality trait scores and grey matter volume values extracted from 3D brain scans. NS correlated positively with grey matter volume in frontal and posterior cingulate regions. HA showed a negative correlation with grey matter volume in orbito-frontal, occipital and parietal structures. RD was negatively correlated with grey matter volume in the caudate nucleus and in the rectal frontal gyrus. PER showed a positive correlation with grey matter volume in the precuneus, paracentral lobule and parahippocampal gyrus. These results indicate that individual differences in the main personality dimensions of NS, HA, RD and PER, may reflect structural variance in specific brain areas.

Structural studies of Pseudomonas and Chromobacterium ω-aminotransferases provide insights into their differing substrate specificity

International Nuclear Information System (INIS)

Sayer, Christopher; Isupov, Michail N.; Westlake, Aaron; Littlechild, Jennifer A.

2013-01-01

The X-ray structures of two ω-aminotransferases from P. aeruginosa and C. violaceum in complex with an inhibitor offer the first detailed insight into the structural basis of the substrate specificity of these industrially important enzymes. The crystal structures and inhibitor complexes of two industrially important ω-aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor β-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-α-methylbenzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabaculine complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ω-aminotransferases

Sensing site-specific structural characteristics and chirality using vibrational circular dichroism of isotope labeled peptides.

Science.gov (United States)

Keiderling, Timothy A

2017-12-01

Isotope labeling has a long history in chemistry as a tool for probing structure, offering enhanced sensitivity, or enabling site selection with a wide range of spectroscopic tools. Chirality sensitive methods such as electronic circular dichroism are global structural tools and have intrinsically low resolution. Consequently, they are generally insensitive to modifications to enhance site selectivity. The use of isotope labeling to modify vibrational spectra with unique resolvable frequency shifts can provide useful site-specific sensitivity, and these methods have been recently more widely expanded in biopolymer studies. While the spectral shifts resulting from changes in isotopic mass can provide resolution of modes from specific parts of the molecule and can allow detection of local change in structure with perturbation, these shifts alone do not directly indicate structure or chirality. With vibrational circular dichroism (VCD), the shifted bands and their resultant sign patterns can be used to indicate local conformations in labeled biopolymers, particularly if multiple labels are used and if their coupling is theoretically modeled. This mini-review discusses selected examples of the use of labeling specific amides in peptides to develop local structural insight with VCD spectra. © 2017 Wiley Periodicals, Inc.

Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic

Energy Technology Data Exchange (ETDEWEB)

Xu, Rui; McBride, Ryan; Nycholat, Corwin M.; Paulson, James C.; Wilson, Ian A. (Scripps)

2012-02-13

Influenza virus hemagglutinin (HA) is the viral envelope protein that mediates viral attachment to host cells and elicits membrane fusion. The HA receptor-binding specificity is a key determinant for the host range and transmissibility of influenza viruses. In human pandemics of the 20th century, the HA normally has acquired specificity for human-like receptors before widespread infection. Crystal structures of the H1 HA from the 2009 human pandemic (A/California/04/2009 [CA04]) in complex with human and avian receptor analogs reveal conserved recognition of the terminal sialic acid of the glycan ligands. However, favorable interactions beyond the sialic acid are found only for {alpha}2-6-linked glycans and are mediated by Asp190 and Asp225, which hydrogen bond with Gal-2 and GlcNAc-3. For {alpha}2-3-linked glycan receptors, no specific interactions beyond the terminal sialic acid are observed. Our structural and glycan microarray analyses, in the context of other high-resolution HA structures with {alpha}2-6- and {alpha}2-3-linked glycans, now elucidate the structural basis of receptor-binding specificity for H1 HAs in human and avian viruses and provide a structural explanation for the preference for {alpha}2-6 siaylated glycan receptors for the 2009 pandemic swine flu virus.

Capturing structured, pulmonary disease-specific data elements in electronic health records.

Science.gov (United States)

Gronkiewicz, Cynthia; Diamond, Edward J; French, Kim D; Christodouleas, John; Gabriel, Peter E

2015-04-01

Electronic health records (EHRs) have the potential to improve health-care quality by allowing providers to make better decisions at the point of care based on electronically aggregated data and by facilitating clinical research. These goals are easier to achieve when key, disease-specific clinical information is documented as structured data elements (SDEs) that computers can understand and process, rather than as free-text/natural-language narrative. This article reviews the benefits of capturing disease-specific SDEs. It highlights several design and implementation considerations, including the impact on efficiency and expressivity of clinical documentation and the importance of adhering to data standards when available. Pulmonary disease-specific examples of collection instruments are provided from two commonly used commercial EHRs. Future developments that can leverage SDEs to improve clinical quality and research are discussed.

Structure And Specificity of a Quorum-Quenching Lactonase (AiiB) From Agrobacterium Tumefaciens

Energy Technology Data Exchange (ETDEWEB)

Liu, D.; Thomas, P.W.; Momb, J.; Hoang, Q.Q.; Petsko, G.A.; Ringe, D.; Fast, W.

2009-06-03

N-Acyl-l-homoserine lactone (AHL) mediated quorum-sensing regulates virulence factor production in a variety of Gram-negative bacteria. Proteins capable of degrading these autoinducers have been called 'quorum-quenching' enzymes, can block many quorum-sensing dependent phenotypes, and represent potentially useful reagents for clinical, agricultural, and industrial applications. The most characterized quorum-quenching enzymes to date are the AHL lactonases, which are metalloproteins that belong to the metallo-beta-lactamase superfamily. Here, we report the cloning, heterologous expression, purification, metal content, substrate specificity, and three-dimensional structure of AiiB, an AHL lactonase from Agrobacterium tumefaciens. Much like a homologous AHL lactonase from Bacillus thuringiensis, AiiB appears to be a metal-dependent AHL lactonase with broad specificity. A phosphate dianion is bound to the dinuclear zinc site and the active-site structure suggests specific mechanistic roles for an active site tyrosine and aspartate. To our knowledge, this is the second representative structure of an AHL lactonase and the first of an AHL lactonase from a microorganism that also produces AHL autoinducers. This work should help elucidate the hydrolytic ring-opening mechanism of this family of enzymes and also facilitate the design of more effective quorum-quenching catalysts.

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Science.gov (United States)

Wlodarski, Tomasz; Kutner, Jan; Towpik, Joanna; Knizewski, Lukasz; Rychlewski, Leszek; Kudlicki, Andrzej; Rowicka, Maga; Dziembowski, Andrzej; Ginalski, Krzysztof

2011-01-01

Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity). Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Directory of Open Access Journals (Sweden)

Tomasz Wlodarski

Full Text Available Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation in S. cerevisiae by conducting a comprehensive structural and functional survey of all the methyltransferases encoded in its genome. Using distant homology detection and fold recognition, we found that the S. cerevisiae methyltransferome comprises 86 MTases (53 well-known and 33 putative with unknown substrate specificity. Structural classification of their catalytic domains shows that these enzymes may adopt nine different folds, the most common being the Rossmann-like. We also analyzed the domain architecture of these proteins and identified several new domain contexts. Interestingly, we found that the majority of MTase genes are periodically expressed during yeast metabolic cycle. This finding, together with calculated isoelectric point, fold assignment and cellular localization, was used to develop a novel approach for predicting substrate specificity. Using this approach, we predicted the general substrates for 24 of 33 putative MTases and confirmed these predictions experimentally in both cases tested. Finally, we show that, in S. cerevisiae, methylation is carried out by 34 RNA MTases, 32 protein MTases, eight small molecule MTases, three lipid MTases, and nine MTases with still unknown substrate specificity.

O'nyong nyong virus molecular determinants of unique vector specificity reside in non-structural protein 3.

Directory of Open Access Journals (Sweden)

Kali D Saxton-Shaw

Full Text Available O'nyong nyong virus (ONNV and Chikungunya virus (CHIKV are two closely related alphaviruses with very different infection patterns in the mosquito, Anopheles gambiae. ONNV is the only alphavirus transmitted by anopheline mosquitoes, but specific molecular determinants of infection of this unique vector specificity remain unidentified. Fifteen distinct chimeric viruses were constructed to evaluate both structural and non-structural regions of the genome and infection patterns were determined through artificial infectious feeds in An. gambiae with each of these chimeras. Only one region, non-structural protein 3 (nsP3, was sufficient to up-regulate infection to rates similar to those seen with parental ONNV. When ONNV non-structural protein 3 (nsP3 replaced nsP3 from CHIKV virus in one of the chimeric viruses, infection rates in An. gambiae went from 0% to 63.5%. No other single gene or viral region addition was able to restore infection rates. Thus, we have shown that a non-structural genome element involved in viral replication is a major element involved in ONNV's unique vector specificity.

Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

Directory of Open Access Journals (Sweden)

David eRoquis

2014-07-01

Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

Magnetic susceptibility, specific heat and magnetic structure of CuNi2(PO4)2

International Nuclear Information System (INIS)

Escobal, Jaione; Pizarro, Jose L.; Mesa, Jose L.; Larranaga, Aitor; Fernandez, Jesus Rodriguez; Arriortua, Maria I.; Rojo, Teofilo

2006-01-01

The CuNi 2 (PO 4 ) 2 phosphate has been synthesized by the ceramic method at 800 deg. C in air. The crystal structure consists of a three-dimensional skeleton constructed from MO 4 (M II =Cu and Ni) planar squares and M 2 O 8 dimers with square pyramidal geometry, which are interconnected by (PO 4 ) 3- oxoanions with tetrahedral geometry. The magnetic behavior has been studied on powdered sample by using susceptibility, specific heat and neutron diffraction data. The bimetallic copper(II)-nickel(II) orthophosphate exhibits a three-dimensional magnetic ordering at, approximately, 29.8 K. However, its complex crystal structure hampers any parametrization of the J-exchange parameter. The specific heat measurements exhibit a three-dimensional magnetic ordering (λ-type) peak at 29.5 K. The magnetic structure of this phosphate shows ferromagnetic interactions inside the Ni 2 O 8 dimers, whereas the sublattice of Cu(II) ions presents antiferromagnetic couplings along the y-axis. The change of the sign in the magnetic unit-cell, due to the [1/2, 0, 1/2] propagation vector determines a purely antiferromagnetic structure. - Graphical abstract: Magnetic structure of CuNi2(PO4)2

Specific "scientific" data structures, and their processing

Directory of Open Access Journals (Sweden)

Jerzy Karczmarczuk

2011-09-01

Full Text Available Programming physicists use, as all programmers, arrays, lists, tuples, records, etc., and this requires some change in their thought patterns while converting their formulae into some code, since the "data structures" operated upon, while elaborating some theory and its consequences, are rather: power series and Padé approximants, differential forms and other instances of differential algebras, functionals (for the variational calculus, trajectories (solutions of differential equations, Young diagrams and Feynman graphs, etc. Such data is often used in a [semi-]numerical setting, not necessarily "symbolic", appropriate for the computer algebra packages. Modules adapted to such data may be "just libraries", but often they become specific, embedded sub-languages, typically mapped into object-oriented frameworks, with overloaded mathematical operations. Here we present a functional approach to this philosophy. We show how the usage of Haskell datatypes and - fundamental for our tutorial - the application of lazy evaluation makes it possible to operate upon such data (in particular: the "infinite" sequences in a natural and comfortable manner.

Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis.

Directory of Open Access Journals (Sweden)

Daniil M Prigozhin

Full Text Available Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

Structural basis of the substrate specificity of Bacillus cereus adenosine phosphorylase

Energy Technology Data Exchange (ETDEWEB)

Dessanti, Paola; Zhang, Yang; Allegrini, Simone; Tozzi, Maria Grazia; Sgarrella, Francesco; Ealick, Steven E. (Cornell); (Sassari); (Pisa)

2012-10-08

Purine nucleoside phosphorylases catalyze the phosphorolytic cleavage of the glycosidic bond of purine (2{prime}-deoxy)nucleosides, generating the corresponding free base and (2{prime}-deoxy)ribose 1-phosphate. Two classes of PNPs have been identified: homotrimers specific for 6-oxopurines and homohexamers that accept both 6-oxopurines and 6-aminopurines. Bacillus cereus adenosine phosphorylase (AdoP) is a hexameric PNP; however, it is highly specific for 6-aminopurines. To investigate the structural basis for the unique substrate specificity of AdoP, the active-site mutant D204N was prepared and kinetically characterized and the structures of the wild-type protein and the D204N mutant complexed with adenosine and sulfate or with inosine and sulfate were determined at high resolution (1.2-1.4 {angstrom}). AdoP interacts directly with the preferred substrate through a hydrogen-bond donation from the catalytically important residue Asp204 to N7 of the purine base. Comparison with Escherichia coli PNP revealed a more optimal orientation of Asp204 towards N7 of adenosine and a more closed active site. When inosine is bound, two water molecules are interposed between Asp204 and the N7 and O6 atoms of the nucleoside, thus allowing the enzyme to find alternative but less efficient ways to stabilize the transition state. The mutation of Asp204 to asparagine led to a significant decrease in catalytic efficiency for adenosine without affecting the efficiency of inosine cleavage.

Combinatorial design of a nanobody that specifically targets structured RNAs.

Science.gov (United States)

Cawez, F; Duray, E; Hu, Y; Vandenameele, J; Romão, E; Vincke, C; Dumoulin, M; Galleni, M; Muyldermans, S; Vandevenne, M

2018-04-11

Recent advances in transcriptome sequencing and analysis have revealed the complexity of the human genome. The majority (≈ 98%) of cellular transcripts is not translated into proteins and represents a vast, unchartered world of functional non-coding RNAs (ncRNAs). Most of them adopt a well-defined 3D structure to achieve their biological functions. However, only very few RNA structures are currently available which reflects the challenges associated with RNA crystallization. Nevertheless, these structures would represent a critical step in understanding functions of ncRNAs and their molecular mechanisms in the cell. The overall goal of this study is to develop an innovative and versatile tool to facilitate the functional study and crystallization of structured RNAs (stRNAs). In this work, we have engineered an antibody fragment from camelid heavy-chain antibody (nanobody) able to specifically bind with low nanomolar affinity to stRNA while no binding could be detected for single-stranded DNA/RNA, double-stranded DNA/RNA or a negatively charged protein. However, this nanobody recognizes different and non-related stRNAs, this observation suggests that it binds to an epitope shared by these stRNAs. Finally, our data also show that the binding of the nanobody doesn't alter the secondary structure content of the stRNA as well as its unfolding/refolding processes during heat treatment. This work constitutes a successful proof-of-concept demonstrating that nanobodies can be engineered to recognize RNA-related epitopes. Copyright © 2018. Published by Elsevier Ltd.

The RecQ helicase-topoisomerase III-Rmi1 complex: a DNA structure-specific 'dissolvasome'?

DEFF Research Database (Denmark)

Mankouri, Hocine W; Hickson, Ian D

2007-01-01

structures, and we propose here that it functions in a coordinated fashion as a DNA structure-specific 'dissolvasome'. Little is known about how the RTR complex might be regulated or targeted to various DNA structures in vivo. Recent findings indicate that the components of the RTR complex might activate...... the cell cycle checkpoint machinery as well as be a target of checkpoint kinases, suggesting that these events are crucial to ensure faithful DNA replication and chromosome segregation....

Polyaniline nanofibers with a high specific surface area and an improved pore structure for supercapacitors

Science.gov (United States)

Xu, Hailing; Li, Xingwei; Wang, Gengchao

2015-10-01

Polyaniline (PANI) with a high specific surface area and an improved pore structure (HSSA-PANI) has been prepared by using a facile method, treating PANI nanofibers with chloroform (CHCl3), and its structure, morphology and pore structure are investigated. The specific surface area and pore volume of HSSA-PANI are 817.3 m2 g-1 and 0.6 cm3 g-1, and those of PANI are 33.6 m2 g-1 and 0.2 cm3 g-1. As electrode materials, a large specific surface area and pore volume can provide high electroactive regions, accelerate the diffusion of ions, and mitigate the electrochemical degradation of active materials. Compared with PANI, the capacity retention rate of HSSA-PANI is 90% with a growth of current density from 5.0 to 30 A g-1, and that of PANI is 29%. At a current density of 30 A g-1, the specific capacitance of HSSA-PANI still reaches 278.3 F g-1, and that of PANI is 86.7 F g-1. At a current density of 5.0 A g-1, the capacitance retention of HSSA-PANI is 53.1% after 2000 cycles, and that of PANI electrode is only 28.1%.

Co-Localisation of Abnormal Brain Structure and Function in Specific Language Impairment

Science.gov (United States)

Badcock, Nicholas A.; Bishop, Dorothy V. M.; Hardiman, Mervyn J.; Barry, Johanna G.; Watkins, Kate E.

2012-01-01

We assessed the relationship between brain structure and function in 10 individuals with specific language impairment (SLI), compared to six unaffected siblings, and 16 unrelated control participants with typical language. Voxel-based morphometry indicated that grey matter in the SLI group, relative to controls, was increased in the left inferior…

Crystal structure of the N domain of human somatic angiotensin I-converting enzyme provides a structural basis for domain-specific inhibitor design.

Science.gov (United States)

Corradi, Hazel R; Schwager, Sylva L U; Nchinda, Aloysius T; Sturrock, Edward D; Acharya, K Ravi

2006-03-31

Human somatic angiotensin I-converting enzyme (sACE) is a key regulator of blood pressure and an important drug target for combating cardiovascular and renal disease. sACE comprises two homologous metallopeptidase domains, N and C, joined by an inter-domain linker. Both domains are capable of cleaving the two hemoregulatory peptides angiotensin I and bradykinin, but differ in their affinities for a range of other substrates and inhibitors. Previously we determined the structure of testis ACE (C domain); here we present the crystal structure of the N domain of sACE (both in the presence and absence of the antihypertensive drug lisinopril) in order to aid the understanding of how these two domains differ in specificity and function. In addition, the structure of most of the inter-domain linker allows us to propose relative domain positions for sACE that may contribute to the domain cooperativity. The structure now provides a platform for the design of "domain-specific" second-generation ACE inhibitors.

Structural Changes of Lumbar Muscles in Non-specific Low Back Pain: A Systematic Review.

Science.gov (United States)

Goubert, Dorien; Oosterwijck, Jessica Van; Meeus, Mira; Danneels, Lieven

2016-01-01

Lumbar muscle dysfunction due to pain might be related to altered lumbar muscle structure. Macroscopically, muscle degeneration in low back pain (LBP) is characterized by a decrease in cross-sectional area and an increase in fat infiltration in the lumbar paraspinal muscles. In addition microscopic changes, such as changes in fiber distribution, might occur. Inconsistencies in results from different studies make it difficult to draw firm conclusions on which structural changes are present in the different types of non-specific LBP. Insights regarding structural muscle alterations in LBP are, however, important for prevention and treatment of non-specific LBP. The goal of this article is to review which macro- and/or microscopic structural alterations of the lumbar muscles occur in case of non-specific chronic low back pain (CLBP), recurrent low back pain (RLBP), and acute low back pain (ALBP). Systematic review. All selected studies were case-control studies. A systematic literature search was conducted in the databases PubMed and Web of Science. Only full texts of original studies regarding structural alterations (atrophy, fat infiltration, and fiber type distribution) in lumbar muscles of patients with non-specific LBP compared to healthy controls were included. All included articles were scored on methodological quality. Fifteen studies were found eligible after screening title, abstract, and full text for inclusion and exclusion criteria. In CLBP, moderate evidence of atrophy was found in the multifidus; whereas, results in the paraspinal and the erector spinae muscle remain inconclusive. Also moderate evidence occurred in RLBP and ALBP, where no atrophy was shown in any lumbar muscle. Conflicting results were seen in undefined LBP groups. Results concerning fat infiltration were inconsistent in CLBP. On the other hand, there is moderate evidence in RLBP that fat infiltration does not occur, although a larger muscle fat index was found in the erector spinae

Structure based protein engineering of Bacillus stearothermophilus {alpha}-amylase: toward a new substrate specificity

Energy Technology Data Exchange (ETDEWEB)

Rasera, Ana Claudia [Sao Paulo Univ., SP (Brazil). Inst. de Ciencias Biomedicas; Iulek, Jorge [Universidade Estadual de Ponta Grossa, PR (Brazil). Inst. de Quimica; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica

1997-12-31

Full text. Structural similarity is observed in all members of {alpha}-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to {alpha}-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus {alpha}-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated {alpha}-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus {alpha}-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to {alpha}-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus

Structure based protein engineering of Bacillus stearothermophilus α-amylase: toward a new substrate specificity

International Nuclear Information System (INIS)

Rasera, Ana Claudia; Iulek, Jorge; Delboni, Luis Fernando; Barbosa, Valma Martins Barbosa

1997-01-01

Full text. Structural similarity is observed in all members of α-amylase family but different products are generated during hydrolysis of starch due to different affinities for intermediate dextrins. In order to understand the structural determinants for this property and to introduce different specificity to α-amylase of Bacillus stearothermophilus we intend to solve the three dimensional structure by X-ray crystallography of the native protein by using synchrotron radiation at Brazilian National Synchrotron Light Laboratory (LNLS). Protein was over expressed in E. coli, purified and crystallization experiments were carried out by using sparse matrix Crystal Screen and Crystal Screen II from Hampton Research (Laguna Hills, CA, USA). Several condition have produced crystals with some defined characteristic: MDP seems to be important to the crystallization: the preferential pH is around 7.5 with organic buffer (HEPES); organic solvent as 2-propanol seems to be also important for the crystallization. On those condition crystals appeared as cluster of needles or small crystals with high number of nucleation. New conditions are being prepared to improve the site and quality of crystals. Data collection of native of Bacillus stearothermophilus α-amylase will e done at Protein Crystallography Station at LNLS. Crystal structure of mutated α-amylase bu site direct mutagenesis of residues suggested by the native crystal structure will be obtained. Co-crystallization of Bacillus stearothermophilus α-amylase and oligosaccharide will be carried out to identify residues involved in the binding site to plan new mutation. In another series of mutation the putative binding site residues, once identified, will be mutated to residues observed in TAKA amylase to confer different specificity to α-amylase. Based on the available TAKA amylase structure, in the primary sequence homology and in the three dimensional model of Bacillus stearothermophilus α-amylase (using Bacillus

Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

Science.gov (United States)

Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

2015-11-03

Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ordering effects on structure and specific heat of nonstoichiometric titanium carbide

International Nuclear Information System (INIS)

Lipatnikov, V.N.; Gusev, A.I.

1999-01-01

The experimental results on the change in the crystal structure and specific heat of the nonstoichiometric titanium carbide TiC y (0.5 2 C phases with cubic and trigonal symmetry and the rhombic ordered Ti 3 C 2 phase are formed in the titanium carbide at the temperature below 1000 K by the phase transitions mechanism. The temperatures and heats of the order-disorder phase transitions are determined [ru

Mushroom Lectins: Specificity, Structure and Bioactivity Relevant to Human Disease

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Mohamed Ali Abol Hassan

2015-04-01

Full Text Available Lectins are non-immunoglobulin proteins that bind diverse sugar structures with a high degree of selectivity. Lectins play crucial role in various biological processes such as cellular signaling, scavenging of glycoproteins from the circulatory system, cell–cell interactions in the immune system, differentiation and protein targeting to cellular compartments, as well as in host defence mechanisms, inflammation, and cancer. Among all the sources of lectins, plants have been most extensively studied. However, more recently fungal lectins have attracted considerable attention due to their antitumor, antiproliferative and immunomodulatory activities. Given that only 10% of mushroom species are known and have been taxonomically classified, mushrooms represent an enormous unexplored source of potentially useful and novel lectins. In this review we provide an up-to-date summary on the biochemical, molecular and structural properties of mushroom lectins, as well as their versatile applications specifically focusing on mushroom lectin bioactivity.

Proximity-activated nanoparticles: in vitro performance of specific structural modification by enzymatic cleavage

Science.gov (United States)

Adam Smith, R; Sewell, Sarah L; Giorgio, Todd D

2008-01-01

The development and in vitro performance of a modular nanoscale system capable of specific structural modification by enzymatic activity is described in this work. Due to its small physical size and adaptable characteristics, this system has the potential for utilization in targeted delivery systems and biosensing. Nanoparticle probes were synthesized containing two distinct fluorescent species including a quantum dot base particle and fluorescently labeled cleavable peptide substrate. Activity of these probes was monitored by gel electrophoresis with quantitative cleavage measurements made by fluorometric analysis. The model proximity-activated nanoparticles studied here exhibit significant susceptibility to cleavage by matrix metalloprotease-7 (MMP-7) at physiologically relevant concentrations, with nearly complete cleavage of available substrate molecules after 24 hours. This response is specific to MMP-7 enzyme activity, as cleavage is completely inhibited with the addition of EDTA. Utilization of enzyme-specific modification is a sensitive approach with broad applications for targeted therapeutics and biosensing. The versatility of this nanoparticle system is highlighted in its modular design, as it has the capability to integrate characteristics for detection, biosensing, targeting, and payload delivery into a single, multifunctional nanoparticle structure. PMID:18488420

Recoveries of rat lymph FA after administration of specific structured C-13-TAG

DEFF Research Database (Denmark)

Vistisen, Bodil; Mu, Huiling; Høy, Carl-Erik

2003-01-01

of intragastrically administered L*L*L*, M*M*M*, ML*M, and ML*L* (where * = C-13-labeled FA) in rats. Lymph lipids were separated into lipid classes and analyzed by GC combustion isotope ratio MS. The recoveries of lymph TAG 18:2n-6 8 h after administration of L*L*L*, ML*M, and ML*L* were 38.6, 48.4, and 49...... rapid recovery of exogenous long-chain FA following administration of specific structured TAG compared with long-chain TAG was probably due to fast hydrolysis. The lymphatic recovery of 8:0 was 2.2% 24 h after administration of M*M*M*. This minor lymphatic recovery of exogenous 8:0 was probably due...... to low stimulation of chylomicron formation. These results demonstrate tendencies toward faster lymphatic recovery of long-chain FA after administration of specific structured TAG compared with long-chain TAG....

Finite Element Analysis and Die Design of Non-specific Engineering Structure of Aluminum Alloy during Extrusion

International Nuclear Information System (INIS)

Chen, D.-C.; Lu, Y.-Y.

2010-01-01

Aluminum extension applies to industrial structure, light load, framework rolls and conveyer system platform. Many factors must be controlled in processing the non-specific engineering structure (hollow shape) of the aluminum alloy during extrusion, to obtain the required plastic strain and desired tolerance values. The major factors include the forming angle of the die and temperature of billet and various materials. This paper employs rigid-plastic finite element (FE) DEFORM 3D software to investigate the plastic deformation behavior of an aluminum alloy (A6061, A5052, A3003) workpiece during extrusion for the engineering structure of the aluminum alloy. This work analyzes effective strain, effective stress, damage and die radius load distribution of the billet under various conditions. The analytical results confirm the suitability of the current finite element software for the non-specific engineering structure of aluminum alloy extrusion.

Function-specific and Enhanced Brain Structural Connectivity Mapping via Joint Modeling of Diffusion and Functional MRI.

Science.gov (United States)

Chu, Shu-Hsien; Parhi, Keshab K; Lenglet, Christophe

2018-03-16

A joint structural-functional brain network model is presented, which enables the discovery of function-specific brain circuits, and recovers structural connections that are under-estimated by diffusion MRI (dMRI). Incorporating information from functional MRI (fMRI) into diffusion MRI to estimate brain circuits is a challenging task. Usually, seed regions for tractography are selected from fMRI activation maps to extract the white matter pathways of interest. The proposed method jointly analyzes whole brain dMRI and fMRI data, allowing the estimation of complete function-specific structural networks instead of interactively investigating the connectivity of individual cortical/sub-cortical areas. Additionally, tractography techniques are prone to limitations, which can result in erroneous pathways. The proposed framework explicitly models the interactions between structural and functional connectivity measures thereby improving anatomical circuit estimation. Results on Human Connectome Project (HCP) data demonstrate the benefits of the approach by successfully identifying function-specific anatomical circuits, such as the language and resting-state networks. In contrast to correlation-based or independent component analysis (ICA) functional connectivity mapping, detailed anatomical connectivity patterns are revealed for each functional module. Results on a phantom (Fibercup) also indicate improvements in structural connectivity mapping by rejecting false-positive connections with insufficient support from fMRI, and enhancing under-estimated connectivity with strong functional correlation.

Linker histones: novel insights into structure-specific recognition of the nucleosome.

Science.gov (United States)

Cutter, Amber R; Hayes, Jeffrey J

2017-04-01

Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.

Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.

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Oleg M Ganichkin

Full Text Available Selenocysteine tRNAs (tRNA(Sec exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec-interacting factors are incompletely understood.We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec. tRNA(Sec lacking the single-stranded 3'-acceptor end ((ΔGCCARNA(Sec yielded a crystal structure at 2.0 Å resolution. The global structure of (ΔGCCARNA(Sec resembles the structure of human tRNA(Sec determined at 3.1 Å resolution. Structural comparisons revealed flexible regions in tRNA(Sec used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Secin vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec.We provide the most highly resolved structure of a tRNA(Sec molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec support its interaction with proteins.

Light-stimulated cargo release from a core–shell structured nanocomposite for site-specific delivery

International Nuclear Information System (INIS)

Cai, Yun; Ling, Li; Li, Xiaofang; Chen, Meng; Su, Likai

2015-01-01

This paper reported a core–shell structured site-specific delivery system with a light switch triggered by low energy light (λ=510 nm). Its core was composed of supermagnetic Fe 3 O 4 nanoparticles for magnetic guiding and targeting. Its outer shell consisted of mesoporous silica molecular sieve MCM-41 which offered highly ordered hexagonal tunnels for cargo capacity. A light switch N1-(4aH-cyclopenta[1,2-b:5,4-b′]dipyridin-5(5aH)-ylidene)benzene-1, 4-diamine (CBD) was covalently grafted into these hexagonal tunnels, serving as light stimuli acceptor with loading content of 1.1 μM/g. This composite was fully characterized and confirmed by SEM, TEM, XRD patterns, N 2 adsorption/desorption, thermogravimetric analysis, IR, UV–vis absorption and emission spectra. Experimental data suggested that this composite had a core as wide as 150 nm and could be magnetically guided to specific sites. Its hexagonal tunnels were as long as 180 nm. Upon light stimuli of “on” and “off” states, controllable release was observed with short release time of ~900 s (90% capacity). - Graphical abstract: A core–shell structured site-specific delivery system with a light switch triggered by yellow light was constructed. Controllable release was observed with short release time of ~900 s (90% capacity). - Highlights: • A core–shell structured site-specific delivery system was constructed. • It consisted of Fe 3 O 4 core and MCM-41 shell grafted with light switch. • This delivery system was triggered by low energy light. • Controllable release was observed with short release time of ~900 s

Light-stimulated cargo release from a core–shell structured nanocomposite for site-specific delivery

Energy Technology Data Exchange (ETDEWEB)

Cai, Yun; Ling, Li; Li, Xiaofang [Department of Neurology, Affiliated Hospital of Hebei University, Baoding 071000 (China); Chen, Meng [Department of Rheumatology, Affiliated Hospital of Hebei University, Baoding 071000 (China); Su, Likai, E-mail: zhangdong19992003@163.com [Department of Neurology, Affiliated Hospital of Hebei University, Baoding 071000 (China)

2015-03-15

This paper reported a core–shell structured site-specific delivery system with a light switch triggered by low energy light (λ=510 nm). Its core was composed of supermagnetic Fe{sub 3}O{sub 4} nanoparticles for magnetic guiding and targeting. Its outer shell consisted of mesoporous silica molecular sieve MCM-41 which offered highly ordered hexagonal tunnels for cargo capacity. A light switch N1-(4aH-cyclopenta[1,2-b:5,4-b′]dipyridin-5(5aH)-ylidene)benzene-1, 4-diamine (CBD) was covalently grafted into these hexagonal tunnels, serving as light stimuli acceptor with loading content of 1.1 μM/g. This composite was fully characterized and confirmed by SEM, TEM, XRD patterns, N{sub 2} adsorption/desorption, thermogravimetric analysis, IR, UV–vis absorption and emission spectra. Experimental data suggested that this composite had a core as wide as 150 nm and could be magnetically guided to specific sites. Its hexagonal tunnels were as long as 180 nm. Upon light stimuli of “on” and “off” states, controllable release was observed with short release time of ~900 s (90% capacity). - Graphical abstract: A core–shell structured site-specific delivery system with a light switch triggered by yellow light was constructed. Controllable release was observed with short release time of ~900 s (90% capacity). - Highlights: • A core–shell structured site-specific delivery system was constructed. • It consisted of Fe{sub 3}O{sub 4} core and MCM-41 shell grafted with light switch. • This delivery system was triggered by low energy light. • Controllable release was observed with short release time of ~900 s.

Lymphatic recovery of exogenous oleic acid in rats on long chain or specific structured triacylglycerol diets

DEFF Research Database (Denmark)

Vistisen, Bodil; Mu, Huiling; Høy, Carl-Erik

2006-01-01

Specific structured triacylglycerols, MLM (M = medium-chain fatty acid, L = long-chain fatty acid), rapidly deliver energy and long-chain fatty acids to the body and are used for longer periods in human enteral feeding. In the present study rats were fed diets of 10 wt% MLM or LLL (L = oleic acid......% and 45%, respectively). However, the recovery of exogenous 18:1 n-9 was higher after a single bolus of MLM compared with a bolus of LLL in rats on the MLM diet (40% and 24%, respectively, P = 0.009). The recovery of lymphatic 18:1 n-9 of the LLL bolus tended to depend on the diet triacylglycerol...... structure and composition (P = 0.07). This study demonstrated that with a diet containing specific structured triacylglycerol, the lymphatic recovery of 18:1 n-9 after a single bolus of fat was dependent on the triacylglycerol structure of the bolus. This indicates that the lymphatic recovery of long...

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity.

Science.gov (United States)

Kouno, Takahide; Silvas, Tania V; Hilbert, Brendan J; Shandilya, Shivender M D; Bohn, Markus F; Kelch, Brian A; Royer, William E; Somasundaran, Mohan; Kurt Yilmaz, Nese; Matsuo, Hiroshi; Schiffer, Celia A

2017-04-28

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

Structural basis for the high specificity of a Trypanosoma congolense immunoassay targeting glycosomal aldolase.

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Joar Pinto

2017-09-01

Full Text Available Animal African trypanosomosis (AAT is a neglected tropical disease which imposes a heavy burden on the livestock industry in Sub-Saharan Africa. Its causative agents are Trypanosoma parasites, with T. congolense and T. vivax being responsible for the majority of the cases. Recently, we identified a Nanobody (Nb474 that was employed to develop a homologous sandwich ELISA targeting T. congolense fructose-1,6-bisphosphate aldolase (TcoALD. Despite the high sequence identity between trypanosomatid aldolases, the Nb474-based immunoassay is highly specific for T. congolense detection. The results presented in this paper yield insights into the molecular principles underlying the assay's high specificity.The structure of the Nb474-TcoALD complex was determined via X-ray crystallography. Together with analytical gel filtration, the structure reveals that a single TcoALD tetramer contains four binding sites for Nb474. Through a comparison with the crystal structures of two other trypanosomatid aldolases, TcoALD residues Ala77 and Leu106 were identified as hot spots for specificity. Via ELISA and surface plasmon resonance (SPR, we demonstrate that mutation of these residues does not abolish TcoALD recognition by Nb474, but does lead to a lack of detection in the Nb474-based homologous sandwich immunoassay.The results show that the high specificity of the Nb474-based immunoassay is not determined by the initial recognition event between Nb474 and TcoALD, but rather by its homologous sandwich design. This (i provides insights into the optimal set-up of the assay, (ii may be of great significance for field applications as it could explain the potential detection escape of certain T. congolense strains, and (iii may be of general interest to those developing similar assays.

Structural diversity and evolution of the N-terminal isoform-specific region of ecdysone receptor-A and -B1 isoforms in insects

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Kubo Takeo

2010-02-01

Full Text Available Abstract Background The ecdysone receptor (EcR regulates various cellular responses to ecdysteroids during insect development. Insects have multiple EcR isoforms with different N-terminal A/B domains that contain the isoform-specific activation function (AF-1 region. Although distinct physiologic functions of the EcR isoforms have been characterized in higher holometabolous insects, they remain unclear in basal direct-developing insects, in which only A isoform has been identified. To examine the structural basis of the EcR isoform-specific AF-1 regions, we performed a comprehensive structural comparison of the isoform-specific region of the EcR-A and -B1 isoforms in insects. Results The EcR isoforms were newly identified in 51 species of insects and non-insect arthropods, including direct-developing ametabolous and hemimetabolous insects. The comprehensive structural comparison revealed that the isoform-specific region of each EcR isoform contained evolutionally conserved microdomain structures and insect subgroup-specific structural modifications. The A isoform-specific region generally contained four conserved microdomains, including the SUMOylation motif and the nuclear localization signal, whereas the B1 isoform-specific region contained three conserved microdomains, including an acidic activator domain-like motif. In addition, the EcR-B1 isoform of holometabolous insects had a novel microdomain at the N-terminal end. Conclusions Given that the nuclear receptor AF-1 is involved in cofactor recruitment and transcriptional regulation, the microdomain structures identified in the isoform-specific A/B domains might function as signature motifs and/or as targets for cofactor proteins that play essential roles in the EcR isoform-specific AF-1 regions. Moreover, the novel microdomain in the isoform-specific region of the holometabolous insect EcR-B1 isoform suggests that the holometabolous insect EcR-B1 acquired additional transcriptional

Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis.

Science.gov (United States)

Komiya, Dai; Hori, Akane; Ishida, Takuya; Igarashi, Kiyohiko; Samejima, Masahiro; Koseki, Takuya; Fushinobu, Shinya

2017-10-15

Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from Aspergillus luchuensis ( Al AXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family. Al AXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from Aspergillus niger indicated that Al AXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of A lAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan. IMPORTANCE Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of

On the specification of structural equation models for ecological systems

Science.gov (United States)

Grace, J.B.; Michael, Anderson T.; Han, O.; Scheiner, S.M.

2010-01-01

The use of structural equation modeling (SEM) is often motivated by its utility for investigating complex networks of relationships, but also because of its promise as a means of representing theoretical concepts using latent variables. In this paper, we discuss characteristics of ecological theory and some of the challenges for proper specification of theoretical ideas in structural equation models (SE models). In our presentation, we describe some of the requirements for classical latent variable models in which observed variables (indicators) are interpreted as the effects of underlying causes. We also describe alternative model specifications in which indicators are interpreted as having causal influences on the theoretical concepts. We suggest that this latter nonclassical specification (which involves another variable type-the composite) will often be appropriate for ecological studies because of the multifaceted nature of our theoretical concepts. In this paper, we employ the use of meta-models to aid the translation of theory into SE models and also to facilitate our ability to relate results back to our theories. We demonstrate our approach by showing how a synthetic theory of grassland biodiversity can be evaluated using SEM and data from a coastal grassland. In this example, the theory focuses on the responses of species richness to abiotic stress and disturbance, both directly and through intervening effects on community biomass. Models examined include both those based on classical forms (where each concept is represented using a single latent variable) and also ones in which the concepts are recognized to be multifaceted and modeled as such. To address the challenge of matching SE models with the conceptual level of our theory, two approaches are illustrated, compositing and aggregation. Both approaches are shown to have merits, with the former being preferable for cases where the multiple facets of a concept have widely differing effects in the

Structure and genetics of the O-specific polysaccharide of Escherichia coli O27.

Science.gov (United States)

Perepelov, Andrei V; Chen, Tingting; Senchenkova, Sofya N; Filatov, Andrei V; Song, Jingjie; Shashkov, Alexander S; Liu, Bin; Knirel, Yuriy A

2018-02-01

The O-specific polysaccharide (O-antigen) is a part of the lipopolysaccharide on the cell surface of Gram-negative bacteria. The O-polysaccharide was obtained by mild acid hydrolysis of the lipopolysaccharide of Escherichia coli O27 and studied by sugar analysis and Smith degradation along with 1 H and 13 C NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established, which is unique among known structures of bacterial polysaccharides:where GlcA is non-stoichiometrically O-acetylated at position 3 (∼22%) or 4 (∼37%). Functions of genes in the O-antigen gene cluster of E. coli O27 were tentatively assigned by comparison with sequences in the available databases and found to be consistent with the O-polysaccharide structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Mapping the MMPI-2-RF Specific Problems Scales Onto Extant Psychopathology Structures.

Science.gov (United States)

Sellbom, Martin

2017-01-01

A main objective in developing the Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF; Ben-Porath & Tellegen, 2008 ) was to link the hierarchical structure of the instrument's scales to contemporary psychopathology and personality models for greater enhancement of construct validity. Initial evidence published with the Restructured Clinical scales has indicated promising results in that the higher order structure of these measures maps onto those reported in the extant psychopathology literature. This study focused on evaluating the internal structure of the Specific Problems and Interest scales, which have not yet been examined in this manner. Two large, mixed-gender outpatient and correctional samples were used. Exploratory factor analyses revealed consistent evidence for a 4-factor structure representing somatization, negative affect, externalizing, and social detachment. Convergent and discriminant validity analyses in the outpatient sample yielded a pattern of results consistent with expectations. These findings add further evidence to indicate that the MMPI-2-RF hierarchy of scales map onto extant psychopathology literature, and also add support to the notion that somatization and detachment should be considered important higher order domains in the psychopathology literature.

Is recursion language-specific? Evidence of recursive mechanisms in the structure of intentional action.

Science.gov (United States)

Vicari, Giuseppe; Adenzato, Mauro

2014-05-01

In their 2002 seminal paper Hauser, Chomsky and Fitch hypothesize that recursion is the only human-specific and language-specific mechanism of the faculty of language. While debate focused primarily on the meaning of recursion in the hypothesis and on the human-specific and syntax-specific character of recursion, the present work focuses on the claim that recursion is language-specific. We argue that there are recursive structures in the domain of motor intentionality by way of extending John R. Searle's analysis of intentional action. We then discuss evidence from cognitive science and neuroscience supporting the claim that motor-intentional recursion is language-independent and suggest some explanatory hypotheses: (1) linguistic recursion is embodied in sensory-motor processing; (2) linguistic and motor-intentional recursions are distinct and mutually independent mechanisms. Finally, we propose some reflections about the epistemic status of HCF as presenting an empirically falsifiable hypothesis, and on the possibility of testing recursion in different cognitive domains. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural basis for type VI secreted peptidoglycan dl-endopeptidase function, specificity and neutralization in Serratia marcescens

Energy Technology Data Exchange (ETDEWEB)

Srikannathasan, Velupillai; English, Grant [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Bui, Nhat Khai [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Trunk, Katharina; O’Rourke, Patrick E. F.; Rao, Vincenzo A. [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom); Vollmer, Waldemar [Newcastle University, Newcastle upon Tyne NE2 4HH (United Kingdom); Coulthurst, Sarah J., E-mail: s.j.coulthurst@dundee.ac.uk; Hunter, William N., E-mail: s.j.coulthurst@dundee.ac.uk [University of Dundee, Dundee DD1 5EH, Scotland (United Kingdom)

2013-12-01

Crystal structures of type VI secretion system-associated immunity proteins, a peptidoglycan endopeptidase and a complex of the endopeptidase and its cognate immunity protein are reported together with assays of endopeptidase activity and functional assessment. Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endopeptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between γ-d-glutamic acid and l-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muropeptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure–activity relationships of Ssp1 and, by comparison, of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1–Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2–Rap2

Structural basis for type VI secreted peptidoglycan dl-endopeptidase function, specificity and neutralization in Serratia marcescens

International Nuclear Information System (INIS)

Srikannathasan, Velupillai; English, Grant; Bui, Nhat Khai; Trunk, Katharina; O’Rourke, Patrick E. F.; Rao, Vincenzo A.; Vollmer, Waldemar; Coulthurst, Sarah J.; Hunter, William N.

2013-01-01

Crystal structures of type VI secretion system-associated immunity proteins, a peptidoglycan endopeptidase and a complex of the endopeptidase and its cognate immunity protein are reported together with assays of endopeptidase activity and functional assessment. Some Gram-negative bacteria target their competitors by exploiting the type VI secretion system to extrude toxic effector proteins. To prevent self-harm, these bacteria also produce highly specific immunity proteins that neutralize these antagonistic effectors. Here, the peptidoglycan endopeptidase specificity of two type VI secretion-system-associated effectors from Serratia marcescens is characterized. These small secreted proteins, Ssp1 and Ssp2, cleave between γ-d-glutamic acid and l-meso-diaminopimelic acid with different specificities. Ssp2 degrades the acceptor part of cross-linked tetratetrapeptides. Ssp1 displays greater promiscuity and cleaves monomeric tripeptides, tetrapeptides and pentapeptides and dimeric tetratetra and tetrapenta muropeptides on both the acceptor and donor strands. Functional assays confirm the identity of a catalytic cysteine in these endopeptidases and crystal structures provide information on the structure–activity relationships of Ssp1 and, by comparison, of related effectors. Functional assays also reveal that neutralization of these effectors by their cognate immunity proteins, which are called resistance-associated proteins (Raps), contributes an essential role to cell fitness. The structures of two immunity proteins, Rap1a and Rap2a, responsible for the neutralization of Ssp1 and Ssp2-like endopeptidases, respectively, revealed two distinct folds, with that of Rap1a not having previously been observed. The structure of the Ssp1–Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. A highly effective steric block of the Ssp1 active site forms the basis of effector neutralization. Comparisons with Ssp2–Rap2

Interleukin-11 binds specific EF-hand proteins via their conserved structural motifs.

Science.gov (United States)

Kazakov, Alexei S; Sokolov, Andrei S; Vologzhannikova, Alisa A; Permyakova, Maria E; Khorn, Polina A; Ismailov, Ramis G; Denessiouk, Konstantin A; Denesyuk, Alexander I; Rastrygina, Victoria A; Baksheeva, Viktoriia E; Zernii, Evgeni Yu; Zinchenko, Dmitry V; Glazatov, Vladimir V; Uversky, Vladimir N; Mirzabekov, Tajib A; Permyakov, Eugene A; Permyakov, Sergei E

2017-01-01

Interleukin-11 (IL-11) is a hematopoietic cytokine engaged in numerous biological processes and validated as a target for treatment of various cancers. IL-11 contains intrinsically disordered regions that might recognize multiple targets. Recently we found that aside from IL-11RA and gp130 receptors, IL-11 interacts with calcium sensor protein S100P. Strict calcium dependence of this interaction suggests a possibility of IL-11 interaction with other calcium sensor proteins. Here we probed specificity of IL-11 to calcium-binding proteins of various types: calcium sensors of the EF-hand family (calmodulin, S100B and neuronal calcium sensors: recoverin, NCS-1, GCAP-1, GCAP-2), calcium buffers of the EF-hand family (S100G, oncomodulin), and a non-EF-hand calcium buffer (α-lactalbumin). A specific subset of the calcium sensor proteins (calmodulin, S100B, NCS-1, GCAP-1/2) exhibits metal-dependent binding of IL-11 with dissociation constants of 1-19 μM. These proteins share several amino acid residues belonging to conservative structural motifs of the EF-hand proteins, 'black' and 'gray' clusters. Replacements of the respective S100P residues by alanine drastically decrease its affinity to IL-11, suggesting their involvement into the association process. Secondary structure and accessibility of the hinge region of the EF-hand proteins studied are predicted to control specificity and selectivity of their binding to IL-11. The IL-11 interaction with the EF-hand proteins is expected to occur under numerous pathological conditions, accompanied by disintegration of plasma membrane and efflux of cellular components into the extracellular milieu.

Specificities of micro-structured reactors for hydrogen production and purification

Energy Technology Data Exchange (ETDEWEB)

Dupont, N.; Germani, G.; Van Veen, A.C.; Schuurman, Y.; Mirodatos, C. [Institut de Recherches sur la Catalyse - CNRS, 2, Avenue Albert Einstein, 69626 Villeurbanne Cedex (France); Schaefer, G. [Atotech Deutschland GmbH, PO Box 210780, 10507 Berlin (Germany)

2007-07-15

This paper presents the specificities of micro-structured reactors as compared to conventional fixed-bed reactors through two case studies devoted to (i) hydrogen production by methanol steam reforming, (ii) hydrogen purification by water-gas shift (WGS). Key features like catalyst coating stability, temperature and pressure management, effects of operating conditions (residence time, pressure drops, etc.) are well identified as controlling the micro-reactor performances for methanol reforming. These devices are also shown to be excellent tools for fast access to reaction kinetics as exemplified for the WGS reaction, subject to operating conditions carefully chosen to ensure proper hydrodynamics, in order to use conventional plug flow reactor models for extracting rate constants. (author)

Testing Fiscal Dominance Hypothesis in a Structural VAR Specification for Pakistan

Directory of Open Access Journals (Sweden)

Shaheen Rozina

2018-03-01

Full Text Available This research aims to test the fiscal dominance hypothesis for Pakistan through a bivariate structural vector auto regression (SVAR specification, covering time period 1977 – 2016. This study employs real primary deficit (non interest government expenditures minus total revenues and real primary liabilities (sum of monetary base and domestic public debt as indicators of fiscal measures and monetary policy respectively. A structural VAR is retrieved both for entire sample period and four sub periods (1977 – 1986, 1987 – 1997, 1998 – 2008, and 2009 – 2016. This study identifies the presence of fiscal dominance for the entire sample period and the sub period from 1987 – 2008. The estimates reveal an interesting phenomenon that fiscal dominance is significant in the elected regimes and weaker in the presence of military regimes in Pakistan. From a policy perspective, this research suggests increased autonomy of central bank to achieve long term price stability and reduced administration costs to ensure efficient democratic regime in Pakistan.

Understanding the mechanism of nanotube synthesis for controlled production of specific (n,m) structures

Energy Technology Data Exchange (ETDEWEB)

Resasco, Daniel E.

2010-02-11

This report shows the extensive research on the mechanism responsible for the formation of single walled carbon nanotubes in order to get control over their structural parameters (diameter and chirality). Catalyst formulations, pre-treatment conditions, and reaction conditions are described in detail as well as mechanisms to produce nanotubes structures of specific arrays (vertical forest, nanotube pillars). Applications of SWNT in different fields are also described in this report. In relation to this project five students have graduated (3 PhD and 2 MS) and 35 papers have been published.

Structural Differences between the Streptococcus agalactiae Housekeeping and Pilus-Specific Sortases: SrtA and SrtC1

Energy Technology Data Exchange (ETDEWEB)

Khare, B.; Krishnan, V.; Rajashankar, K.R.; I-Hsiu, H.; Xin, M.; Ton-That, H.; Narayana, S.V. (Texas-HSC); (Cornell); (UAB)

2011-10-21

The assembly of pili on the cell wall of Gram-positive bacteria requires transpeptidase enzymes called sortases. In Streptococcus agalactiae, the PI-1 pilus island of strain 2603V/R encodes two pilus-specific sortases (SrtC1 and SrtC2) and three pilins (GBS80, GBS52 and GBS104). Although either pilus-specific sortase is sufficient for the polymerization of the major pilin, GBS80, incorporation of the minor pilins GBS52 and GBS104 into the pilus structure requires SrtC1 and SrtC2, respectively. The S. agalactiae housekeeping sortase, SrtA, whose gene is present at a different location and does not catalyze pilus polymerization, was shown to be involved in cell wall anchoring of pilus polymers. To understand the structural basis of sortases involved in such diverse functions, we determined the crystal structures of S. agalactiae SrtC1 and SrtA. Both enzymes are made of an eight-stranded beta-barrel core with variations in their active site architecture. SrtA exhibits a catalytic triad arrangement similar to that in Streptococcus pyogenes SrtA but different from that in Staphylococcus aureus SrtA. In contrast, the SrtC1 enzyme contains an N-terminal helical domain and a 'lid' in its putative active site, which is similar to that seen in Streptococcus pneumoniae pilus-specific sortases, although with subtle differences in positioning and composition. To understand the effect of such differences on substrate recognition, we have also determined the crystal structure of a SrtC1 mutant, in which the conserved DP(W/F/Y) motif was replaced with the sorting signal motif of GBS80, IPNTG. By comparing the structures of WT wild type SrtA and SrtC1 and the 'lid' mutant of SrtC1, we propose that structural elements within the active site and the lid may be important for defining the role of specific sortase in pili biogenesis.

Structural differences between the Streptococcus agalactiae housekeeping and pilus-specific sortases: SrtA and SrtC1.

Directory of Open Access Journals (Sweden)

B Khare

Full Text Available The assembly of pili on the cell wall of Gram-positive bacteria requires transpeptidase enzymes called sortases. In Streptococcus agalactiae, the PI-1 pilus island of strain 2603V/R encodes two pilus-specific sortases (SrtC1 and SrtC2 and three pilins (GBS80, GBS52 and GBS104. Although either pilus-specific sortase is sufficient for the polymerization of the major pilin, GBS80, incorporation of the minor pilins GBS52 and GBS104 into the pilus structure requires SrtC1 and SrtC2, respectively. The S. agalactiae housekeeping sortase, SrtA, whose gene is present at a different location and does not catalyze pilus polymerization, was shown to be involved in cell wall anchoring of pilus polymers. To understand the structural basis of sortases involved in such diverse functions, we determined the crystal structures of S. agalactiae SrtC1 and SrtA. Both enzymes are made of an eight-stranded beta-barrel core with variations in their active site architecture. SrtA exhibits a catalytic triad arrangement similar to that in Streptococcus pyogenes SrtA but different from that in Staphylococcus aureus SrtA. In contrast, the SrtC1 enzyme contains an N-terminal helical domain and a 'lid' in its putative active site, which is similar to that seen in Streptococcus pneumoniae pilus-specific sortases, although with subtle differences in positioning and composition. To understand the effect of such differences on substrate recognition, we have also determined the crystal structure of a SrtC1 mutant, in which the conserved DP(W/F/Y motif was replaced with the sorting signal motif of GBS80, IPNTG. By comparing the structures of WT wild type SrtA and SrtC1 and the 'lid' mutant of SrtC1, we propose that structural elements within the active site and the lid may be important for defining the role of specific sortase in pili biogenesis.

Crystal structure of inulosucrase from Lactobacillus: insights into the substrate specificity and product specificity of GH68 fructansucrases.

Science.gov (United States)

Pijning, Tjaard; Anwar, Munir A; Böger, Markus; Dobruchowska, Justyna M; Leemhuis, Hans; Kralj, Slavko; Dijkhuizen, Lubbert; Dijkstra, Bauke W

2011-09-09

Fructansucrases (FSs) catalyze a transfructosylation reaction with sucrose as substrate to produce fructo-oligosaccharides and fructan polymers that contain either β-2,1 glycosidic linkages (inulin) or β-2,6 linkages (levan). Levan-synthesizing FSs (levansucrases) have been most extensively investigated, while detailed information on inulosucrases is limited. Importantly, the molecular basis of the different product specificities of levansucrases and inulosucrases is poorly understood. We have elucidated the three-dimensional structure of a truncated active bacterial GH68 inulosucrase, InuJ of Lactobacillus johnsonii NCC533 (residues 145-708), in its apo form, with a bound substrate (sucrose), and with a transfructosylation product. The sucrose binding pocket and the sucrose binding mode are virtually identical with those of GH68 levansucrases, confirming that both enzyme types use the same fully conserved structural framework for the binding and cleavage of the donor substrate sucrose in the active site. The binding mode of the first transfructosylation product 1-kestose (Fru-β(2-1)-Fru-α(2-1)-Glc, where Fru=fructose and Glc=glucose) in subsites -1 to +2 shows for the first time how inulin-type fructo-oligosaccharide bind in GH68 FS and how an inulin-type linkage can be formed. Surprisingly, observed interactions with the sugar in subsites +1 and +2 are provided by residues that are also present in levansucrases. The binding mode of 1-kestose and the presence of a more distant sucrose binding site suggest that residues beyond the +2 subsite, in particular residues from the nonconserved 1B-1C loop, determine product linkage type specificity in GH68 FSs. Copyright © 2011 Elsevier Ltd. All rights reserved.

Sensory memory of structure-from-motion is shape-specific.

Science.gov (United States)

Pastukhov, Alexander; Füllekrug, Jana; Braun, Jochen

2013-08-01

Perceptual priming can stabilize the phenomenal appearance of multistable visual displays (Leopold, Wilke, Maier, & Logothetis, Nature Neuroscience, 5, 605-609, 2002). Prior exposure to such displays induces a sensory memory of their appearance, which persists over long intervals and intervening stimulation, and which facilitates renewed perception of the same appearance. Here, we investigated perceptual priming for the apparent rotation in depth of ambiguous structure-from-motion (SFM) displays. Specifically, we generated SFM objects with different three-dimensional shapes and presented them in random order and with intervening blank periods. To assess perceptual priming, we established the probability that a perceived direction of rotation would persist between successive objects. In general, persistence was greatest between identical objects, intermediate between similar objects, and negligible between dissimilar objects. These results demonstrate unequivocally that sensory memory for apparent rotation is specific to three-dimensional shape, contrary to previous reports (e.g., Maier, Wilke, Logothetis, & Leopold, Current Biology, 13, 1076-1085, 2003). Because persistence did not depend on presentation order for any pair of objects, it provides a commutative measure for the similarity of object shapes. However, it is not clear exactly which features or aspects of object shape determine similarity. At least, we did not find simple, low-level features (such as volume overlap, heterogeneity, or rotational symmetry) that could have accounted for all observations. Accordingly, it seems that sensory memory of SFM (which underlies priming of ambiguous rotation) engages higher-level representations of object surface and shape.

Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Science.gov (United States)

Vacchi-Suzzi, Caterina; Hahne, Florian; Scheubel, Philippe; Marcellin, Magali; Dubost, Valerie; Westphal, Magdalena; Boeglen, Catherine; Büchmann-Møller, Stine; Cheung, Ming Sin; Cordier, André; De Benedetto, Christopher; Deurinck, Mark; Frei, Moritz; Moulin, Pierre; Oakeley, Edward; Grenet, Olivier; Grevot, Armelle; Stull, Robert; Theil, Diethilde; Moggs, Jonathan G; Marrer, Estelle; Couttet, Philippe

2013-01-01

MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves) in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744) and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*). The relative abundance of myocardium-enriched (miR-1) and valve-enriched (miR-125b-5p and miR-204) microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

Heart structure-specific transcriptomic atlas reveals conserved microRNA-mRNA interactions.

Directory of Open Access Journals (Sweden)

Caterina Vacchi-Suzzi

Full Text Available MicroRNAs are short non-coding RNAs that regulate gene expression at the post-transcriptional level and play key roles in heart development and cardiovascular diseases. Here, we have characterized the expression and distribution of microRNAs across eight cardiac structures (left and right ventricles, apex, papillary muscle, septum, left and right atrium and valves in rat, Beagle dog and cynomolgus monkey using microRNA sequencing. Conserved microRNA signatures enriched in specific heart structures across these species were identified for cardiac valve (miR-let-7c, miR-125b, miR-127, miR-199a-3p, miR-204, miR-320, miR-99b, miR-328 and miR-744 and myocardium (miR-1, miR-133b, miR-133a, miR-208b, miR-30e, miR-499-5p, miR-30e*. The relative abundance of myocardium-enriched (miR-1 and valve-enriched (miR-125b-5p and miR-204 microRNAs was confirmed using in situ hybridization. MicroRNA-mRNA interactions potentially relevant for cardiac functions were explored using anti-correlation expression analysis and microRNA target prediction algorithms. Interactions between miR-1/Timp3, miR-125b/Rbm24, miR-204/Tgfbr2 and miR-208b/Csnk2a2 were identified and experimentally investigated in human pulmonary smooth muscle cells and luciferase reporter assays. In conclusion, we have generated a high-resolution heart structure-specific mRNA/microRNA expression atlas for three mammalian species that provides a novel resource for investigating novel microRNA regulatory circuits involved in cardiac molecular physiopathology.

Universal and Language-Specific Patterns in the Acquisition of Verb Argument Structures in German

Science.gov (United States)

Leischner, Franziska N.; Weissenborn, Jürgen; Naigles, Letitia R.

2016-01-01

The study investigated the influence of universal and language-specific morpho-syntactic properties (i.e., flexible word order, case) on the acquisition of verb argument structures in German compared with English. To this end, 65 three- to nine-year-old German learning children and adults were asked to act out grammatical ("The sheep…

Electronic Health Record in Occupational Medicine: Specific Aspects and Requirements of Data Structuring and Standardization

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Dorin TRIFF

2009-07-01

Full Text Available The service of occupational medicine of a specific economic agent, as integrated part of the System of Labor Health and Safety, requires efficient, well-organized information management through standardized and computerized data processing and exploitation. Legal requirements and practical aspects of information management in occupational medicine trigger necessary operational modifications in the Electronic Health File. The goal of the paper is to present basic requirements of structuring the electronic health file and the necessary standards in recording specific data.

Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family.

Science.gov (United States)

Xu, Qingping; Mengin-Lecreulx, Dominique; Patin, Delphine; Grant, Joanna C; Chiu, Hsiu-Ju; Jaroszewski, Lukasz; Knuth, Mark W; Godzik, Adam; Lesley, Scott A; Elsliger, Marc-André; Deacon, Ashley M; Wilson, Ian A

2014-12-02

GlcNAc-1,6-anhydro-MurNAc-tetrapeptide is a major peptidoglycan degradation intermediate and a cytotoxin. It is generated by lytic transglycosylases and further degraded and recycled by various enzymes. We have identified and characterized a highly specific N-acetylmuramoyl-L-alanine amidase (AmiA) from Bacteroides uniformis, a member of the DUF1460 protein family, that hydrolyzes GlcNAc-1,6-anhydro-MurNAc-peptide into disaccharide and stem peptide. The high-resolution apo structure at 1.15 Å resolution shows that AmiA is related to NlpC/P60 γ-D-Glu-meso-diaminopimelic acid amidases and shares a common catalytic core and cysteine peptidase-like active site. AmiA has evolved structural adaptations that reconfigure the substrate recognition site. The preferred substrates for AmiA were predicted in silico based on structural and bioinformatics data, and subsequently were characterized experimentally. Further crystal structures of AmiA in complexes with GlcNAc-1,6-anhydro-MurNAc and GlcNAc have enabled us to elucidate substrate recognition and specificity. DUF1460 is highly conserved in structure and defines another amidase family. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of cocoa butter triacylglycerides and minor compounds on oil migration.

Science.gov (United States)

Wang, Hao; Maleky, Farnaz

2018-04-01

In a multi-component chocolate product, oil migration, from high oil content filling into chocolate, is one of the major contributors to the product quality loss. Among various parameters influencing oil diffusivity, cocoa butter is studied intensively. Studies have shown that the rate of oil transportion in cocoa butter is affected by its composition, the way that it is crystallized, and also the storage conditions. To model and study effects of cocoa butter type and processing conditions on oil migration, five different cocoa butter samples were studied in this work. Samples' chemical compositions in addition to their structural properties were analyzed to understand and compare oil migrations in the networks. Crystallized cocoa butter samples were placed in contact with a cream as a source of liquid oil. Using Magnetic Resonance Imaging, the movement of liquid oil into samples was investigated. The effects of minor differences in the cocoa butter chemical compositions on oil migrations rate are shown clearly. The highest effective diffusion coefficient was observed in the sample with the higher unsaturated fatty acids and phospholipids content. Although shearing at 250s -1 delayed oil migration in all the samples and a significantly lower diffusion coefficient was observed in the dynamic samples, the effects of chemical composition were still dominant. This study successfully highlighted that even minor differences in cocoa butter composition affect the network mass transfer phenomenon dramatically and that it is not easy to diminish these possessions by just crystallization processes. Published by Elsevier Ltd.

Mitochondrial DNA paradox: sex-specific genetic structure in a marine mussel – despite maternal inheritance and passive dispersal

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Teske Peter R

2012-06-01

Full Text Available Abstract Background When genetic structure is identified using mitochondrial DNA (mtDNA, but no structure is identified using biparentally-inherited nuclear DNA, the discordance is often attributed to differences in dispersal potential between the sexes. Results We sampled the intertidal rocky shore mussel Perna perna in a South African bay and along the nearby open coast, and sequenced maternally-inherited mtDNA (there is no evidence for paternally-inherited mtDNA in this species and a biparentally-inherited marker. By treating males and females as different populations, we identified significant genetic structure on the basis of mtDNA data in the females only. Conclusions This is the first study to report sex-specific differences in genetic structure based on matrilineally-inherited mtDNA in a passively dispersing species that lacks social structure or sexual dimorphism. The observed pattern most likely stems from females being more vulnerable to selection in habitats from which they did not originate, which also manifests itself in a male-biased sex ratio. Our results have three important implications for the interpretation of population genetic data. First, even when mtDNA is inherited exclusively in the female line, it also contains information about males. For that reason, using it to identify sex-specific differences in genetic structure by contrasting it with biparentally-inherited markers is problematic. Second, the fact that sex-specific differences were found in a passively dispersing species in which sex-biased dispersal is unlikely highlights the fact that significant genetic structure is not necessarily a function of low dispersal potential or physical barriers. Third, even though mtDNA is typically used to study historical demographic processes, it also contains information about contemporary processes. Higher survival rates of males in non-native habitats can erase the genetic structure present in their mothers within a single

First applications of structural pattern recognition methods to the investigation of specific physical phenomena at JET

International Nuclear Information System (INIS)

Ratta, G.A.; Vega, J.; Pereira, A.; Portas, A.; Luna, E. de la; Dormido-Canto, S.; Farias, G.; Dormido, R.; Sanchez, J.; Duro, N.; Vargas, H.; Santos, M.; Pajares, G.; Murari, A.

2008-01-01

Structural pattern recognition techniques allow the identification of plasma behaviours. Physical properties are encoded in the morphological structure of signals. Intelligent access methods have been applied to JET databases to retrieve data according to physical criteria. On the one hand, the structural form of signals has been used to develop general purpose data retrieval systems to search for both similar entire waveforms and similar structural shapes inside waveforms. On the other hand, domain dependent knowledge was added to the structural information of signals to create particular data retrieval methods for specific physical phenomena. The inclusion of explicit knowledge assists in data analysis. The latter has been applied in JET to look for first, cut-offs in ECE heterodyne radiometer signals and, second, L-H transitions

First applications of structural pattern recognition methods to the investigation of specific physical phenomena at JET

Energy Technology Data Exchange (ETDEWEB)

Ratta, G.A. [Asociacion EURATOM/CIEMAT para Fusion (Spain)], E-mail: giuseppe.ratta@ciemat.es; Vega, J.; Pereira, A.; Portas, A.; Luna, E. de la [Asociacion EURATOM/CIEMAT para Fusion (Spain); Dormido-Canto, S.; Farias, G.; Dormido, R.; Sanchez, J.; Duro, N.; Vargas, H. [Dpto. Informatica y Automatica-UNED, 28040 Madrid (Spain); Santos, M.; Pajares, G. [Dpto. Arquitectura de Computadores y Automatica-UCM, 28040 Madrid (Spain); Murari, A. [Consorzio RFX-Associazione EURATOM ENEA per la Fusione, Padua (Italy)

2008-04-15

Structural pattern recognition techniques allow the identification of plasma behaviours. Physical properties are encoded in the morphological structure of signals. Intelligent access methods have been applied to JET databases to retrieve data according to physical criteria. On the one hand, the structural form of signals has been used to develop general purpose data retrieval systems to search for both similar entire waveforms and similar structural shapes inside waveforms. On the other hand, domain dependent knowledge was added to the structural information of signals to create particular data retrieval methods for specific physical phenomena. The inclusion of explicit knowledge assists in data analysis. The latter has been applied in JET to look for first, cut-offs in ECE heterodyne radiometer signals and, second, L-H transitions.

Specific chemical and structural damage to proteins produced by synchrotron radiation.

Science.gov (United States)

Weik, M; Ravelli, R B; Kryger, G; McSweeney, S; Raves, M L; Harel, M; Gros, P; Silman, I; Kroon, J; Sussman, J L

2000-01-18

Radiation damage is an inherent problem in x-ray crystallography. It usually is presumed to be nonspecific and manifested as a gradual decay in the overall quality of data obtained for a given crystal as data collection proceeds. Based on third-generation synchrotron x-ray data, collected at cryogenic temperatures, we show for the enzymes Torpedo californica acetylcholinesterase and hen egg white lysozyme that synchrotron radiation also can cause highly specific damage. Disulfide bridges break, and carboxyl groups of acidic residues lose their definition. Highly exposed carboxyls, and those in the active site of both enzymes, appear particularly susceptible. The catalytic triad residue, His-440, in acetylcholinesterase, also appears to be much more sensitive to radiation damage than other histidine residues. Our findings have direct practical implications for routine x-ray data collection at high-energy synchrotron sources. Furthermore, they provide a direct approach for studying the radiation chemistry of proteins and nucleic acids at a detailed, structural level and also may yield information concerning putative "weak links" in a given biological macromolecule, which may be of structural and functional significance.

Crystal Structure and Substrate Specificity of Drosophila 3,4-Dihydroxyphenylalanine Decarboxylase

Energy Technology Data Exchange (ETDEWEB)

Han, Q.; Ding, H; Robinson, H; Christensen, B; Li, J

2010-01-01

3,4-Dihydroxyphenylalanine decarboxylase (DDC), also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses. In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82 and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine. The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.

Preschool externalizing behavior predicts gender-specific variation in adolescent neural structure.

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Jessica Z K Caldwell

Full Text Available Dysfunction in the prefrontal cortex, amygdala, and hippocampus is believed to underlie the development of much psychopathology. However, to date only limited longitudinal data relate early behavior with neural structure later in life. Our objective was to examine the relationship of early life externalizing behavior with adolescent brain structure. We report here the first longitudinal study linking externalizing behavior during preschool to brain structure during adolescence. We examined the relationship of preschool externalizing behavior with amygdala, hippocampus, and prefrontal cortex volumes at age 15 years in a community sample of 76 adolescents followed longitudinally since their mothers' pregnancy. A significant gender by externalizing behavior interaction revealed that males-but not females-with greater early childhood externalizing behavior had smaller amygdala volumes at adolescence (t = 2.33, p = .023. No significant results were found for the hippocampus or the prefrontal cortex. Greater early externalizing behavior also related to smaller volume of a cluster including the angular gyrus and tempoparietal junction across genders. Results were not attributable to the impact of preschool anxiety, preschool maternal stress, school-age internalizing or externalizing behaviors, or adolescent substance use. These findings demonstrate a novel, gender-specific relationship between early-childhood externalizing behavior and adolescent amygdala volume, as well as a cross-gender result for the angular gyrus and tempoparietal junction.

Structural and functional plasticity specific to musical training with wind instruments

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Uk-Su eChoi

2015-10-01

Full Text Available Numerous neuroimaging studies have shown structural and functional changes resulting from musical training. Among these studies, changes in primary sensory areas are mostly related to motor functions. In this study, we looked for some similar functional and structural changes in other functional modalities, such as somatosensory function, by examining the effects of musical training with wind instruments. We found significant changes in two aspects of neuroplasticity, cortical thickness and resting-state neuronal networks. A group of subjects with several years of continuous musical training and who are currently playing in university wind ensembles showed differences in cortical thickness in lip- and tongue-related brain areas versus non-music playing subjects. Cortical thickness in lip-related brain areas was significantly thicker and that in tongue-related areas was significantly thinner in the music playing group compared with that in the non-music playing group. Association analysis of lip-related areas in the music playing group showed that the increase in cortical thickness was caused by musical training. In addition, seed-based correlation analysis showed differential activation in the precentral gyrus and supplementary motor areas between the music and non-music playing groups. These results suggest that high-intensity training with specific musical instruments could induce structural changes in related anatomical areas and could also generate a new functional neuronal network in the brain.

Crystal structure and substrate specificity of Drosophila 3,4-dihydroxyphenylalanine decarboxylase.

Directory of Open Access Journals (Sweden)

Qian Han

2010-01-01

Full Text Available 3,4-Dihydroxyphenylalanine decarboxylase (DDC, also known as aromatic L-amino acid decarboxylase, catalyzes the decarboxylation of a number of aromatic L-amino acids. Physiologically, DDC is responsible for the production of dopamine and serotonin through the decarboxylation of 3,4-dihydroxyphenylalanine and 5-hydroxytryptophan, respectively. In insects, both dopamine and serotonin serve as classical neurotransmitters, neuromodulators, or neurohormones, and dopamine is also involved in insect cuticle formation, eggshell hardening, and immune responses.In this study, we expressed a typical DDC enzyme from Drosophila melanogaster, critically analyzed its substrate specificity and biochemical properties, determined its crystal structure at 1.75 Angstrom resolution, and evaluated the roles residues T82 and H192 play in substrate binding and enzyme catalysis through site-directed mutagenesis of the enzyme. Our results establish that this DDC functions exclusively on the production of dopamine and serotonin, with no activity to tyrosine or tryptophan and catalyzes the formation of serotonin more efficiently than dopamine.The crystal structure of Drosophila DDC and the site-directed mutagenesis study of the enzyme demonstrate that T82 is involved in substrate binding and that H192 is used not only for substrate interaction, but for cofactor binding of drDDC as well. Through comparative analysis, the results also provide insight into the structure-function relationship of other insect DDC-like proteins.

Changes in cell surface structure by viral transformation studied by binding of lectins differing in sugar specificity.

Science.gov (United States)

Tsuda, M; Kurokawa, T; Takeuchi, M; Sugino, Y

1975-10-01

Changes in cell surface structure by viral transformation were studied by examining changes in the binding of various lectins differing in carbohydrate specificities. Binding of lectins was assayed directly using cells grown in coverslips. The following 125I-lectins were used: Concanavalin-A (specific for glucose and mannose), wheat germ agglutinin (specific for N-acetylglucosamine), castor bean agglutinin (specific for galactose), Wistaria floribunda agglutinin (specific for N-acetylgalactosamine), and soybean agglutinin (specific for N-acetyl-galactosamine). Cells for a clone, SS7, transformed by bovine adenovirus type-3, were found to bind 5 to 6 times more Wistaria floribunda agglutinin than the normal counterpart cells (clone C31, from C3H mouse kidney). In contrast, the binding of soybean agglutinin, which has a sugar specificity similar to Wistaria floribunda agglutinin, to normal and transformed cells was similar. The binding of wheat germ agglutinin and castor bean agglutinin, respectively, to normal and transformed cells was also similar. However, normal cells bound twice as much concanavalin-A as transformed cells. Only half as much Wistaria floribunda agglutinin was bound to transformed cells when they had been dispersed with EDTA. These changes in the number of lectin binding sites on transformation are thought to reflect alteration of the cell surface structure. The amount of lectins bound per cell decreased with increase in cell density, especially in the case of binding of Wistaria floribunda agglutinin to normal cells.

Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

Science.gov (United States)

Dos Santos, Helena G; Siltberg-Liberles, Jessica

2016-09-19

One of the largest multigene families in Metazoa are the tyrosine kinases (TKs). These are important multifunctional proteins that have evolved as dynamic switches that perform tyrosine phosphorylation and other noncatalytic activities regulated by various allosteric mechanisms. TKs interact with each other and with other molecules, ultimately activating and inhibiting different signaling pathways. TKs are implicated in cancer and almost 30 FDA-approved TK inhibitors are available. However, specific binding is a challenge when targeting an active site that has been conserved in multiple protein paralogs for millions of years. A cassette domain (CD) containing SH3-SH2-Tyrosine Kinase domains reoccurs in vertebrate nonreceptor TKs. Although part of the CD function is shared between TKs, it also presents TK specific features. Here, the evolutionary dynamics of sequence, structure, and phosphorylation across the CD in 17 TK paralogs have been investigated in a large-scale study. We establish that TKs often have ortholog-specific structural disorder and phosphorylation patterns, while secondary structure elements, as expected, are highly conserved. Further, domain-specific differences are at play. Notably, we found the catalytic domain to fluctuate more in certain secondary structure elements than the regulatory domains. By elucidating how different properties evolve after gene duplications and which properties are specifically conserved within orthologs, the mechanistic understanding of protein evolution is enriched and regions supposedly critical for functional divergence across paralogs are highlighted. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Rapid discovery of peptide capture candidates with demonstrated specificity for structurally similar toxins

Science.gov (United States)

Sarkes, Deborah A.; Hurley, Margaret M.; Coppock, Matthew B.; Farrell, Mikella E.; Pellegrino, Paul M.; Stratis-Cullum, Dimitra N.

2016-05-01

Peptides have emerged as viable alternatives to antibodies for molecular-based sensing due to their similarity in recognition ability despite their relative structural simplicity. Various methods for peptide capture reagent discovery exist, including phage display, yeast display, and bacterial display. One of the primary advantages of peptide discovery by bacterial display technology is the speed to candidate peptide capture agent, due to both rapid growth of bacteria and direct utilization of the sorted cells displaying each individual peptide for the subsequent round of biopanning. We have previously isolated peptide affinity reagents towards protective antigen of Bacillus anthracis using a commercially available automated magnetic sorting platform with improved enrichment as compared to manual magnetic sorting. In this work, we focus on adapting our automated biopanning method to a more challenging sort, to demonstrate the specificity possible with peptide capture agents. This was achieved using non-toxic, recombinant variants of ricin and abrin, RiVax and abrax, respectively, which are structurally similar Type II ribosomal inactivating proteins with significant sequence homology. After only two rounds of biopanning, enrichment of peptide capture candidates binding abrax but not RiVax was achieved as demonstrated by Fluorescence Activated Cell Sorting (FACS) studies. Further sorting optimization included negative sorting against RiVax, proper selection of autoMACS programs for specific sorting rounds, and using freshly made buffer and freshly thawed protein target for each round of biopanning for continued enrichment over all four rounds. Most of the resulting candidates from biopanning for abrax binding peptides were able to bind abrax but not RiVax, demonstrating that short peptide sequences can be highly specific even at this early discovery stage.

Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation.

Science.gov (United States)

Kim, Kuglae; Cha, Jeong Seok; Cho, Yong-Soon; Kim, Hoyoung; Chang, Nienping; Kim, Hye-Jung; Cho, Hyun-Soo

2018-04-07

Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia. Copyright © 2018 Elsevier Ltd. All rights reserved.

Play in two societies: pervasiveness of process, specificity of structure.

Science.gov (United States)

Bornstein, M H; Haynes, O M; Pascual, L; Painter, K M; Galperín, C

1999-01-01

The present study compared Argentine (N = 39) and U.S. (N = 43) children and their mothers on exploratory, symbolic, and social play and interaction when children were 20 months of age. Patterns of cultural similarity and difference emerged. In both cultures, boys engaged in more exploratory play than girls, and girls engaged in more symbolic play than boys; mothers of boys engaged in more exploratory play than mothers of girls, and mothers of girls engaged in more symbolic play than mothers of boys. Moreover, in both cultures, individual variation in children's exploratory and symbolic play was specifically associated with individual variation in mothers' exploratory and symbolic play, respectively. Between cultures, U.S. children and their mothers engaged in more exploratory play, whereas Argentine children and their mothers engaged in more symbolic play. Moreover, Argentine mothers exceeded U.S. mothers in social play and verbal praise of their children. During an early period of mental and social growth, general developmental processes in play may be pervasive, but dyadic and cultural structures are apparently specific. Overall, Argentine and U.S. dyads utilized different modes of exploration, representation, and interaction--emphasizing "other-directed" acts of pretense versus "functional" and "combinatorial" exploration, for example--and these individual and dyadic allocentric versus idiocentric stresses accord with larger cultural concerns of collectivism versus individualism in the two societies.

Quantitative MR imaging of intra-orbital structures: Tissue-specific measurements and age dependency compared to extra-orbital structures using multispectral quantitative MR imaging.

Science.gov (United States)

Watanabe, Memi; Buch, Karen; Fujita, Akifumi; Jara, Hernán; Qureshi, Muhammad Mustafa; Sakai, Osamu

2017-08-01

The orbit can be affected by unique pathologic conditions and often requires MRI evaluation. The purpose of this study was to investigate the age-related changes in multiple intra-orbital structures using quantitative MRI (qMRI). Thirty-eight subjects (20 males, 18 females; ages 0.5-87 years) underwent MRI with a mixed turbo spin echo sequence. T1 and T2 measurements were obtained within ROI in 6 intra-orbital structures (medial and lateral rectus muscles, medial and lateral retrobulbar fat, lacrimal gland, and optic nerve), and compared with those of corresponding extra-orbital structures (masseter muscle, subcutaneous cheek fat, buccal fat, parotid gland, and frontal white matter). Statistical analyses were performed using Pearson's correlation coefficients. T1 and T2 values of the extra-ocular muscles increased with age, with higher T1 and T2 values compared to the masseter muscles. Retrobulbar fat showed significant age-associated increases in T1 values in the lateral side and in T2 values in both sides. T1 and T2 values in the lacrimal gland increased with age, while the parotid gland showed an age-associated increase in T2 values and decrease in T1 values. Optic nerves demonstrated age-related changes, similar to that of frontal white matter; rapid decreases with age in T1 and T2 times in early stages of life, and slight increases in T1 and T2 times later in life. Intra-orbital structures demonstrated specific qMRI measurements and aging patterns, which were different from extra-orbital structures. Location-specific age-related changes of intra-orbital structures should be considered in the qMRI assessment of the orbital pathology.

High Lipid Induction in Microalgae for Biodiesel Production

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Peer M. Schenk

2012-05-01

Full Text Available Oil-accumulating microalgae have the potential to enable large-scale biodiesel production without competing for arable land or biodiverse natural landscapes. High lipid productivity of dominant, fast-growing algae is a major prerequisite for commercial production of microalgal oil-derived biodiesel. However, under optimal growth conditions, large amounts of algal biomass are produced, but with relatively low lipid contents, while species with high lipid contents are typically slow growing. Major advances in this area can be made through the induction of lipid biosynthesis, e.g., by environmental stresses. Lipids, in the form of triacylglycerides typically provide a storage function in the cell that enables microalgae to endure adverse environmental conditions. Essentially algal biomass and triacylglycerides compete for photosynthetic assimilate and a reprogramming of physiological pathways is required to stimulate lipid biosynthesis. There has been a wide range of studies carried out to identify and develop efficient lipid induction techniques in microalgae such as nutrients stress (e.g., nitrogen and/or phosphorus starvation, osmotic stress, radiation, pH, temperature, heavy metals and other chemicals. In addition, several genetic strategies for increased triacylglycerides production and inducibility are currently being developed. In this review, we discuss the potential of lipid induction techniques in microalgae and also their application at commercial scale for the production of biodiesel.

The Structural Model of Spirituality and Psychological Well-Being for Pregnancy-Specific Stress.

Science.gov (United States)

Dolatian, Mahrokh; Mahmoodi, Zohreh; Dilgony, Taibeh; Shams, Jamal; Zaeri, Farid

2017-12-01

Women experience different types of stress in their lifetime. The present study was conducted to examine the structural model of spirituality and psychological well-being for pregnancy-specific stress. The present descriptive correlational study was conducted on 450 pregnant Iranian women (150 women from each trimester) in Dehdasht city in 2015. Data were collected using the personal-social questionnaire, the pregnancy-specific stress questionnaire, the spirituality questionnaire and the psychological well-being questionnaire and were then analyzed in SPSS-16 and Lisrel-8.8 for carrying out a path analysis. The fit indices of the model indicate the good fit and high compatibility of the model and rational relationships between the variables (GFI = 0.94, NFI = 0.85, CFI = 0.94 and RMSEA = 0.048). Of the variables that affected pregnancy-specific stress through both paths, spirituality had a positive effect (B = 0.11) and the personal-social variable a negative effect (B = -0.37). Psychological well-being affected pregnancy-specific stress negatively and directly and through one path only (B = -0.59). The results obtained through the model confirm the effect of spirituality and psychological well-being in reducing pregnancy-specific stress. Given that handling stress has a major role in the quality of daily life in pregnant women, stress management skills are recommended to be promoted among pregnant women so as to mitigate stress and its negative consequences.

Structure and anticoagulant activity of a sulfated galactan from the red alga, Gelidium crinale. Is there a specific structural requirement for the anticoagulant action?

Science.gov (United States)

Pereira, Maria G; Benevides, Norma M B; Melo, Marcia R S; Valente, Ana Paula; Melo, Fábio R; Mourão, Paulo A S

2005-09-05

Marine red algae are an abundant source of sulfated galactans with potent anticoagulant activity. However, the specific structural motifs that confer biological activity remain to be elucidated. We have now isolated and purified a sulfated galactan from the marine red alga, Gellidium crinale. The structure of this polysaccharide was determined using NMR spectroscopy. It is composed of the repeating structure -4-alpha-Galp-(1-->3)-beta-Galp1--> but with a variable sulfation pattern. Clearly 15% of the total alpha-units are 2,3-di-sulfated and another 55% are 2-sulfated. No evidence for the occurrence of 3,6-anhydro alpha-galactose units was observed in the NMR spectra. We also compared the anticoagulant activity of this sulfated galactan with a polysaccharide from the species, Botryocladia occidentalis, with a similar saccharide chain but with higher amounts of 2,3-di-sulfated alpha-units. The sulfated galactan from G. crinale has a lower anticoagulant activity on a clotting assay when compared with the polysaccharide from B. occidentalis. When tested in assays using specific proteases and coagulation inhibitors, these two galactans showed significant differences in their activity. They do not differ in thrombin inhibition mediated by antithrombin, but in assays where heparin cofactor II replaces antithrombin, the sulfated galactan from G. crinale requires a significantly higher concentration to achieve the same inhibitory effect as the polysaccharide from B. occidentalis. In contrast, when factor Xa instead of thrombin is used as the target protease, the sulfated galactan from G. crinale is a more potent anticoagulant. These observations suggest that the proportion and/or the distribution of 2,3-di-sulfated alpha-units along the galactan chain may be a critical structural motif to promote the interaction of the protease with specific protease and coagulation inhibitors.

2.4. Kinetics of voids structure change according to the specific properties of the concrete mix

International Nuclear Information System (INIS)

Saidov, D.Kh.

2011-01-01

This work is devoted to kinetics of voids structure changes according to the specific properties of concrete mix. The influence of concrete mix mobility on durability and watertightness of concrete was studied. The influence of cement expenditure on concrete durability was examined.

Production of specific-structured lipids by enzymatic interesterification: elucidation of acyl migration by response surface design

DEFF Research Database (Denmark)

Xu, Xuebing; Skands, Anja; Høy, Carl-Erik

1998-01-01

Production of specific-structured lipids (SSL) by lipase-catalyzed interesterification has been attracting more and more attention recently. However, it was found that acyl migration occurs during the reaction and causes the production of by-products. In this paper, the elucidation of acyl...

Production of specific structured lipids by enzymatic interesterification: optimization of the reaction by response surface design

DEFF Research Database (Denmark)

Xu, Xuebing; Skands, Anja Rebecca Havegaard; Adler-Nissen, Jens

1998-01-01

Rapeseed oil and capric acid were interesterified in solvent-free media catalyzed by Lipozyme IM (Rhizomucor miehei) to produce specific-structured lipids (SSLs). The process was optimized by response surface design concerning the effects of acyl migration and the by-products of diacylglycerols...

Molecular simulation of the water-triolein-oleic acid mixture: Local structure and thermodynamic properties

Science.gov (United States)

Couallier, E.; Riaublanc, A.; David Briand, E.; Rousseau, B.

2018-05-01

An artificial oil-in-water emulsion analogous to those found in bioresources or food matrices is simulated and studied experimentally. It is composed of one of the major natural free fatty acids (the oleic acid, OA) and the corresponding triacylglyceride (trioleic glyceride, or triolein, GTO). Because of the large time and length scales involved, the molecular simulations are done with the Martini force field, a coarse-grained model. This allowed us to study the water-OA-GTO system at different compositions with more than 20 000 molecules and up to 2 μs. Interfacial tension was measured using the pendant drop method and compared with molecular simulation results. We observe very good agreement at high OA concentrations and deviations up to 15% at low OA concentrations. The water solubility in the lipid phase is in fair agreement with experiments, between 0.03 and 0.32 mol/l, rising with the OA content. The area occupied by OA and GTO at the interface between water and the pure product fitted with experimental data (AOA = 36.6 Å2 and AGTO = 152.1 Å2). The consistency between simulation and experimental results allowed a structural analysis of the interface. A bilayer structure of the lipids at the water/oil interface is proposed, containing preferentially oleic acid but also triolein. Through all these results, the usefulness of coarse-grained simulation for the description of water-oil interfacial organization is demonstrated. This method will be used later to bring local information on the organization of target compounds, necessary in biomass fractionation processes or food additive formulations, for example.

High affinity antigen recognition of the dual specific variants of herceptin is entropy-driven in spite of structural plasticity.

Directory of Open Access Journals (Sweden)

Jenny Bostrom

Full Text Available The antigen-binding site of Herceptin, an anti-human Epidermal Growth Factor Receptor 2 (HER2 antibody, was engineered to add a second specificity toward Vascular Endothelial Growth Factor (VEGF to create a high affinity two-in-one antibody bH1. Crystal structures of bH1 in complex with either antigen showed that, in comparison to Herceptin, this antibody exhibited greater conformational variability, also called "structural plasticity". Here, we analyzed the biophysical and thermodynamic properties of the dual specific variants of Herceptin to understand how a single antibody binds two unrelated protein antigens. We showed that while bH1 and the affinity-improved bH1-44, in particular, maintained many properties of Herceptin including binding affinity, kinetics and the use of residues for antigen recognition, they differed in the binding thermodynamics. The interactions of bH1 and its variants with both antigens were characterized by large favorable entropy changes whereas the Herceptin/HER2 interaction involved a large favorable enthalpy change. By dissecting the total entropy change and the energy barrier for dual interaction, we determined that the significant structural plasticity of the bH1 antibodies demanded by the dual specificity did not translate into the expected increase of entropic penalty relative to Herceptin. Clearly, dual antigen recognition of the Herceptin variants involves divergent antibody conformations of nearly equivalent energetic states. Hence, increasing the structural plasticity of an antigen-binding site without increasing the entropic cost may play a role for antibodies to evolve multi-specificity. Our report represents the first comprehensive biophysical analysis of a high affinity dual specific antibody binding two unrelated protein antigens, furthering our understanding of the thermodynamics that drive the vast antigen recognition capacity of the antibody repertoire.

Direct methods and residue type specific isotope labeling in NMR structure determination and model-driven sequential assignment

International Nuclear Information System (INIS)

Schedlbauer, Andreas; Auer, Renate; Ledolter, Karin; Tollinger, Martin; Kloiber, Karin; Lichtenecker, Roman; Ruedisser, Simon; Hommel, Ulrich; Schmid, Walther; Konrat, Robert; Kontaxis, Georg

2008-01-01

Direct methods in NMR based structure determination start from an unassigned ensemble of unconnected gaseous hydrogen atoms. Under favorable conditions they can produce low resolution structures of proteins. Usually a prohibitively large number of NOEs is required, to solve a protein structure ab-initio, but even with a much smaller set of distance restraints low resolution models can be obtained which resemble a protein fold. One problem is that at such low resolution and in the absence of a force field it is impossible to distinguish the correct protein fold from its mirror image. In a hybrid approach these ambiguous models have the potential to aid in the process of sequential backbone chemical shift assignment when 13 C β and 13 C' shifts are not available for sensitivity reasons. Regardless of the overall fold they enhance the information content of the NOE spectra. These, combined with residue specific labeling and minimal triple-resonance data using 13 C α connectivity can provide almost complete sequential assignment. Strategies for residue type specific labeling with customized isotope labeling patterns are of great advantage in this context. Furthermore, this approach is to some extent error-tolerant with respect to data incompleteness, limited precision of the peak picking, and structural errors caused by misassignment of NOEs

Structural insights into Rhino-Deadlock complex for germline piRNA cluster specification.

Science.gov (United States)

Yu, Bowen; Lin, Yu An; Parhad, Swapnil S; Jin, Zhaohui; Ma, Jinbiao; Theurkauf, William E; Zhang, Zz Zhao; Huang, Ying

2018-06-01

PIWI-interacting RNAs (piRNAs) silence transposons in germ cells to maintain genome stability and animal fertility. Rhino, a rapidly evolving heterochromatin protein 1 (HP1) family protein, binds Deadlock in a species-specific manner and so defines the piRNA-producing loci in the Drosophila genome. Here, we determine the crystal structures of Rhino-Deadlock complex in Drosophila melanogaster and simulans In both species, one Rhino binds the N-terminal helix-hairpin-helix motif of one Deadlock protein through a novel interface formed by the beta-sheet in the Rhino chromoshadow domain. Disrupting the interface leads to infertility and transposon hyperactivation in flies. Our structural and functional experiments indicate that electrostatic repulsion at the interaction interface causes cross-species incompatibility between the sibling species. By determining the molecular architecture of this piRNA-producing machinery, we discover a novel HP1-partner interacting mode that is crucial to piRNA biogenesis and transposon silencing. We thus explain the cross-species incompatibility of two sibling species at the molecular level. © 2018 The Authors.

The structure-specific endonuclease Ercc1-Xpf is required for targeted gene replacement in embryonic stem cells

NARCIS (Netherlands)

L.J. Niedernhofer (Laura); J. Essers (Jeroen); G. Weeda (Geert); H.B. Beverloo (Berna); J. de Wit (Jan); M. Muijtjens (Manja); H. Odijk (Hanny); J.H.J. Hoeijmakers (Jan); R. Kanaar (Roland)

2001-01-01

textabstractThe Ercc1-Xpf heterodimer, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair and homologous recombination. Erccl-Xpf incises

A specific PFT and sub-canopy structure for simulating oil palm in the Community Land Model

Science.gov (United States)

Fan, Y.; Knohl, A.; Roupsard, O.; Bernoux, M.; LE Maire, G.; Panferov, O.; Kotowska, M.; Meijide, A.

2015-12-01

Towards an effort to quantify the effects of rainforests to oil palm conversion on land-atmosphere carbon, water and energy fluxes, a specific plant functional type (PFT) and sub-canopy structure are developed for simulating oil palm within the Community Land Model (CLM4.5). Current global land surface models only simulate annual crops beside natural vegetation. In this study, a multilayer oil palm subroutine is developed in CLM4.5 for simulating oil palm's phenology and carbon and nitrogen allocation. The oil palm has monopodial morphology and sequential phenology of around 40 stacked phytomers, each carrying a large leaf and a fruit bunch, forming a natural multilayer canopy. A sub-canopy phenological and physiological parameterization is thus introduced, so that multiple phytomer components develop simultaneously but according to their different phenological steps (growth, yield and senescence) at different canopy layers. This specific multilayer structure was proved useful for simulating canopy development in terms of leaf area index (LAI) and fruit yield in terms of carbon and nitrogen outputs in Jambi, Sumatra (Fan et al. 2015). The study supports that species-specific traits, such as palm's monopodial morphology and sequential phenology, are necessary representations in terrestrial biosphere models in order to accurately simulate vegetation dynamics and feedbacks to climate. Further, oil palm's multilayer structure allows adding all canopy-level calculations of radiation, photosynthesis, stomatal conductance and respiration, beside phenology, also to the sub-canopy level, so as to eliminate scale mismatch problem among different processes. A series of adaptations are made to the CLM model. Initial results show that the adapted multilayer radiative transfer scheme and the explicit represention of oil palm's canopy structure improve on simulating photosynthesis-light response curve. The explicit photosynthesis and dynamic leaf nitrogen calculations per canopy

Human lactoferricin derived di-peptides deploying loop structures induce apoptosis specifically in cancer cells through targeting membranous phosphatidylserine.

Science.gov (United States)

Riedl, Sabrina; Leber, Regina; Rinner, Beate; Schaider, Helmut; Lohner, Karl; Zweytick, Dagmar

2015-11-01

Host defense-derived peptides have emerged as a novel strategy for the development of alternative anticancer therapies. In this study we report on characteristic features of human lactoferricin (hLFcin) derivatives which facilitate specific killing of cancer cells of melanoma, glioblastoma and rhabdomyosarcoma compared with non-specific derivatives and the synthetic peptide RW-AH. Changes in amino acid sequence of hLFcin providing 9-11 amino acids stretched derivatives LF11-316, -318 and -322 only yielded low antitumor activity. However, the addition of the repeat (di-peptide) and the retro-repeat (di-retro-peptide) sequences highly improved cancer cell toxicity up to 100% at 20 μM peptide concentration. Compared to the complete parent sequence hLFcin the derivatives showed toxicity on the melanoma cell line A375 increased by 10-fold and on the glioblastoma cell line U-87mg by 2-3-fold. Reduced killing velocity, apoptotic blebbing, activation of caspase 3/7 and formation of apoptotic DNA fragments proved that the active and cancer selective peptides, e.g. R-DIM-P-LF11-322, trigger apoptosis, whereas highly active, though non-selective peptides, such as DIM-LF11-318 and RW-AH seem to kill rapidly via necrosis inducing membrane lyses. Structural studies revealed specific toxicity on cancer cells by peptide derivatives with loop structures, whereas non-specific peptides comprised α-helical structures without loop. Model studies with the cancer membrane mimic phosphatidylserine (PS) gave strong evidence that PS only exposed by cancer cells is an important target for specific hLFcin derivatives. Other negatively charged membrane exposed molecules as sialic acid, heparan and chondroitin sulfate were shown to have minor impact on peptide activity. Copyright © 2015. Published by Elsevier B.V.

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

Science.gov (United States)

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

2011-01-01

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. We present the first crystal structure of the human CD147 Ig0 domain and show that the CD147 Ig0 domain is a crystallographic dimer with an I-type domain structure, which is maintained in solution. Furthermore, we have utilized our structural data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Finally, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation. PMID:21620857

Structural basis for the site-specific incorporation of lysine derivatives into proteins.

Directory of Open Access Journals (Sweden)

Veronika Flügel

Full Text Available Posttranslational modifications (PTMs of proteins determine their structure-function relationships, interaction partners, as well as their fate in the cell and are crucial for many cellular key processes. For instance chromatin structure and hence gene expression is epigenetically regulated by acetylation or methylation of lysine residues in histones, a phenomenon known as the 'histone code'. Recently it was shown that these lysine residues can furthermore be malonylated, succinylated, butyrylated, propionylated and crotonylated, resulting in significant alteration of gene expression patterns. However the functional implications of these PTMs, which only differ marginally in their chemical structure, is not yet understood. Therefore generation of proteins containing these modified amino acids site specifically is an important tool. In the last decade methods for the translational incorporation of non-natural amino acids using orthogonal aminoacyl-tRNA synthetase (aaRS:tRNAaaCUA pairs were developed. A number of studies show that aaRS can be evolved to use non-natural amino acids and expand the genetic code. Nevertheless the wild type pyrrolysyl-tRNA synthetase (PylRS from Methanosarcina mazei readily accepts a number of lysine derivatives as substrates. This enzyme can further be engineered by mutagenesis to utilize a range of non-natural amino acids. Here we present structural data on the wild type enzyme in complex with adenylated ε-N-alkynyl-, ε-N-butyryl-, ε-N-crotonyl- and ε-N-propionyl-lysine providing insights into the plasticity of the PylRS active site. This shows that given certain key features in the non-natural amino acid to be incorporated, directed evolution of this enzyme is not necessary for substrate tolerance.

Structural basis for subtype-specific inhibition of the P2X7 receptor

Energy Technology Data Exchange (ETDEWEB)

Karasawa, Akira; Kawate, Toshimitsu (Cornell)

2016-12-09

The P2X7 receptor is a non-selective cation channel activated by extracellular adenosine triphosphate (ATP). Chronic activation of P2X7 underlies many health problems such as pathologic pain, yet we lack effective antagonists due to poorly understood mechanisms of inhibition. Here we present crystal structures of a mammalian P2X7 receptor complexed with five structurally-unrelated antagonists. Unexpectedly, these drugs all bind to an allosteric site distinct from the ATP-binding pocket in a groove formed between two neighboring subunits. This novel drug-binding pocket accommodates a diversity of small molecules mainly through hydrophobic interactions. Functional assays propose that these compounds allosterically prevent narrowing of the drug-binding pocket and the turret-like architecture during channel opening, which is consistent with a site of action distal to the ATP-binding pocket. These novel mechanistic insights will facilitate the development of P2X7-specific drugs for treating human diseases.

Structural characterization of a D-isomer specific 2-hydroxyacid dehydrogenase from Lactobacillus delbrueckii ssp. bulgaricus.

Science.gov (United States)

Holton, Simon J; Anandhakrishnan, Madhankumar; Geerlof, Arie; Wilmanns, Matthias

2013-02-01

Hydroxyacid dehydrogenases, responsible for the stereospecific conversion of 2-keto acids to 2-hydroxyacids in lactic acid producing bacteria, have a range of biotechnology applications including antibiotic synthesis, flavor development in dairy products and the production of valuable synthons. The genome of Lactobacillus delbrueckii ssp. bulgaricus, a member of the heterogeneous group of lactic acid bacteria, encodes multiple hydroxyacid dehydrogenases whose structural and functional properties remain poorly characterized. Here, we report the apo and coenzyme NAD⁺ complexed crystal structures of the L. bulgaricusD-isomer specific 2-hydroxyacid dehydrogenase, D2-HDH. Comparison with closely related members of the NAD-dependent dehydrogenase family reveals that whilst the D2-HDH core fold is structurally conserved, the substrate-binding site has a number of non-canonical features that may influence substrate selection and thus dictate the physiological function of the enzyme. Copyright © 2012 Elsevier Inc. All rights reserved.

Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease

International Nuclear Information System (INIS)

Lin, Ying-Chuan; Perryman, Alexander L.; Olson, Arthur J.; Torbett, Bruce E.; Elder, John H.; Stout, C. David

2011-01-01

Crystal structures of the 6s-98S FIV protease chimera with darunavir and lopinavir bound have been determined at 1.7 and 1.8 Å resolution, respectively. A chimeric feline immunodeficiency virus (FIV) protease (PR) has been engineered that supports infectivity but confers sensitivity to the human immunodeficiency virus (HIV) PR inhibitors darunavir (DRV) and lopinavir (LPV). The 6s-98S PR has five replacements mimicking homologous residues in HIV PR and a sixth which mutated from Pro to Ser during selection. Crystal structures of the 6s-98S FIV PR chimera with DRV and LPV bound have been determined at 1.7 and 1.8 Å resolution, respectively. The structures reveal the role of a flexible 90s loop and residue 98 in supporting Gag processing and infectivity and the roles of residue 37 in the active site and residues 55, 57 and 59 in the flap in conferring the ability to specifically recognize HIV PR drugs. Specifically, Ile37Val preserves tertiary structure but prevents steric clashes with DRV and LPV. Asn55Met and Val59Ile induce a distinct kink in the flap and a new hydrogen bond to DRV. Ile98Pro→Ser and Pro100Asn increase 90s loop flexibility, Gln99Val contributes hydrophobic contacts to DRV and LPV, and Pro100Asn forms compensatory hydrogen bonds. The chimeric PR exhibits a comparable number of hydrogen bonds, electrostatic interactions and hydrophobic contacts with DRV and LPV as in the corresponding HIV PR complexes, consistent with IC 50 values in the nanomolar range

The bats (Chiroptera; Mammalia of Mordovia: specific structure and features of distribution

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Oleg N. Artaev

2016-05-01

Full Text Available This article presents the specific structure and distribution of the bats made in the territory of the Republic of Mordovia (Central Russia from the first half of the 20th century to the present. Occurence, relative abundance and patterns of distribution are briefly assessed for rare species. On this base, recommendations for inclusion these bats in the regional Red Data Book are presented. .In Mordovia twelve species of bats have been observed. There are widespread and numerous species: Pipistrellus nathusii, Myotis daubentonii, M. dasycneme, Nyctalus noctula and Vespertilio murinus. Widespread but less numerous species are: Myotis brandtii and Plecotus auritus. Finally, rare species are: Myotis nattereri, Nyctalus lasiopterus, N. leisleri, Pipistrellus pygmaeus and P. kuhlii.

Partitioning of polychlorinated biphenyls into human cells and adipose tissues: evaluation of octanol, triolein, and liposomes as surrogates

NARCIS (Netherlands)

Quinn, Cristina L.; Van Der Heijden, Stephan A.; Wania, Frank; Jonker, Michiel T O

2014-01-01

Whereas octanol, triacylglycerides, and liposomes have all been proposed as surrogates for measuring the affinity of hydrophobic organic contaminants to human lipids, no comparative evaluation of their suitability exists. Here we conducted batch sorption experiments with polyoxymethylene passive

Minor milk constituents are affected by protein concentration and forage digestibility in the feed ration

DEFF Research Database (Denmark)

Larsen, Torben; Alstrup, Lene; Weisbjerg, Martin Riis

2016-01-01

The present study was conducted in order to investigate if selected minor milk components would be indicative for the nutritional situation of the cow. Forty-eight dairy cows were offered a high digestible ration vs. a lower digestible ration combined with 2 protein levels in a 4 × 4 Latin square...... design. Milk glucose, glucose-6-phosphate, cholesterol, triacylglycerides (TAG), uric acid and β-hydroxybutyrate (BHBA) were measured and correlated mutually and towards other milking parameters (yield, h since last milking, days in milk (DIM), urea, etc). The variation range of the suggested variables...... were broad, a fact that may support their utilisation as predictive parameters. The content of milk metabolites was significantly affected by the change in rations as milk glucose, glucose-6-phosphate, uric acid, and the ratio cholesterol: triacylglycerides increased with higher energy intake while...

Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9.

Science.gov (United States)

Hirano, Seiichi; Nishimasu, Hiroshi; Ishitani, Ryuichiro; Nureki, Osamu

2016-03-17

The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets bearing a PAM (protospacer adjacent motif) and complementarity to the guide RNA. A recent study showed that, whereas wild-type Streptococcus pyogenes Cas9 (SpCas9) recognizes the 5'-NGG-3' PAM, the engineered VQR, EQR, and VRER SpCas9 variants recognize the 5'-NGA-3', 5'-NGAG-3', and 5'-NGCG-3' PAMs, respectively, thus expanding the targetable sequences in Cas9-mediated genome editing applications. Here, we present the high-resolution crystal structures of the three SpCas9 variants in complexes with a single-guide RNA and its altered PAM-containing, partially double-stranded DNA targets. A structural comparison of the three SpCas9 variants with wild-type SpCas9 revealed that the multiple mutations synergistically induce an unexpected displacement in the phosphodiester backbone of the PAM duplex, thereby allowing the SpCas9 variants to directly recognize the altered PAM nucleotides. Our findings explain the altered PAM specificities of the SpCas9 variants and establish a framework for further rational engineering of CRISPR-Cas9. Copyright © 2016 Elsevier Inc. All rights reserved.

In vivo study about specific captation of 125 I-insulin by rat brain structures

International Nuclear Information System (INIS)

Sanvitto, G.L.

1986-01-01

The specific captation of 125 I-insulin was evaluated by brain structures, as olfactory bulbous, hypothalamus and cerebellum in rats, from in vivo experiences that including two different aspects: captation measure of 125 I-insulin after the intravenous injection of the labelled hormone, in fed rats and in rats with 48 h of fast or convulsion, procedure by the pentylene tetrazole; captation measure of 125 I-insulin after intra-cerebral-ventricular injection of the labelled hormone in fed rats. (C.G.C.)

Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity.

Science.gov (United States)

Weeks, Amy M; Coyle, Scott M; Jinek, Martin; Doudna, Jennifer A; Chang, Michelle C Y

2010-11-02

We have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme A (CoA) specific thioesterase (FlK) from Streptomyces cattleya. Our data establish that FlK is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-CoA (k(cat)/K(M) = 5 × 10⁷ M⁻¹ s⁻¹) and acetyl-CoA (k(cat)/K(M) = 30 M⁻¹ s⁻¹) based on a single fluorine substitution that originates from differences in both substrate reactivity and binding. We show that Thr 42, Glu 50, and His 76 are key catalytic residues and identify several factors that influence substrate selectivity. We propose that FlK minimizes interaction with the thioester carbonyl, leading to selection against acetyl-CoA binding that can be recovered in part by new C═O interactions in the T42S and T42C mutants. We hypothesize that the loss of these interactions is compensated by the entropic driving force for fluorinated substrate binding in a hydrophobic binding pocket created by a lid structure, containing Val 23, Leu 26, Phe 33, and Phe 36, that is not found in other structurally characterized members of this superfamily. We further suggest that water plays a critical role in fluorine specificity based on biochemical and structural studies focused on the unique Phe 36 "gate" residue, which functions to exclude water from the active site. Taken together, the findings from these studies offer molecular insights into organofluorine recognition and design of fluorine-specific enzymes.

Sequence- and structure-dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA

International Nuclear Information System (INIS)

Spaltenstein, A.; Robinson, B.H.; Hopkins, P.B.

1989-01-01

A nitroxide spin-labeled analogue of thymidine (1a), in which the methyl group is replaced by an acetylene-tethered nitroxide, was evaluated as a probe for structural and dynamics studies of sequence specifically spin-labeled DNA. Residue 1a was incorporated into synthetic deoxyoligonucleotides by using automated phosphite triester methods. 1 H NMR, CD, and thermal denaturation studies indicate that 1a (T) does not significantly alter the structure of 5'-d(CGCGAATT*CGCG) from that of the native dodecamer. EPR studies on monomer, single-stranded, and duplexed DNA show that 1a readily distinguishes environments of different rigidity. Comparison of the general line-shape features of the observed EPR spectra of several small duplexes (12-mer, 24-mer) with simulated EPR spectra assuming isotropic motion suggests that probe 1a monitors global tumbling of small duplexes. Increasing the length of the DNA oligomers results in significant deviation from isotropic motion, with line-shape features similar to those of calculated spectra of objects with isotropic rotational correlation times of 20-100 ns. EPR spectra of a spin-labeled GT mismatch and a T bulge in long DNAs are distinct from those of spin-labeled Watson-Crick paired DNAs, further demonstrating the value of EPR as a tool in the evaluation of local dynamic and structural features in macromolecules

Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease

Energy Technology Data Exchange (ETDEWEB)

Lin, Ying-Chuan; Perryman, Alexander L.; Olson, Arthur J.; Torbett, Bruce E.; Elder, John H.; Stout, C. David, E-mail: dave@scripps.edu [The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (United States)

2011-06-01

Crystal structures of the 6s-98S FIV protease chimera with darunavir and lopinavir bound have been determined at 1.7 and 1.8 Å resolution, respectively. A chimeric feline immunodeficiency virus (FIV) protease (PR) has been engineered that supports infectivity but confers sensitivity to the human immunodeficiency virus (HIV) PR inhibitors darunavir (DRV) and lopinavir (LPV). The 6s-98S PR has five replacements mimicking homologous residues in HIV PR and a sixth which mutated from Pro to Ser during selection. Crystal structures of the 6s-98S FIV PR chimera with DRV and LPV bound have been determined at 1.7 and 1.8 Å resolution, respectively. The structures reveal the role of a flexible 90s loop and residue 98 in supporting Gag processing and infectivity and the roles of residue 37 in the active site and residues 55, 57 and 59 in the flap in conferring the ability to specifically recognize HIV PR drugs. Specifically, Ile37Val preserves tertiary structure but prevents steric clashes with DRV and LPV. Asn55Met and Val59Ile induce a distinct kink in the flap and a new hydrogen bond to DRV. Ile98Pro→Ser and Pro100Asn increase 90s loop flexibility, Gln99Val contributes hydrophobic contacts to DRV and LPV, and Pro100Asn forms compensatory hydrogen bonds. The chimeric PR exhibits a comparable number of hydrogen bonds, electrostatic interactions and hydrophobic contacts with DRV and LPV as in the corresponding HIV PR complexes, consistent with IC{sub 50} values in the nanomolar range.

Crystal structure and novel recognition motif of rho ADP-ribosylating C3 exoenzyme from Clostridium botulinum: structural insights for recognition specificity and catalysis.

Science.gov (United States)

Han, S; Arvai, A S; Clancy, S B; Tainer, J A

2001-01-05

Clostridium botulinum C3 exoenzyme inactivates the small GTP-binding protein family Rho by ADP-ribosylating asparagine 41, which depolymerizes the actin cytoskeleton. C3 thus represents a major family of the bacterial toxins that transfer the ADP-ribose moiety of NAD to specific amino acids in acceptor proteins to modify key biological activities in eukaryotic cells, including protein synthesis, differentiation, transformation, and intracellular signaling. The 1.7 A resolution C3 exoenzyme structure establishes the conserved features of the core NAD-binding beta-sandwich fold with other ADP-ribosylating toxins despite little sequence conservation. Importantly, the central core of the C3 exoenzyme structure is distinguished by the absence of an active site loop observed in many other ADP-ribosylating toxins. Unlike the ADP-ribosylating toxins that possess the active site loop near the central core, the C3 exoenzyme replaces the active site loop with an alpha-helix, alpha3. Moreover, structural and sequence similarities with the catalytic domain of vegetative insecticidal protein 2 (VIP2), an actin ADP-ribosyltransferase, unexpectedly implicates two adjacent, protruding turns, which join beta5 and beta6 of the toxin core fold, as a novel recognition specificity motif for this newly defined toxin family. Turn 1 evidently positions the solvent-exposed, aromatic side-chain of Phe209 to interact with the hydrophobic region of Rho adjacent to its GTP-binding site. Turn 2 evidently both places the Gln212 side-chain for hydrogen bonding to recognize Rho Asn41 for nucleophilic attack on the anomeric carbon of NAD ribose and holds the key Glu214 catalytic side-chain in the adjacent catalytic pocket. This proposed bipartite ADP-ribosylating toxin turn-turn (ARTT) motif places the VIP2 and C3 toxin classes into a single ARTT family characterized by analogous target protein recognition via turn 1 aromatic and turn 2 hydrogen-bonding side-chain moieties. Turn 2 centrally anchors

Biodiesel from soybean oil: experimental procedure of transesterification for organic chemistry laboratories

International Nuclear Information System (INIS)

Geris, Regina; Santos, Nadia Alessandra Carmo dos; Amaral, Bruno Andrade; Maia, Isabelle de Souza; Castro, Vinicius Dourado; Carvalho, Jose Roque Mota

2007-01-01

The transesterification procedure of triacylglycerides from soybean oil (in natura and waste oil) to give biodiesel was adapted to semi-micro laboratory scale as an additional experimental technique of nucleophilic acyl substitution for undergraduate courses in Chemistry and related areas. (author)

UPF201 Archaeal Specific Family Members Reveals Structural Similarity to RNA-Binding Proteins but Low Likelihood for RNA-Binding Function

Energy Technology Data Exchange (ETDEWEB)

Rao, K.N.; Swaminathan, S.; Burley, S. K.

2008-12-11

We have determined X-ray crystal structures of four members of an archaeal specific family of proteins of unknown function (UPF0201; Pfam classification: DUF54) to advance our understanding of the genetic repertoire of archaea. Despite low pairwise amino acid sequence identities (10-40%) and the absence of conserved sequence motifs, the three-dimensional structures of these proteins are remarkably similar to one another. Their common polypeptide chain fold, encompassing a five-stranded antiparallel {beta}-sheet and five {alpha}-helices, proved to be quite unexpectedly similar to that of the RRM-type RNA-binding domain of the ribosomal L5 protein, which is responsible for binding the 5S- rRNA. Structure-based sequence alignments enabled construction of a phylogenetic tree relating UPF0201 family members to L5 ribosomal proteins and other structurally similar RNA binding proteins, thereby expanding our understanding of the evolutionary purview of the RRM superfamily. Analyses of the surfaces of these newly determined UPF0201 structures suggest that they probably do not function as RNA binding proteins, and that this domain specific family of proteins has acquired a novel function in archaebacteria, which awaits experimental elucidation.

Structure elucidation of female-specific volatiles released by the parasitoid wasp Trichogramma turkestanica (Hymenoptera: Trichogrammatidae

Directory of Open Access Journals (Sweden)

Armin Tröger

2014-04-01

Full Text Available Females of the parasitoid wasp Trichogramma turkestanica produce the putative polydeoxypropionates (2E,4E,6S,8S,10S-4,6,8,10-tetramethyltrideca-2,4-diene and (2E,4E,6S,8S,10S-4,6,8,10-tetramethyltrideca-2,4-dien-1-ol or their enantiomers as sex specific volatiles. The structures were assigned on the basis of GC–MS investigations using synthetic reference compounds.

Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.

Science.gov (United States)

Camproux, A C; Tufféry, P

2005-08-05

Understanding and predicting protein structures depend on the complexity and the accuracy of the models used to represent them. We have recently set up a Hidden Markov Model to optimally compress protein three-dimensional conformations into a one-dimensional series of letters of a structural alphabet. Such a model learns simultaneously the shape of representative structural letters describing the local conformation and the logic of their connections, i.e. the transition matrix between the letters. Here, we move one step further and report some evidence that such a model of protein local architecture also captures some accurate amino acid features. All the letters have specific and distinct amino acid distributions. Moreover, we show that words of amino acids can have significant propensities for some letters. Perspectives point towards the prediction of the series of letters describing the structure of a protein from its amino acid sequence.

Dietary Energy Source in Dairy Cows in Early Lactation: Metabolites and Metabolic Hormones

NARCIS (Netherlands)

Knegsel, van A.T.M.; Brand, van den H.; Graat, E.A.M.; Dijkstra, J.; Jorritsma, R.; Decuypere, M.P.; Tamminga, S.; Kemp, B.

2007-01-01

Negative energy balance-related metabolic disorders suggest that the balance between available lipogenic and glucogenic nutrients is important. The objectives of this study were to compare the effects of a glucogenic or a lipogenic diet on liver triacylglycerides (TAG), metabolites, and metabolic

Biodiesel de soja: reação de transesterificação para aulas práticas de química orgânica Biodiesel from soybean oil: experimental procedure of transesterification for organic chemistry laboratories

Directory of Open Access Journals (Sweden)

Regina Geris

2007-10-01

Full Text Available The transesterification procedure of triacylglycerides from soybean oil (in natura and waste oil to give biodiesel was adapted to semi-micro laboratory scale as an additional experimental technique of nucleophilic acyl substitution for undergraduate courses in Chemistry and related areas.

Specific uptake of DHA by the brain from a structured phospholipid, AceDoPC®

Directory of Open Access Journals (Sweden)

Bernoud-Hubac Nathalie

2017-03-01

Full Text Available Docosahexaenoic acid (DHA; 22:6 ω-3 is highly enriched in the brain and is required for proper brain development and function. Its deficiency has been shown to be linked with the emergence of neurological diseases. Dietary ω-3 fatty acid supplements including DHA have been suggested to improve neuronal development and enhance cognitive functions. Findings suggested that DHA is better incorporated into the brain when esterified at the sn-2 position of a lysophosphatidylcholine (LysoPC-DHA. AceDoPC® is a structured phospholipid or acetyl-LysoPC-DHA. As previously shown for LysoPC-DHA, AceDoPC® is a specific and preferred carrier of DHA to the brain. When AceDoPC® was injected to rats that were subjected to an ischemic stroke, it prevents the extension of brain lesions. Regarding the essential role of DHA for cerebral functions, targeting the brain with specific carriers of DHA might provide novel therapeutic approaches to neurodegenerative diseases.

Comparison of lipases for in vitro models of gastric digestion

DEFF Research Database (Denmark)

Sassene, P J; Fanø, M; Mu, H

2016-01-01

Lipase (ROL), Rabbit Gastric Lipase (RGL) and recombinant HGL (rHGL), were used to catalyze the in vitro digestion of two infant formulas (a medium-chain triacylglyceride enriched formula (MC-IF) and a predominantly long-chain triacylglyceride formula (LC-IF)). Digesta were withdrawn after 0, 5, 15, 30......, 60 min of gastric digestion and after 90 or 180 min of intestinal digestion with or without the presence of pancreatic enzymes, respectively. The digesta were analyzed by scanning electron microscopy and gas chromatography to quantify the release of fatty acids (FAs). Digestions of both formulas......, catalyzed by ROL, showed that the extent of gastric digestion was higher than expected from previously published in vivo data. ROL was furthermore insensitive to FA chain length and all FAs were released at the same pace. RGL and rHGL favoured the release of MC-FAs in both formulas, but rHGL did also...

Real-time specifications

DEFF Research Database (Denmark)

David, A.; Larsen, K.G.; Legay, A.

2015-01-01

A specification theory combines notions of specifications and implementations with a satisfaction relation, a refinement relation, and a set of operators supporting stepwise design. We develop a specification framework for real-time systems using Timed I/O Automata as the specification formalism......, with the semantics expressed in terms of Timed I/O Transition Systems. We provide constructs for refinement, consistency checking, logical and structural composition, and quotient of specifications-all indispensable ingredients of a compositional design methodology. The theory is implemented in the new tool Ecdar...

Structural Basis for the Specific Neutralization of Stx2a with a Camelid Single Domain Antibody Fragment

Directory of Open Access Journals (Sweden)

Robert Alvin Bernedo-Navarro

2018-03-01

Full Text Available Background: Shiga toxin-producing Escherichia coli (STEC are a subset of pathogens leading to illnesses such as diarrhea, hemolytic uremic syndrome and even death. The Shiga toxins are the main virulence factors and divided in two groups: Stx1 and Stx2, of which the latter is more frequently associated with severe pathologies in humans. Results: An immune library of nanobodies (Nbs was constructed after immunizing an alpaca with recombinant Shiga toxin-2a B subunit (rStx2aB, to retrieve multiple rStx2aB-specific Nbs. The specificity of five Nbs towards rStx2aB was confirmed in ELISA and Western blot. Nb113 had the highest affinity (9.6 nM and its bivalent construct exhibited a 100-fold higher functional affinity. The structure of the Nb113 in complex with rStx2aB was determined via X-ray crystallography. The crystal structure of the Nb113–rStx2aB complex revealed that five copies of Nb113 bind to the rStx2aB pentamer and that the Nb113 epitope overlaps with the Gb3 binding site, thereby providing a structural basis for the neutralization of Stx2a by Nb113 that was observed on Vero cells. Finally, the tandem-repeated, bivalent Nb1132 exhibits a higher toxin neutralization capacity compared to monovalent Nb113. Conclusions: The Nb of highest affinity for rStx2aB is also the best Stx2a and Stx2c toxin neutralizing Nb, especially in a bivalent format. This lead Nb neutralizes Stx2a by competing for the Gb3 receptor. The fusion of the bivalent Nb1132 with a serum albumin specific Nb is expected to combine high toxin neutralization potential with prolonged blood circulation.

Study of hypocholesterolemic activity of Algerian Pistacia lentiscus leaves extracts in vivo

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Mohammed Cheurfa

Full Text Available Abstract Plants are a large source of new bioactive molecules with therapeutic potentials. However, only a small amount of worldwide plants have been phytochemically investigated. The aqueous and ethanolic extracts of Pistacia lentiscus L., Anacardiaceae, leaves were evaluated for hypocholesterolemic activity in vivo. In this study, hypercholesterolemia was induced in animals by feeding them high cholesterol (1% food. The extracts of P. lentiscus were orally administered at a dose of 200 mg/kg body weight along with a high cholesterol diet for thirty successive days. Lipid parameters such as total cholesterol, triacylglyceride, low density lipoprotein, very low density lipoprotein and high density lipoprotein were measured in the plasma. Total phenol and flavonoid contents were also evaluated. Flavonoid content was found to be more present in the ethanolic extract (8.218 ± 0.009 mg of QE/g compared to the aqueous extract (3.107 ± 0.014 mg of QE/g. The administration of P. lentiscus extracts produced a significant decrease in total cholesterol, triacylglyceride and low density lipoprotein-cholesterol (154.6 ± 18.10, 71.2 ± 4.38 and 99.36 ± 18.77 mg/dl respectively in the ethanolic extract, while the aqueous extract showed a significant decrease in total cholesterol and triacylglyceride (203.6 ± 9.18 and 97.6 ± 3.57 mg/dl respectively. The results of the investigation demonstrated that P. lentiscus leaf extract has hypocholesterolemic properties and might be used for the prevention of hypercholesterolemia associated disorders.

Progresses in studies on 2-alkylcyclobutanones in irradiated lipid-containing foods

International Nuclear Information System (INIS)

Zhang Haiwei; Ha Yiming; Wang Feng

2007-01-01

When foods are irradiated, the free fatty acids and triacylglycerides in the food are decomposed to 2-alkylcyclobutanones (2-ACBs), which have been one of the focuses in food irradiation studies since they were dis- covered in irradiated lipid-containing foods. As specific markers, 2-ACBs could be used to detect irradiated food. The production and stability of 2-ACBs are affected strongly by the irradiation does and temperature and preservation conditions, etc. On the other hand, potential health hazard assessments of 2-ACBs have been studied extensively. Re- cent progresses in 2-ACBs detecting methods from irradiated food, toxicological studies on 2-ACBs, and factors affecting production and stability of 2-ACBs are reviewed in this paper. (authors)

Motor Skill Development in Italian Pre-School Children Induced by Structured Activities in a Specific Playground.

Science.gov (United States)

Tortella, Patrizia; Haga, Monika; Loras, Håvard; Sigmundsson, Hermundur; Fumagalli, Guido

2016-01-01

This study examined the effects and specificity of structured and unstructured activities played at the playground Primo Sport 0246 in Northern Italy on motor skill competence in five years old children. The playground was specifically designed to promote gross motor skills in preschool children; in this study 71 children from local kindergartens came to the park once a week for ten consecutive weeks and were exposed to 30 minutes of free play and 30 minutes of structured activities. Before and after the ten visits, each child completed nine tests to assess levels of motor skills, three for fine-motor skills and six for gross-motor skills. As control, motor skills were also assessed on 39 children from different kindergartens who did not come to the park. The results show that the experimental group who practiced gross-motor activities in the playground for 1 hour a week for 10 weeks improved significantly in 4 out of the 6 gross motor tasks and in none of the fine motor tasks. The data indicate that limited transfer occurred between tasks referring to different domains of motor competences while suggesting cross feeding for improvement of gross-motor skills between different exercises when domains related to physical fitness and strength of specific muscle groups are involved. These results are relevant to the issue of condition(s) appropriate for maintaining and developing motor skills in this age group as well as for the planning, organization and implementation of play and physical activities in kindergartens.

Motor Skill Development in Italian Pre-School Children Induced by Structured Activities in a Specific Playground.

Directory of Open Access Journals (Sweden)

Patrizia Tortella

Full Text Available This study examined the effects and specificity of structured and unstructured activities played at the playground Primo Sport 0246 in Northern Italy on motor skill competence in five years old children. The playground was specifically designed to promote gross motor skills in preschool children; in this study 71 children from local kindergartens came to the park once a week for ten consecutive weeks and were exposed to 30 minutes of free play and 30 minutes of structured activities. Before and after the ten visits, each child completed nine tests to assess levels of motor skills, three for fine-motor skills and six for gross-motor skills. As control, motor skills were also assessed on 39 children from different kindergartens who did not come to the park. The results show that the experimental group who practiced gross-motor activities in the playground for 1 hour a week for 10 weeks improved significantly in 4 out of the 6 gross motor tasks and in none of the fine motor tasks. The data indicate that limited transfer occurred between tasks referring to different domains of motor competences while suggesting cross feeding for improvement of gross-motor skills between different exercises when domains related to physical fitness and strength of specific muscle groups are involved. These results are relevant to the issue of condition(s appropriate for maintaining and developing motor skills in this age group as well as for the planning, organization and implementation of play and physical activities in kindergartens.

Motor Skill Development in Italian Pre-School Children Induced by Structured Activities in a Specific Playground

Science.gov (United States)

Tortella, Patrizia; Haga, Monika; Loras, Håvard

2016-01-01

This study examined the effects and specificity of structured and unstructured activities played at the playground Primo Sport 0246 in Northern Italy on motor skill competence in five years old children. The playground was specifically designed to promote gross motor skills in preschool children; in this study 71 children from local kindergartens came to the park once a week for ten consecutive weeks and were exposed to 30 minutes of free play and 30 minutes of structured activities. Before and after the ten visits, each child completed nine tests to assess levels of motor skills, three for fine-motor skills and six for gross-motor skills. As control, motor skills were also assessed on 39 children from different kindergartens who did not come to the park. The results show that the experimental group who practiced gross-motor activities in the playground for 1 hour a week for 10 weeks improved significantly in 4 out of the 6 gross motor tasks and in none of the fine motor tasks. The data indicate that limited transfer occurred between tasks referring to different domains of motor competences while suggesting cross feeding for improvement of gross-motor skills between different exercises when domains related to physical fitness and strength of specific muscle groups are involved. These results are relevant to the issue of condition(s) appropriate for maintaining and developing motor skills in this age group as well as for the planning, organization and implementation of play and physical activities in kindergartens. PMID:27462985

Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities

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Ul-Haq Zaheer

2012-11-01

Full Text Available Abstract Background X-converting enzyme (XCE involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characterized homologue endothelin-converting enzyme-1 (ECE-1 showed broad substrate specificity and acts as endopeptidase as well as dipeptidase. To explore the structural differences between XCE and ECE-1, homology model of XCE was built using the complex structure of ECE-1 with phosphoramidon (pdb-id: 3DWB as template. Phosphoramidon was docked into the binding site of XCE whereas phosphate oxygen of the inhibitor was used as water molecule to design the apo forms of both enzymes. Molecular dynamics simulation of both enzymes was performed to analyze the dynamic nature of their active site residues in the absence and presence of the inhibitor. Results Homology model of XCE explained the role of non-conserved residues of its S2’ subsite. Molecular dynamics (MD simulations identified the flexible transitions of F149/I150, N566/N571, W714/W719, and R145/R723 residues of ECE-1/XCE for the strong binding of the inhibitor. Secondary structure calculations using DSSP method reveals the folding of R145/R723 residue of ECE-1/XCE into β-sheet structure while unfolding of the S2’ subsite residues in aECE-1 and sustained compact folding of that of aXCE. The results evaluated are in good agreement with available experimental data, thus providing detailed molecular models which can explain the structural and specificities differences between both zinc peptidases. Conclusions Secondary structure changes of both enzymes during the simulation time revealed the importance of β-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the α-helix comprising the S2’ subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may

Selection of oleaginous yeasts for fatty acid production

NARCIS (Netherlands)

Lamers, Dennis; Biezen, van Nick; Martens, Dirk; Peters, Linda; Zilver, van de Eric; Jacobs-van Dreumel, Nicole; Wijffels, René H.; Lokman, Christien

2016-01-01

Background: Oleaginous yeast species are an alternative for the production of lipids or triacylglycerides (TAGs). These yeasts are usually non-pathogenic and able to store TAGs ranging from 20 % to 70 % of their cell mass depending on culture conditions. TAGs originating from oleaginous yeasts

Raman imaging and lipidomic analysis of lipid droplets in (activated) hepatic stellate cells

NARCIS (Netherlands)

Vaandrager, A.B.; Testerink, N.; Ajat, M.; Houweling, M.; Brouwers, J.F.H.M.; Pully, V.V.; van Manen, H.J.; Otto, Cornelis; Helms, J.B.

2009-01-01

In eukaryotic cells the excess of hydrophobic molecules is stored in special organelles named lipid droplets (LDs). These droplets contain triacylglycerides, cholesteryl esters and/or retinyl esters, depending on the function of the cell in which they reside. Retinyl esters, the storage form of

Mesenchymal Stem Cells in Oriented PLGA/ACECM Composite Scaffolds Enhance Structure-Specific Regeneration of Hyaline Cartilage in a Rabbit Model.

Science.gov (United States)

Guo, Weimin; Zheng, Xifu; Zhang, Weiguo; Chen, Mingxue; Wang, Zhenyong; Hao, Chunxiang; Huang, Jingxiang; Yuan, Zhiguo; Zhang, Yu; Wang, Mingjie; Peng, Jiang; Wang, Aiyuan; Wang, Yu; Sui, Xiang; Xu, Wenjing; Liu, Shuyun; Lu, Shibi; Guo, Quanyi

2018-01-01

Articular cartilage lacks a blood supply and nerves. Hence, articular cartilage regeneration remains a major challenge in orthopedics. Decellularized extracellular matrix- (ECM-) based strategies have recently received particular attention. The structure of native cartilage exhibits complex zonal heterogeneity. Specifically, the development of a tissue-engineered scaffold mimicking the aligned structure of native cartilage would be of great utility in terms of cartilage regeneration. Previously, we fabricated oriented PLGA/ACECM (natural, nanofibrous, articular cartilage ECM) composite scaffolds. In vitro, we found that the scaffolds not only guided seeded cells to proliferate in an aligned manner but also exhibited high biomechanical strength. To detect whether oriented cartilage regeneration was possible in vivo, we used mesenchymal stem cell (MSC)/scaffold constructs to repair cartilage defects. The results showed that cartilage defects could be completely regenerated. Histologically, these became filled with hyaline cartilage and subchondral bone. Moreover, the aligned structure of cartilage was regenerated and was similar to that of native tissue. In conclusion, the MSC/scaffold constructs enhanced the structure-specific regeneration of hyaline cartilage in a rabbit model and may be a promising treatment strategy for the repair of human cartilage defects.

The structure of bradyzoite-specific enolase from Toxoplasma gondii reveals insights into its dual cytoplasmic and nuclear functions

Energy Technology Data Exchange (ETDEWEB)

Ruan, Jiapeng [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Mouveaux, Thomas [Université Lille Nord de France, (France); Light, Samuel H.; Minasov, George; Anderson, Wayne F. [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); Tomavo, Stanislas [Université Lille Nord de France, (France); Ngô, Huân M., E-mail: h-ngo@northwestern.edu [Northwestern University, 320 E. Superior Street, Morton 7-601, Chicago, IL 60611 (United States); BrainMicro LLC, 21 Pendleton Street, New Haven, CT 06511 (United States)

2015-03-01

The second crystal structure of a parasite protein preferentially enriched in the brain cyst of T. gondii has been solved at 2.75 Å resolution. Bradyzoite enolase 1 is reported to have differential functions as a glycolytic enzyme and a transcriptional regulator in bradyzoites. In addition to catalyzing a central step in glycolysis, enolase assumes a remarkably diverse set of secondary functions in different organisms, including transcription regulation as documented for the oncogene c-Myc promoter-binding protein 1. The apicomplexan parasite Toxoplasma gondii differentially expresses two nuclear-localized, plant-like enolases: enolase 1 (TgENO1) in the latent bradyzoite cyst stage and enolase 2 (TgENO2) in the rapidly replicative tachyzoite stage. A 2.75 Å resolution crystal structure of bradyzoite enolase 1, the second structure to be reported of a bradyzoite-specific protein in Toxoplasma, captures an open conformational state and reveals that distinctive plant-like insertions are located on surface loops. The enolase 1 structure reveals that a unique residue, Glu164, in catalytic loop 2 may account for the lower activity of this cyst-stage isozyme. Recombinant TgENO1 specifically binds to a TTTTCT DNA motif present in the cyst matrix antigen 1 (TgMAG1) gene promoter as demonstrated by gel retardation. Furthermore, direct physical interactions of both nuclear TgENO1 and TgENO2 with the TgMAG1 gene promoter are demonstrated in vivo using chromatin immunoprecipitation (ChIP) assays. Structural and biochemical studies reveal that T. gondii enolase functions are multifaceted, including the coordination of gene regulation in parasitic stage development. Enolase 1 provides a potential lead in the design of drugs against Toxoplasma brain cysts.

Bioaccessibility of hydroxytyrosol and n-3 fatty acids as affected by the delivery system: simple, double and gelled double emulsions.

Science.gov (United States)

Cofrades, Susana; Bou, Ricard; Flaiz, Linda; Garcimartín, Alba; Benedí, Juana; Mateos, Raquel; Sánchez-Muniz, Francisco J; Olivero-David, Raúl; Jiménez-Colmenero, Francisco

2017-06-01

This study examines the influence of different food-grade n-3 PUFA-enriched simple emulsion (SE), double emulsion (DE) and gelled double emulsion (GDE) delivery systems on the extent of lipolysis, antioxidant capacity and the bioaccessibility of hydroxytyrosol (HTy). GDE emulsion offered better protection for HTy (89%) than the other systems (79% in SE and DE). The reducing capacity of the emulsions containing HTy were not altered during oral digestion. However, "in vitro" gastric and intestinal phases significantly reduced the antioxidant activity of all systems. The structural and physical state of GDE entailed a slowing-down of triacylglyceride hydrolysis (36.4%) in comparison with that of SE and DE (22.7 and 24.8% for SE and DE, respectively).

Structure-function relationship of substituted bromomethylcoumarins in nucleoside specificity of RNA alkylation.

Science.gov (United States)

Kellner, Stefanie; Kollar, Laura Bettina; Ochel, Antonia; Ghate, Manjunath; Helm, Mark

2013-01-01

Selective alkylation of RNA nucleotides is an important field of RNA biochemistry, e.g. in applications of fluorescent labeling or in structural probing experiments, yet detailed structure-function studies of labeling agents are rare. Here, bromomethylcoumarins as reactive compounds for fluorescent labeling of RNA are developed as an attractive scaffold on which electronic properties can be modulated by varying the substituents. Six different 4-bromomethyl-coumarins of various substitution patterns were tested for nucleotide specificity of RNA alkylation using tRNA from Escherichia coli as substrate. Using semi-quantitative LC-MS/MS analysis, reactions at mildly acidic and slightly alkaline pH were compared. For all tested compounds, coumarin conjugates with 4-thiouridine, pseudouridine, guanosine, and uridine were identified, with the latter largely dominating. This data set shows that selectivity of ribonucleotide alkylation depends on the substitution pattern of the reactive dye, and even more strongly on the modulation of the reaction conditions. The latter should be therefore carefully optimized when striving to achieve selectivity. Interestingly, the highest selectivity for labeling of a modified nucleoside, namely of 4-thiouridine, was achieved with a compound whose selectivity was somewhat less dependent on reaction conditions than the other compounds. In summary, bromomethylcoumarin derivatives are a highly interesting class of compounds, since their selectivity for 4-thiouridine can be efficiently tuned by variation of substitution pattern and reaction conditions.

Structure-guided mutational analysis reveals the functional requirements for product specificity of DOT1 enzymes.

Science.gov (United States)

Dindar, Gülcin; Anger, Andreas M; Mehlhorn, Christine; Hake, Sandra B; Janzen, Christian J

2014-11-12

DOT1 enzymes are conserved methyltransferases that catalyse the methylation of lysine 79 on histone H3 (H3K79). Most eukaryotes contain one DOT1 enzyme, whereas African trypanosomes have two homologues, DOT1A and DOT1B, with different enzymatic activities. DOT1A mediates mono- and dimethylation of H3K76, the homologue of H3K79 in other organisms, whereas DOT1B additionally catalyses H3K76 trimethylation. However, it is unclear how these different enzymatic activities are achieved. Here we employ a trypanosomal nucleosome reconstitution system and structure-guided homology modelling to identify critical residues within and outside the catalytic centre that modulate product specificity. Exchange of these residues transfers the product specificity from one enzyme to the other, and reveals the existence of distinct regulatory domains adjacent to the catalytic centre. Our study provides the first evidence that a few crucial residues in DOT1 enzymes are sufficient to catalyse methyl-state-specific reactions. These results might also have far-reaching consequences for the functional understanding of homologous enzymes in higher eukaryotes.

CASL, the Common Algebraic Specification Language

DEFF Research Database (Denmark)

Mossakowski, Till; Haxthausen, Anne Elisabeth; Sannella, Donald

2008-01-01

CASL is an expressive specification language that has been designed to supersede many existing algebraic specification languages and provide a standard. CASL consists of several layers, including basic (unstructured) specifications, structured specifications and architectural specifications...

Guide Structures in CD-ROM Dictionaries, with Specific Reference ...

African Journals Online (AJOL)

Since the appearance of that article, various academics have written articles and read ... The access and mediostructures of the Microsoft Encarta World English ... structures, inner access structure, inner search path, internet, mediostructure, ...

Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

Directory of Open Access Journals (Sweden)

Amy L Bauer

2010-11-01

Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

Inter-specific coral chimerism: Genetically distinct multicellular structures associated with tissue loss in Montipora capitata

Science.gov (United States)

Work, Thierry M.; Forsman, Zac H.; Szabo, Zoltan; Lewis, Teresa D.; Aeby, Greta S.; Toonen, Robert J.

2011-01-01

Montipora white syndrome (MWS) results in tissue-loss that is often lethal to Montipora capitata, a major reef building coral that is abundant and dominant in the Hawai'ian Archipelago. Within some MWS-affected colonies in Kane'ohe Bay, Oahu, Hawai'i, we saw unusual motile multicellular structures within gastrovascular canals (hereafter referred to as invasive gastrovascular multicellular structure-IGMS) that were associated with thinning and fragmentation of the basal body wall. IGMS were in significantly greater densities in coral fragments manifesting tissue-loss compared to paired normal fragments. Mesenterial filaments from these colonies yielded typical M. capitata mitochondrial haplotypes (CO1, CR), while IGMS from the same colony consistently yielded distinct haplotypes previously only found in a different Montipora species (Montipora flabellata). Protein profiles showed consistent differences between paired mesenterial filaments and IGMS from the same colonies as did seven microsatellite loci that also exhibited an excess of alleles per locus inconsistent with a single diploid organism. We hypothesize that IGMS are a parasitic cellular lineage resulting from the chimeric fusion between M. capitata and M. flabellata larvae followed by morphological reabsorption of M. flabellata and subsequent formation of cell-lineage parasites. We term this disease Montiporaiasis. Although intra-specific chimerism is common in colonial animals, this is the first suspected inter-specific example and the first associated with tissue loss.

Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

Science.gov (United States)

Xie, Jianming [San Diego, CA; Wang, Lei [San Diego, CA; Wu, Ning [Boston, MA; Schultz, Peter G [La Jolla, CA

2008-07-15

Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

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Xueyong Zhu

2015-11-01

Full Text Available Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA mutants from ferret-transmissible H5N1 viruses of A/Vietnam/1203/2004 and A/Indonesia/5/2005 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6-linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3-linked sialosides. Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogs reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.

Structural evolution and tissue-specific expression of tetrapod-specific second isoform of secretory pathway Ca2+-ATPase

International Nuclear Information System (INIS)

Pestov, Nikolay B.; Dmitriev, Ruslan I.; Kostina, Maria B.; Korneenko, Tatyana V.; Shakhparonov, Mikhail I.; Modyanov, Nikolai N.

2012-01-01

Highlights: ► Full-length secretory pathway Ca-ATPase (SPCA2) cloned from rat duodenum. ► ATP2C2 gene (encoding SPCA2) exists only in genomes of Tetrapoda. ► Rat and pig SPCA2 are expressed in intestines, lung and some secretory glands. ► Subcellular localization of SPCA2 may depend on tissue type. ► In rat duodenum, SPCA2 is localized in plasma membrane-associated compartments. -- Abstract: Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1. The rat SPCA2 sequence is also highly homologous to putative human protein KIAA0703, however, the latter seems to have an aberrant N-terminus originating from intron 2. The tissue-specificity of SPCA2 expression is different from ubiquitous SPCA1. Rat SPCA2 transcripts were detected predominantly in gastrointestinal tract, lung, trachea, lactating mammary gland, skin and preputial gland. In the newborn pig, the expression profile is very similar with one remarkable exception: porcine bulbourethral gland gave the strongest signal. Upon overexpression in cultured cells, SPCA2 shows an intracellular distribution with remarkable enrichment in Golgi. However, in vivo SPCA2 may be localized in compartments that differ among various tissues: it is intracellular in epidermis, but enriched in plasma membranes of the intestinal epithelium. Analysis of SPCA2 sequences from various vertebrate species argue that ATP2C2 gene radiated from ATP2C1 (encoding SPCA1) during adaptation of tetrapod ancestors to terrestrial habitats.

High resolution bone material property assignment yields robust subject specific finite element models of complex thin bone structures.

Science.gov (United States)

Pakdel, Amirreza; Fialkov, Jeffrey; Whyne, Cari M

2016-06-14

Accurate finite element (FE) modeling of complex skeletal anatomy requires high resolution in both meshing and the heterogeneous mapping of material properties onto the generated mesh. This study introduces Node-based elastic Modulus Assignment with Partial-volume correction (NMAP) as a new approach for FE material property assignment to thin bone structures. The NMAP approach incorporates point spread function based deblurring of CT images, partial-volume correction of CT image voxel intensities and anisotropic interpolation and mapping of CT intensity assignment to FE mesh nodes. The NMAP procedure combined with a derived craniomaxillo-facial skeleton (CMFS) specific density-isotropic elastic modulus relationship was applied to produce specimen-specific FE models of 6 cadaveric heads. The NMAP procedure successfully generated models of the complex thin bone structures with surface elastic moduli reflective of cortical bone material properties. The specimen-specific CMFS FE models were able to accurately predict experimental strains measured under in vitro temporalis and masseter muscle loading (r=0.93, slope=1.01, n=5). The strength of this correlation represents a robust validation for CMFS FE modeling that can be used to better understand load transfer in this complex musculoskeletal system. The developed methodology offers a systematic process-flow able to address the complexity of the CMFS that can be further applied to create high-fidelity models of any musculoskeletal anatomy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

Science.gov (United States)

Mavhunga, Elizabeth

2018-04-01

Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

ReMixT: clone-specific genomic structure estimation in cancer.

Science.gov (United States)

McPherson, Andrew W; Roth, Andrew; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P E; Eirew, Peter; Bouchard-Côté, Alexandre; Aparicio, Sam; Sahinalp, S Cenk; Shah, Sohrab P

2017-07-27

Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .

Common genetic variation near MC4R has a sex-specific impact on human brain structure and eating behavior.

Directory of Open Access Journals (Sweden)

Annette Horstmann

Full Text Available Obesity is associated with genetic and environmental factors but the underlying mechanisms remain poorly understood. Recent genome-wide association studies (GWAS identified obesity- and type 2 diabetes-associated genetic variants located within or near genes that modulate brain activity and development. Among the top hits is rs17782313 near MC4R, encoding for the melanocortin-4-receptor, which is expressed in brain regions that regulate eating. Here, we hypothesized rs17782313-associated changes in human brain regions that regulate eating behavior. Therefore, we examined effects of common variants at rs17782313 near MC4R on brain structure and eating behavior. Only in female homozygous carriers of the risk allele we found significant increases of gray matter volume (GMV in the right amygdala, a region known to influence eating behavior, and the right hippocampus, a structure crucial for memory formation and learning. Further, we found bilateral increases in medial orbitofrontal cortex, a multimodal brain structure encoding the subjective value of reinforcers, and bilateral prefrontal cortex, a higher order regulation area. There was no association between rs17782313 and brain structure in men. Moreover, among female subjects only, we observed a significant increase of 'disinhibition', and, more specifically, on 'emotional eating' scores of the Three Factor Eating Questionnaire in carriers of the variant rs17782313's risk allele. These findings suggest that rs17782313's effect on eating behavior is mediated by central mechanisms and that these effects are sex-specific.

Fat emulsions based on structured lipids (1,3-specific triglycerides): an investigation of the in vivo fate.

Science.gov (United States)

Hedeman, H; Brøndsted, H; Müllertz, A; Frokjaer, S

1996-05-01

Structured lipids (1,3-specific triglycerides) are new chemical entities made by enzymatic transesterification of the fatty acids in the 1,3 positions of the triglyceride. The purpose of this study is to characterize structured lipids with either short chain fatty acids or medium chain fatty acids in the 1,3 positions with regard to their hydrophobicity, and investigate the in vivo fate in order to evaluate the potential of structured lipids as core material in fat emulsions used as parenteral drug delivery system. The lipids were characterized by employing reversed phase high performance liquid chromatography. The biodistribution of radioactively labeled emulsions was studied in rats. By employing high performance liquid chromatography a rank order of the hydrophobicities of the lipids could be given, with the triglycerides containing long chain fatty acids being the most hydrophobic and the structured lipid with short chain fatty acids in the 1,3 positions the least. When formulated as fat emulsions, the emulsion based on structured lipids with short fatty acids in the 1,3 positions was removed slower from the general blood circulation compared to emulsions based on lipids with long chain fatty acids in the 1,3 positions. The type of core material influences the in vivo circulation time of fat emulsions.

Review of technical specifications

International Nuclear Information System (INIS)

Bedrich, M.; Scholz, D.

1980-01-01

The present paper deals with position and function of technical specifications before and during the manufacturing of reactor components, their structure and reasons for specific regulations due to safety philosophy and explains the cooperation of supplier, manufacturer, utilities and supervisory organizations. (RW)

1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

International Nuclear Information System (INIS)

Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

1988-01-01

Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages.

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Mikael Altun

Full Text Available Ovarian tumor domain containing proteases cleave ubiquitin (Ub and ubiquitin-like polypeptides from proteins. Here we report the crystal structure of human otubain 2 (OTUB2 in complex with a ubiquitin-based covalent inhibitor, Ub-Br2. The ubiquitin binding mode is oriented differently to how viral otubains (vOTUs bind ubiquitin/ISG15, and more similar to yeast and mammalian OTUs. In contrast to OTUB1 which has exclusive specificity towards Lys48 poly-ubiquitin chains, OTUB2 cleaves different poly-Ub linked chains. N-terminal tail swapping experiments between OTUB1 and OTUB2 revealed how the N-terminal structural motifs in OTUB1 contribute to modulating enzyme activity and Ub-chain selectivity, a trait not observed in OTUB2, supporting the notion that OTUB2 may affect a different spectrum of substrates in Ub-dependent pathways.

Evolution of Substrate Specificity within a Diverse Family of [beta/alpha]-Barrel-fold Basic Amino Acid Decarboxylases X-ray Structure Determination of Enzymes with Specificity for L-Arginine and Carboxynorspermidine

Energy Technology Data Exchange (ETDEWEB)

Deng, Xiaoyi; Lee, Jeongmi; Michael, Anthony J.; Tomchick, Diana R.; Goldsmith, Elizabeth J.; Phillips, Margaret A. (Sungkyunkwan); (UTSMC)

2010-08-26

Pyridoxal 5{prime}-phosphate (PLP)-dependent basic amino acid decarboxylases from the {beta}/{alpha}-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2.3- and 2.0-{angstrom} resolution, solved as product complexes with agmatine and norspermidine. Despite low overall sequence identity, the monomeric and dimeric structures are similar to other enzymes in the family, with the active sites formed between the {beta}/{alpha}-barrel domain of one subunit and the {beta}-barrel of the other. ADC contains both a unique interdomain insertion (4-helical bundle) and a C-terminal extension (3-helical bundle) and it packs as a tetramer in the asymmetric unit with the insertions forming part of the dimer and tetramer interfaces. Analytical ultracentrifugation studies confirmed that the ADC solution structure is a tetramer. Specificity for different basic amino acids appears to arise primarily from changes in the position of, and amino acid replacements in, a helix in the {beta}-barrel domain we refer to as the 'specificity helix.' Additionally, in CANSDC a key acidic residue that interacts with the distal amino group of other substrates is replaced by Leu{sup 314}, which interacts with the aliphatic portion of norspermidine. Neither product, agmatine in ADC nor norspermidine in CANSDC, form a Schiff base to pyridoxal 5{prime}-phosphate, suggesting that the product complexes may promote product release by slowing the back reaction. These studies provide insight into the structural basis for the evolution of novel function within a common structural-fold.

Structural modeling of age specific fertility curves in Peninsular Malaysia: An approach of Lee Carter method

Science.gov (United States)

Hanafiah, Hazlenah; Jemain, Abdul Aziz

2013-11-01

In recent years, the study of fertility has been getting a lot of attention among research abroad following fear of deterioration of fertility led by the rapid economy development. Hence, this study examines the feasibility of developing fertility forecasts based on age structure. Lee Carter model (1992) is applied in this study as it is an established and widely used model in analysing demographic aspects. A singular value decomposition approach is incorporated with an ARIMA model to estimate age specific fertility rates in Peninsular Malaysia over the period 1958-2007. Residual plots is used to measure the goodness of fit of the model. Fertility index forecast using random walk drift is then utilised to predict the future age specific fertility. Results indicate that the proposed model provides a relatively good and reasonable data fitting. In addition, there is an apparent and continuous decline in age specific fertility curves in the next 10 years, particularly among mothers' in their early 20's and 40's. The study on the fertility is vital in order to maintain a balance between the population growth and the provision of facilities related resources.

Structure of ‘linkerless’ hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket

Energy Technology Data Exchange (ETDEWEB)

Tabackman, Alexa A.; Frankson, Rochelle; Marsan, Eric S.; Perry, Kay; Cole, Kathryn E. (Ithaca); (Cornell); (Christopher Newport U)

2016-11-04

Histone deacetylases (HDACs) catalyze the hydrolysis of acetylated lysine side chains in histone and non-histone proteins, and play a critical role in the regulation of many biological processes, including cell differentiation, proliferation, senescence, and apoptosis. Aberrant HDAC activity is associated with cancer, making these enzymes important targets for drug design. In general, HDAC inhibitors (HDACi) block the proliferation of tumor cells by inducing cell differentiation, cell cycle arrest, and/or apoptosis, and comprise some of the leading therapies in cancer treatments. To date, four HDACi have been FDA approved for the treatment of cancers: suberoylanilide hydroxamic acid (SAHA, Vorinostat, Zolinza®), romidepsin (FK228, Istodax®), belinostat (Beleodaq®), and panobinostat (Farydak®). Most current inhibitors are pan-HDACi, and non-selectively target a number of HDAC isoforms. Six previously reported HDACi were rationally designed, however, to target a unique sub-pocket found only in HDAC8. While these inhibitors were indeed potent against HDAC8, and even demonstrated specificity for HDAC8 over HDACs 1 and 6, there were no structural data to confirm the mode of binding. Here we report the X-ray crystal structure of Compound 6 complexed with HDAC8 to 1.98 Å resolution. We also describe the use of molecular docking studies to explore the binding interactions of the other 5 related HDACi. Our studies confirm that the HDACi induce the formation of and bind in the HDAC8-specific subpocket, offering insights into isoform-specific inhibition.

Development of a patient-specific anatomical foot model from structured light scan data.

Science.gov (United States)

Lochner, Samuel J; Huissoon, Jan P; Bedi, Sanjeev S

2014-01-01

The use of anatomically accurate finite element (FE) models of the human foot in research studies has increased rapidly in recent years. Uses for FE foot models include advancing knowledge of orthotic design, shoe design, ankle-foot orthoses, pathomechanics, locomotion, plantar pressure, tissue mechanics, plantar fasciitis, joint stress and surgical interventions. Similar applications but for clinical use on a per-patient basis would also be on the rise if it were not for the high costs associated with developing patient-specific anatomical foot models. High costs arise primarily from the expense and challenges of acquiring anatomical data via magnetic resonance imaging (MRI) or computed tomography (CT) and reconstructing the three-dimensional models. The proposed solution morphs detailed anatomy from skin surface geometry and anatomical landmarks of a generic foot model (developed from CT or MRI) to surface geometry and anatomical landmarks acquired from an inexpensive structured light scan of a foot. The method yields a patient-specific anatomical foot model at a fraction of the cost of standard methods. Average error for bone surfaces was 2.53 mm for the six experiments completed. Highest accuracy occurred in the mid-foot and lowest in the forefoot due to the small, irregular bones of the toes. The method must be validated in the intended application to determine if the resulting errors are acceptable.

Molecular mechanisms of conformational specificity: A study of Hox in vivo target DNA binding specificities and the structure of a Ure2p mutation that affects fibril formation rates

Science.gov (United States)

Bauer, William Joseph, Jr.

The fate of an individual cell, or even an entire organism, is often determined by minute, yet very specific differences in the conformation of a single protein species. Very often, proteins take on alternate folds or even side chain conformations to deal with different situations present within the cell. These differences can be as large as a whole domain or as subtle as the alteration of a single amino acid side chain. Yet, even these seemingly minor side chain conformational differences can determine the development of a cell type during differentiation or even dictate whether a cell will live or die. Two examples of situations where minor conformational differences within a specific protein could lead to major differences in the life cycle of a cell are described herein. The first example describes the variations seen in DNA conformations which can lead to slightly different Hox protein binding conformations responsible for recognizing biologically relevant regulatory sites. These specific differences occur in the minor groove of the bound DNA and are limited to the conformation of only two side chains. The conformation of the bound DNA, however, is not solely determined by the sequence of the DNA, as multiple sequences can result in the same DNA conformation. The second example takes place in the context of a yeast prion protein which contains a mutation that decreases the frequency at which fibrils form. While the specific interactions leading to this physiological change were not directly detected, it can be ascertained from the crystal structure that the structural changes are subtle and most likely involve another binding partner. In both cases, these conformational changes are very slight but have a profound effect on the downstream processes.

Probe specificity

International Nuclear Information System (INIS)

Laget, J.M.

1986-11-01

Specificity and complementarity of hadron and electron probes must be systematically developed to answer three questions currently asked in intermediate energy nuclear physics: what is nucleus structure at short distances, what is nature of short range correlations, what is three body force nature [fr

Non-verbal emotion communication training induces specific changes in brain function and structure.

Science.gov (United States)

Kreifelts, Benjamin; Jacob, Heike; Brück, Carolin; Erb, Michael; Ethofer, Thomas; Wildgruber, Dirk

2013-01-01

The perception of emotional cues from voice and face is essential for social interaction. However, this process is altered in various psychiatric conditions along with impaired social functioning. Emotion communication trainings have been demonstrated to improve social interaction in healthy individuals and to reduce emotional communication deficits in psychiatric patients. Here, we investigated the impact of a non-verbal emotion communication training (NECT) on cerebral activation and brain structure in a controlled and combined functional magnetic resonance imaging (fMRI) and voxel-based morphometry study. NECT-specific reductions in brain activity occurred in a distributed set of brain regions including face and voice processing regions as well as emotion processing- and motor-related regions presumably reflecting training-induced familiarization with the evaluation of face/voice stimuli. Training-induced changes in non-verbal emotion sensitivity at the behavioral level and the respective cerebral activation patterns were correlated in the face-selective cortical areas in the posterior superior temporal sulcus and fusiform gyrus for valence ratings and in the temporal pole, lateral prefrontal cortex and midbrain/thalamus for the response times. A NECT-induced increase in gray matter (GM) volume was observed in the fusiform face area. Thus, NECT induces both functional and structural plasticity in the face processing system as well as functional plasticity in the emotion perception and evaluation system. We propose that functional alterations are presumably related to changes in sensory tuning in the decoding of emotional expressions. Taken together, these findings highlight that the present experimental design may serve as a valuable tool to investigate the altered behavioral and neuronal processing of emotional cues in psychiatric disorders as well as the impact of therapeutic interventions on brain function and structure.

Structural evolution and tissue-specific expression of tetrapod-specific second isoform of secretory pathway Ca{sup 2+}-ATPase

Energy Technology Data Exchange (ETDEWEB)

Pestov, Nikolay B., E-mail: korn@mail.ibch.ru [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Dmitriev, Ruslan I.; Kostina, Maria B. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Korneenko, Tatyana V. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Department of Physiology and Pharmacology, University of Toledo College of Medicine, 3000 Arlington Ave., Toledo, OH 43614 (United States); Shakhparonov, Mikhail I. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871 (Russian Federation); Modyanov, Nikolai N., E-mail: nikolai.modyanov@utoledo.edu [Department of Physiology and Pharmacology, University of Toledo College of Medicine, 3000 Arlington Ave., Toledo, OH 43614 (United States)

2012-01-27

Highlights: Black-Right-Pointing-Pointer Full-length secretory pathway Ca-ATPase (SPCA2) cloned from rat duodenum. Black-Right-Pointing-Pointer ATP2C2 gene (encoding SPCA2) exists only in genomes of Tetrapoda. Black-Right-Pointing-Pointer Rat and pig SPCA2 are expressed in intestines, lung and some secretory glands. Black-Right-Pointing-Pointer Subcellular localization of SPCA2 may depend on tissue type. Black-Right-Pointing-Pointer In rat duodenum, SPCA2 is localized in plasma membrane-associated compartments. -- Abstract: Secretory pathway Ca-ATPases are less characterized mammalian calcium pumps than plasma membrane Ca-ATPases and sarco-endoplasmic reticulum Ca-ATPases. Here we report analysis of molecular evolution, alternative splicing, tissue-specific expression and subcellular localization of the second isoform of the secretory pathway Ca-ATPase (SPCA2), the product of the ATP2C2 gene. The primary structure of SPCA2 from rat duodenum deduced from full-length transcript contains 944 amino acid residues, and exhibits 65% sequence identity with known SPCA1. The rat SPCA2 sequence is also highly homologous to putative human protein KIAA0703, however, the latter seems to have an aberrant N-terminus originating from intron 2. The tissue-specificity of SPCA2 expression is different from ubiquitous SPCA1. Rat SPCA2 transcripts were detected predominantly in gastrointestinal tract, lung, trachea, lactating mammary gland, skin and preputial gland. In the newborn pig, the expression profile is very similar with one remarkable exception: porcine bulbourethral gland gave the strongest signal. Upon overexpression in cultured cells, SPCA2 shows an intracellular distribution with remarkable enrichment in Golgi. However, in vivo SPCA2 may be localized in compartments that differ among various tissues: it is intracellular in epidermis, but enriched in plasma membranes of the intestinal epithelium. Analysis of SPCA2 sequences from various vertebrate species argue that ATP2C2

Nitrides and carbides of molybdenum and tungsten with high specific-surface area: their synthesis, structure, and catalytic properties

International Nuclear Information System (INIS)

Volpe, L.

1985-01-01

Temperature-programmed reactions between trioxides of molybdenum or tungsten and ammonia provide a new method to synthesize dimolybdenum and ditungsten nitrides with specific surface areas to two-hundred-and-twenty and ninety-one square meters per gram, respectively. These are the highest values on record for any unsupported metallic powders. They correspond to three-four nonometer particles. The reaction of molybdenum trioxide with ammonia is topotactic in the sense that one-zero-zero planes of dimolybdenum nitride are parallel to zero-one-zero planes of molybdenum trioxide. As the trioxide transforms, it passes through an oxynitride intermediate with changing bulk structure and increasing surface area and extent of reduction. The nitride product consists of platelets, pseudomorphous with the original trioxide, which can be regarded as highly porous defect single crystals. By treating small particles of dimolybdenum or ditungsten nitride with methane-dihydrogen mixtures it is possible to replace interstitial nitrogen atoms by carbon atoms, without sintering, and thus to prepare carbides of molybdenum and tungsten with very high specific surface areas. Molybdenum nitride powders catalyze ammonia synthesis. A pronounced increase in the catalytic activity with increasing particle size confirms the structure-sensitive character of this reaction

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng

2015-09-09

To detect and evaluate the similarities between the three-dimensional (3D) structures of two molecules, various kinds of methods have been proposed for the pairwise structure alignment problem [6, 9, 7, 11]. The problem plays important roles when studying the function and the evolution of biological molecules. Recently, pairwise structure alignment methods have been extended and applied on surface pocket structures [10, 3, 5] and interaction interface structures [8, 4]. The results show that, even when there are no global similarities discovered between the global sequences and the global structures, biological molecules or complexes could share similar functions because of well conserved pockets and interfaces. Thus, pairwise pocket and interface structure alignments are promising to unveil such shared functions that cannot be discovered by the well-studied global sequence and global structure alignments. State-of-the-art methods for pairwise pocket and interface structure alignments [4, 5] are direct extensions of the classic pairwise protein structure alignment methods, and thus such methods share a few limitations. First, the goal of the classic protein structure alignment methods is to align single-chain protein structures (i.e., a single fragment of residues connected by peptide bonds). However, we observed that pockets and interfaces tend to consist of tens of extremely short backbone fragments (i.e., three or fewer residues connected by peptide bonds). Thus, existing pocket and interface alignment methods based on the protein structure alignment methods still rely on the existence of long-enough backbone fragments, and the fragmentation issue of pockets and interfaces rises the risk of missing the optimal alignments. Moreover, existing interface structure alignment methods focus on protein-protein interfaces, and require a "blackbox preprocessing" before aligning protein-DNA and protein-RNA interfaces. Therefore, we introduce the PROtein STucture Alignment

Site-specific issues related to structural/seismic design of an underground independent spent fuel storage installation (ISFSI)

International Nuclear Information System (INIS)

Tripathi, B.P.

2005-01-01

Utilities owning and operating commercial nuclear power plants (NPP) in USA may choose to build an underground Independent Spent Fuel Storage Installation (ISFSI) to store the spent nuclear fuels. The regulatory requirements and other guidance are based on 10 CFR Part 72, Regulatory Guide RG 3.73, Standard Review Plans NUREG-1536 and NUREG-1567, and Interim staff Guidance (ISG) documents as applicable. Structures, Systems, and Components (SSCs) classified as important to safety are designed to withstand the effects of site-specific environmental conditions and natural phenomena such as earthquake, tornado, flood, etc. An underground ISFSI for storage of spent nuclear fuel, presents some unique analysis and design challenges. This paper will briefly address some of these challenges and discuss site-specific loads, including seismic for the ISFSI design. (authors)

The Chemically-Specific Structure of an Amorphous Molybdenum Germanium Alloy by Anomalous X-ray Scattering

Energy Technology Data Exchange (ETDEWEB)

Ishii, H. A.

2002-06-11

Since its inception in the late 1970s, anomalous x-ray scattering (AXS) has been employed for chemically-specific structure determination in a wide variety of noncrystalline materials. These studies have successfully produced differential distribution functions (DDFs) which provide information about the compositionally-averaged environment of a specific atomic species in the sample. Despite the wide success in obtaining DDFs, there are very few examples of successful extraction of the fully-chemically-specific partial pair distribution functions (PPDFs), the most detailed description of an amorphous sample possible by x-ray scattering. Extracting the PPDFs is notoriously difficult since the matrix equation involved is ill-conditioned and thus extremely sensitive to errors present in the experimental quantities that enter the equation. Instead of addressing this sensitivity by modifying the data through mathematical methods, sources of error have been removed experimentally: A focusing analyzer crystal was combined with a position-sensitive linear detector to experimentally eliminate unwanted inelastic scattering intensity over most of the reciprocal space range probed. This instrumentation has been used in data collection for the extraction of PPDFs from amorphous (a)-MoGe{sub 3}. This composition arises as a phase separation endpoint in the Ge-rich region of the vapor-deposited Mo-Ge amorphous alloy system but is not present at equilibrium. Since the first Ge-rich compound in the Mo-Ge equilibrium system is MoGe{sub 2}, previous workers have speculated that perhaps a unique MoGe{sub 3} compound exists in the amorphous system. Rather than indicating a distinct MoGe{sub 3} compound with definitive local structure, however, the coordination results are more consistent with a densely-packed alloy having a wide range of solid solubility. Significant improvement in the quality and reliability of experimental PPDFs from a-MoGe{sub 3} by AXS has been achieved solely

An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.

Science.gov (United States)

Ingemarsdotter, Carin K; Zeng, Jingwei; Long, Ziqi; Lever, Andrew M L; Kenyon, Julia C

2018-03-14

NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594

Industry-specificities and Size of Corporations: Determinants of Ownership Structures

NARCIS (Netherlands)

van der Elst, C.

This paper analyses ownership concentration in six European countries and empirically studies the rent-seeking theory. This theory states that ownership concentration not only depends on the level of investor protection but also on company-specific and industry-specific parameters. This study

Structural and Kinetic Properties of the Aldehyde Dehydrogenase NahF, a Broad Substrate Specificity Enzyme for Aldehyde Oxidation.

Science.gov (United States)

Coitinho, Juliana B; Pereira, Mozart S; Costa, Débora M A; Guimarães, Samuel L; Araújo, Simara S; Hengge, Alvan C; Brandão, Tiago A S; Nagem, Ronaldo A P

2016-09-27

The salicylaldehyde dehydrogenase (NahF) catalyzes the oxidation of salicylaldehyde to salicylate using NAD(+) as a cofactor, the last reaction of the upper degradation pathway of naphthalene in Pseudomonas putida G7. The naphthalene is an abundant and toxic compound in oil and has been used as a model for bioremediation studies. The steady-state kinetic parameters for oxidation of aliphatic or aromatic aldehydes catalyzed by 6xHis-NahF are presented. The 6xHis-NahF catalyzes the oxidation of aromatic aldehydes with large kcat/Km values close to 10(6) M(-1) s(-1). The active site of NahF is highly hydrophobic, and the enzyme shows higher specificity for less polar substrates than for polar substrates, e.g., acetaldehyde. The enzyme shows α/β folding with three well-defined domains: the oligomerization domain, which is responsible for the interlacement between the two monomers; the Rossmann-like fold domain, essential for nucleotide binding; and the catalytic domain. A salicylaldehyde molecule was observed in a deep pocket in the crystal structure of NahF where the catalytic C284 and E250 are present. Moreover, the residues G150, R157, W96, F99, F274, F279, and Y446 were thought to be important for catalysis and specificity for aromatic aldehydes. Understanding the molecular features responsible for NahF activity allows for comparisons with other aldehyde dehydrogenases and, together with structural information, provides the information needed for future mutational studies aimed to enhance its stability and specificity and further its use in biotechnological processes.

Production of specifically structured lipids by enzymatic interesterification in a pilot enzyme bed reactor: process optimization by response surface methodology

DEFF Research Database (Denmark)

Xu, Xuebing; Mu, Huiling; Høy, Carl-Erik

1999-01-01

Pilot production of specifically structured lipids by Lipozyme IM-catalyzed interesterification was carried out in a continuous enzyme bed reactor without the use of solvent. Medium chain triacylglycerols and oleic acid were used as model substrates. Response surface methodology was applied...... and the production of mono-incorporated and di-incorporated structured lipids with multiple regression and backward elimination. The coefficient of determination (R2) for the incorporation was 0.93, and that for the di-incorporated products was 0.94. The optimal conditions were flow rate, 2 ml/min; temperature, 65...

Structural basis for the substrate specificity and the absence of dehalogenation activity in 2-chloromuconate cycloisomerase from Rhodococcus opacus 1CP.

Science.gov (United States)

Kolomytseva, Marina; Ferraroni, Marta; Chernykh, Alexey; Golovleva, Ludmila; Scozzafava, Andrea

2014-09-01

2-Chloromuconate cycloisomerase from the Gram-positive bacterium Rhodococcus opacus 1CP (Rho-2-CMCI) is an enzyme of a modified ortho-pathway, in which 2-chlorophenol is degraded using 3-chlorocatechol as the central intermediate. In general, the chloromuconate cycloisomerases catalyze not only the cycloisomerization, but also the process of dehalogenation of the chloromuconate to dienelactone. However Rho-2-CMCI, unlike the homologous enzymes from the Gram-negative bacteria, is very specific for only one position of the chloride on the substrate chloromuconate. Furthermore, Rho-2-CMCI is not able to dehalogenate the 5-chloromuconolactone and therefore it cannot generate the dienelactone. The crystallographic structure of the homooctameric Rho-2-CMCI was solved by molecular replacement using the coordinates of the structure of chloromuconate cycloisomerase from Pseudomonas putida PRS2000. The structure was analyzed and compared to the other already known structures of (chloro)muconate cycloisomerases. In addition to this, molecular docking calculations were carried out, which allowed us to determine the residues responsible for the high substrate specificity and the lack of dehalogenation activity of Rho-2-CMCI. Our studies highlight that a histidine, located in a loop that closes the active site cavity upon the binding of the substrate, could be related to the dehalogenation inability of Rho-2-CMCI and in general of the muconate cycloisomerases. Copyright © 2014 Elsevier B.V. All rights reserved.

Structure of a bacterial glycoside hydrolase family 63 enzyme in complex with its glycosynthase product, and insights into the substrate specificity.

Science.gov (United States)

Miyazaki, Takatsugu; Ichikawa, Megumi; Yokoi, Gaku; Kitaoka, Motomitsu; Mori, Haruhide; Kitano, Yoshikazu; Nishikawa, Atsushi; Tonozuka, Takashi

2013-09-01

Proteins belonging to glycoside hydrolase family 63 (GH63) are found in bacteria, archaea and eukaryotes. Although the eukaryotic GH63 proteins have been identified as processing α-glucosidase I, the substrate specificities of the bacterial and archaeal GH63 proteins are not clear. Here, we converted a bacterial GH63 enzyme, Escherichia coli YgjK, to a glycosynthase to probe its substrate specificity. Two mutants of YgjK (E727A and D324N) were constructed, and both mutants showed glycosynthase activity. The reactions of E727A with β-D-glucosyl fluoride and monosaccharides showed that the largest amount of glycosynthase product accumulated when galactose was employed as an acceptor molecule. The crystal structure of E727A complexed with the reaction product indicated that the disaccharide bound at the active site was 2-O-α-D-glucopyranosyl-α-D-galactopyranose (Glc12Gal). A comparison of the structures of E727A-Glc12Gal and D324N-melibiose showed that there were two main types of conformation: the open and closed forms. The structure of YgjK adopted the closed form when subsite -1 was occupied by glucose. These results suggest that sugars containing the Glc12Gal structure are the most likely candidates for natural substrates of YgjK. © 2013 FEBS.

Crystal structures of the human G3BP1 NTF2-like domain visualize FxFG Nup Repeat Specificity

DEFF Research Database (Denmark)

Vognsen, Tina Reinholdt; Möller, Ingvar Rúnar; Kristensen, Ole

2013-01-01

Ras GTPase Activating Protein SH3 Domain Binding Protein (G3BP) is a potential anti-cancer drug target implicated in several cellular functions. We have used protein crystallography to solve crystal structures of the human G3BP1 NTF2-like domain both alone and in complex with an FxFG Nup repeat...... peptide. Despite high structural similarity, the FxFG binding site is located between two alpha helices in the G3BP1 NTF2-like domain and not at the dimer interface as observed for nuclear transport factor 2. ITC studies showed specificity towards the FxFG motif but not FG and GLFG motifs. The unliganded...

45S5 bioglass: modifications in the structural arrangement to meet specific needs in bone regeneration

International Nuclear Information System (INIS)

Silva, A.C.; Braga, J.F.C.; Aparecida, A.H.

2011-01-01

After surgical implantation the osteoinductivity property, observed in bioactive materials, is mainly due to the formation of calcium phosphate on these materials surface when in body fluids contact. The dissolution and diffusion phenomena in bioglass are result of it's structural arrangement and govern the osteoinductivity property. In structural arrangement of bioglass, silica segments are linked by phosphate groups, defining the distance between the vitreous network segments and thereby influence of cations diffusion rate through the network and the dissolution rate. Thus, the induced changes in arrangement of phosphate groups can control the intensity of material osteoinductivity in order to fit bone regeneration requirements. In this study, P_2O_5 nanoclusters formation were induced in bioglass 45S5 network structure. The bioactive glasses were prepared by melting at 1500°C in platinum crucibles and annealed between 2 and 24 h at 500°C. The characterization was performed using the following techniques, X-ray diffraction (XRD), Infrared spectroscopy (FT-IR) and hydrolytic resistance. In bioglasses 24 hours heat-treated, there was evidence of nanocrystals formation, dissolution rate, significant increase and consequently the property of osteoinductive. The obtained results indicated the potential of development of biomaterials for specific applications in bone regeneration. (author)

Physiological and transcriptional characterization of Saccharomyces cerevisiae engineered for production of fatty acid ethyl esters

DEFF Research Database (Denmark)

de Jong, Bouke Wim; Siewers, Verena; Nielsen, Jens

2016-01-01

gene (ws2) and strain BdJ15, containing disruptions of genes DGA1, LRO1, ARE1, ARE2 and POX1, which prevent the conversion of acyl-CoA to sterol esters, triacylglycerides and the degradation to acetyl-CoA, triggered oxidative stress that consequently influenced cellular growth. In the latter strain...

Genome-wide analysis of the expansin gene superfamily reveals grapevine-specific structural and functional characteristics.

Directory of Open Access Journals (Sweden)

Silvia Dal Santo

Full Text Available BACKGROUND: Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP comprises four distinct families: expansin A (EXPA, expansin B (EXPB, expansin-like A (EXLA and expansin-like B (EXLB. There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far. METHODOLOGY/PRINCIPAL FINDINGS: We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon-intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa, compared to those from Arabidopsis thaliana and rice (Oryza sativa. We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering. CONCLUSION: Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the

Universal fine structure of the specific heat at the critical λ-point for an ideal Bose gas in an arbitrary trap

International Nuclear Information System (INIS)

Tarasov, S V; Kocharovsky, Vl V; Kocharovsky, V V

2014-01-01

We analytically find the universal fine structure of the noted discontinuity in the value and/or derivative of the specific heat of an ideal Bose gas in an arbitrary trap in the whole critical region around the λ-point of the Bose–Einstein condensation. The result reveals a remarkable dependence of the λ-point structure on the trap's form and boundary conditions, even for a macroscopically large system. We suggest measuring this strong effect in the experiments with a controllable trap potential. (paper)

FATTY ACID ETHYL ESTERS FROM MICROALGAE OF Scenedesmus ecornis BY ENZYMATIC AND ACID CATALYSIS

Directory of Open Access Journals (Sweden)

Gabryelle F. de Almeida

Full Text Available Microalgae are an indispensable food source for the various growth stages of mollusks, crustaceans, and several fish species. Using a microalgae biomass present in the Amazonian ecosystem (Macapá-AP, we study extraction methods for fatty acid such as solvent extraction (magnetic stirring and/or Soxhlet and/or hydrolysis (acid and/or enzymatic catalysis followed by esterification and/or direct transesterification. Extraction of crude triacylglycerides by mechanical stirring at room temperature was more efficient than continuous reflux (Soxhlet. Subsequently, the lipid extract was subject to transesterification with ethanol and CAL-B as a biocatalyst, leading to production of fatty acid ethyl esters (FAEE. Additionally, FAEEs were prepared by hydrolysis of crude triacylglycerides followed by acid-mediated esterification or enzymatic catalysis (lipase. In this case, the type of catalyst did not significantly influence FAEE yields. In the lipid extract, we identified palmitic, linoleic, oleic, and stearic acids with palmitic acid being the most abundant. Our results suggest that enzymatic catalysis is a viable method for the extraction of lipids in the microalga, Scenedesmus ecornis.

The Structural Basis of Cryptosporidium-Specific IMP Dehydrogenase Inhibitor Selectivity

Energy Technology Data Exchange (ETDEWEB)

MacPherson, Iain S.; Kirubakaran, Sivapriya; Gorla, Suresh Kumar; Riera, Thomas V.; D’Aquino, J. Alejandro; Zhang, Minjia; Cuny, Gregory D.; Hedstrom, Lizbeth (BWH); (Brandeis)

2010-03-29

Cryptosporidium parvum is a potential biowarfare agent, an important AIDS pathogen, and a major cause of diarrhea and malnutrition. No vaccines or effective drug treatment exist to combat Cryptosporidium infection. This parasite relies on inosine 5{prime}-monophosphate dehydrogenase (IMPDH) to obtain guanine nucleotides, and inhibition of this enzyme blocks parasite proliferation. Here, we report the first crystal structures of CpIMPDH. These structures reveal the structural basis of inhibitor selectivity and suggest a strategy for further optimization. Using this information, we have synthesized low-nanomolar inhibitors that display 10{sup 3} selectivity for the parasite enzyme over human IMPDH2.

Determination and analysis of site-specific 125I decay-induced DNA double-strand break end-group structures.

Science.gov (United States)

Datta, Kamal; Weinfeld, Michael; Neumann, Ronald D; Winters, Thomas A

2007-02-01

End groups contribute to the structural complexity of radiation-induced DNA double-strand breaks (DSBs). As such, end-group structures may affect a cell's ability to repair DSBs. The 3'-end groups of strand breaks caused by gamma radiation, or oxidative processes, under oxygenated aqueous conditions have been shown to be distributed primarily between 3'-phosphoglycolate and 3'-phosphate, with 5'-phosphate ends in both cases. In this study, end groups of the high-LET-like DSBs caused by 125I decay were investigated. Site-specific DNA double-strand breaks were produced in plasmid pTC27 in the presence or absence of 2 M DMSO by 125I-labeled triplex-forming oligonucleotide targeting. End-group structure was assessed enzymatically as a function of the DSB end to serve as a substrate for ligation and various forms of end labeling. Using this approach, we have demonstrated 3'-hydroxyl (3'-OH) and 3'-phosphate (3'-P) end groups and 5'-ends (> or = 42%) terminated by phosphate. A 32P postlabeling assay failed to detect 3'-phosphoglycolate in a restriction fragment terminated by the 125I-induced DNA double-strand break, and this is likely due to restricted oxygen diffusion during irradiation as a frozen aqueous solution. Even so, end-group structure and relative distribution varied as a function of the free radical scavenging capacity of the irradiation buffer.

Lsd1 Ablation Triggers Metabolic Reprogramming of Brown Adipose Tissue

Directory of Open Access Journals (Sweden)

Delphine Duteil

2016-10-01

Full Text Available Previous work indicated that lysine-specific demethylase 1 (Lsd1 can positively regulate the oxidative and thermogenic capacities of white and beige adipocytes. Here we investigate the role of Lsd1 in brown adipose tissue (BAT and find that BAT-selective Lsd1 ablation induces a shift from oxidative to glycolytic metabolism. This shift is associated with downregulation of BAT-specific and upregulation of white adipose tissue (WAT-selective gene expression. This results in the accumulation of di- and triacylglycerides and culminates in a profound whitening of BAT in aged Lsd1-deficient mice. Further studies show that Lsd1 maintains BAT properties via a dual role. It activates BAT-selective gene expression in concert with the transcription factor Nrf1 and represses WAT-selective genes through recruitment of the CoREST complex. In conclusion, our data uncover Lsd1 as a key regulator of gene expression and metabolic function in BAT.

Towards Patient-Tailored Perimetry: Automated Perimetry Can Be Improved by Seeding Procedures With Patient-Specific Structural Information

Science.gov (United States)

Denniss, Jonathan; McKendrick, Allison M.; Turpin, Andrew

2013-01-01

Purpose: To explore the performance of patient-specific prior information, for example, from structural imaging, in improving perimetric procedures. Methods: Computer simulation was used to determine the error distribution and presentation count for Structure–Zippy Estimation by Sequential Testing (ZEST), a Bayesian procedure with prior distribution centered on a threshold prediction from structure. Structure-ZEST (SZEST) was trialled for single locations with combinations of true and predicted thresholds between 1 to 35 dB, and compared with a standard procedure with variability similar to Swedish Interactive Thresholding Algorithm (SITA) (Full-Threshold, FT). Clinical tests of glaucomatous visual fields (n = 163, median mean deviation −1.8 dB, 90% range +2.1 to −22.6 dB) were also compared between techniques. Results: For single locations, SZEST typically outperformed FT when structural predictions were within ± 9 dB of true sensitivity, depending on response errors. In damaged locations, mean absolute error was 0.5 to 1.8 dB lower, SD of threshold estimates was 1.2 to 1.5 dB lower, and 2 to 4 (29%–41%) fewer presentations were made for SZEST. Gains were smaller across whole visual fields (SZEST, mean absolute error: 0.5 to 1.2 dB lower, threshold estimate SD: 0.3 to 0.8 dB lower, 1 [17%] fewer presentation). The 90% retest limits of SZEST were median 1 to 3 dB narrower and more consistent (interquartile range 2–8 dB narrower) across the dynamic range than those for FT. Conclusion: Seeding Bayesian perimetric procedures with structural measurements can reduce test variability of perimetry in glaucoma, despite imprecise structural predictions of threshold. Translational Relevance: Structural data can reduce the variability of current perimetric techniques. A strong structure–function relationship is not necessary, however, structure must predict function within ±9 dB for gains to be realized. PMID:24049720

Relationship of binding specificity and structural property of the technetium-99m complexes for tumor hypoxia and tumor angiogenesis imaging

International Nuclear Information System (INIS)

Su, Z.F.

2005-01-01

The growth of tumor requires nutrition and oxygen. Tumor cells will become hypoxic when the supply of oxygen is insufficient. Hypoxic tumor cells will not only resist radiation therapy and chemotherapy, but also induce angiogenesis for oxygen supply and for metastasis. Therefore, detection of tumor hypoxia and tumor angiogenesis with high sensitive radio labeled imaging agents is important. Hypoxic tumor cells may display some molecules as tumor markers for the specific binding with radiopharmaceuticals. Radiopharmaceuticals, unlike the non-radioactive drugs, are trace compounds in a given dosage. Due to the extreme low concentration, the non-specific accumulation of the radiotracers by blood cells and proteins, tissues, and organs can be even more serious compared to the non-radioactive drugs. The non-specific accumulation of the radiotracers can make the ratios of tumor/tissue (in terms of i.d.%/g) falling to the range of 2∼7 [1-2]. Non-specific binding of radiopharmaceuticals is common, but detailed studies on it are poor documented. This presentation reports the study of the relationship of non-specific accumulation and the structural property of two type of 99m TC labeled compounds: (a) 99m Tc-(amine o xime) containing either 2-nitroimidazole (2-NI, as hypoxia tumor cells specific agents), or 4-nitro- imidazole (4-NI, as control), or aniline (as reference) groups; (b) 99m Tc-(arginine-glycine- aspartic acid, RGD, as tumor angiogenesis specific agents) and 99m Tc-(arginine-glycine- glutarmic acid, RGE, as control). The 99m Tc-(amine-oxime) complexes, in addition to the 2-NI, 4-NI, and aniline groups, contain methyl-, ethyl-, propyl-, iso-butyl-, t-butyl-, phenyl-, and Benzyl- groups as well to make the radiotracers differing in structure and in lipophilicity , while the lipophilicity of a radiotracer plays an important role in non-specific cellular accumulation and protein binding, The results demonstrated that (1) the complex containing 2-NI showed specific

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.

Science.gov (United States)

Johnson, Jennifer L; Entzminger, Kevin C; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P; Morales, Ivan A; Sheppard, Aly; Gumbart, James C; Maynard, Jennifer A; Lieberman, Raquel L

2015-04-01

Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.

Amplification of the active site of BnLIP3 gene of Brassica napus L ...

African Journals Online (AJOL)

Lipases are useful enzymes that are responsible for the hydrolysis of triacylglycerides and play an important role in plant growth. In this study, we report a rapid molecular method to amplify a partial sequence of the lipase class 3 family designated BnLIP3 gene of Brassica napus L. in order to follow its expression and ...

Disorder-specific predictive classification of adolescents with attention deficit hyperactivity disorder (ADHD relative to autism using structural magnetic resonance imaging.

Directory of Open Access Journals (Sweden)

Lena Lim

Full Text Available Attention Deficit Hyperactivity Disorder (ADHD is a neurodevelopmental disorder, but diagnosed by subjective clinical and rating measures. The study's aim was to apply Gaussian process classification (GPC to grey matter (GM volumetric data, to assess whether individual ADHD adolescents can be accurately differentiated from healthy controls based on objective, brain structure measures and whether this is disorder-specific relative to autism spectrum disorder (ASD.Twenty-nine adolescent ADHD boys and 29 age-matched healthy and 19 boys with ASD were scanned. GPC was applied to make disorder-specific predictions of ADHD diagnostic status based on individual brain structure patterns. In addition, voxel-based morphometry (VBM analysis tested for traditional univariate group level differences in GM.The pattern of GM correctly classified 75.9% of patients and 82.8% of controls, achieving an overall classification accuracy of 79.3%. Furthermore, classification was disorder-specific relative to ASD. The discriminating GM patterns showed higher classification weights for ADHD in earlier developing ventrolateral/premotor fronto-temporo-limbic and stronger classification weights for healthy controls in later developing dorsolateral fronto-striato-parieto-cerebellar networks. Several regions were also decreased in GM in ADHD relative to healthy controls in the univariate VBM analysis, suggesting they are GM deficit areas.The study provides evidence that pattern recognition analysis can provide significant individual diagnostic classification of ADHD patients and healthy controls based on distributed GM patterns with 79.3% accuracy and that this is disorder-specific relative to ASD. Findings are a promising first step towards finding an objective differential diagnostic tool based on brain imaging measures to aid with the subjective clinical diagnosis of ADHD.

Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling

Energy Technology Data Exchange (ETDEWEB)

Ren, Xiaoming; Gelinas, Amy D.; von Carlowitz, Ira; Janjic, Nebojsa; Pyle, Anna Marie (Yale); (SomaLogic)

2017-10-09

IL-1α is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1α and inhibits its signaling pathway. By solving the crystal structure of the IL-1α/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1α/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1α uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.

The structures of bacteriophages K1E and K1-5 explain processive degradation of polysaccharide capsules and evolution of new host specificities.

Science.gov (United States)

Leiman, Petr G; Battisti, Anthony J; Bowman, Valorie D; Stummeyer, Katharina; Mühlenhoff, Martina; Gerardy-Schahn, Rita; Scholl, Dean; Molineux, Ian J

2007-08-17

External polysaccharides of many pathogenic bacteria form capsules protecting the bacteria from the animal immune system and phage infection. However, some bacteriophages can digest these capsules using glycosidases displayed on the phage particle. We have utilized cryo-electron microscopy to determine the structures of phages K1E and K1-5 and thereby establish the mechanism by which these phages attain and switch their host specificity. Using a specific glycosidase, both phages penetrate the capsule and infect the neuroinvasive human pathogen Escherichia coli K1. In addition to the K1-specific glycosidase, each K1-5 particle carries a second enzyme that allows it to infect E. coli K5, whose capsule is chemically different from that of K1. The enzymes are organized into a multiprotein complex attached via an adapter protein to the virus portal vertex, through which the DNA is ejected during infection. The structure of the complex suggests a mechanism for the apparent processivity of degradation that occurs as the phage drills through the polysaccharide capsule. The enzymes recognize the adapter protein by a conserved N-terminal sequence, providing a mechanism for phages to acquire different enzymes and thus to evolve new host specificities.

Structural modeling of tissue-specific mitochondrial alanyl-tRNA synthetase (AARS2 defects predicts differential effects on aminoacylation

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Liliya eEuro

2015-02-01

Full Text Available The accuracy of mitochondrial protein synthesis is dependent on the coordinated action of nuclear-encoded mitochondrial aminoacyl-tRNA synthetases (mtARSs and the mitochondrial DNA-encoded tRNAs. The recent advances in whole-exome sequencing have revealed the importance of the mtARS proteins for mitochondrial pathophysiology since nearly every nuclear gene for mtARS (out of 19 is now recognized as a disease gene for mitochondrial disease. Typically, defects in each mtARS have been identified in one tissue-specific disease, most commonly affecting the brain, or in one syndrome. However, mutations in the AARS2 gene for mitochondrial alanyl-tRNA synthetase (mtAlaRS have been reported both in patients with infantile-onset cardiomyopathy and in patients with childhood to adulthood-onset leukoencephalopathy. We present here an investigation of the effects of the described mutations on the structure of the synthetase, in an effort to understand the tissue-specific outcomes of the different mutations.The mtAlaRS differs from the other mtARSs because in addition to the aminoacylation domain, it has a conserved editing domain for deacylating tRNAs that have been mischarged with incorrect amino acids. We show that the cardiomyopathy phenotype results from a single allele, causing an amino acid change p.R592W in the editing domain of AARS2, whereas the leukodystrophy mutations are located in other domains of the synthetase. Nevertheless, our structural analysis predicts that all mutations reduce the aminoacylation activity of the synthetase, because all mtAlaRS domains contribute to tRNA binding for aminoacylation. According to our model, the cardiomyopathy mutations severely compromise aminoacylation whereas partial activity is retained by the mutation combinations found in the leukodystrophy patients. These predictions provide a hypothesis for the molecular basis of the distinct tissue-specific phenotypic outcomes.

Sex specific differences in hepatic and plasma lipid profiles in healthy cats pre and post spaying and neutering: relationship with feline hepatic lipidosis.

Science.gov (United States)

Valtolina, Chiara; Vaandrager, Arie B; Favier, Robert P; Tuohetahuntila, Maidina; Kummeling, Anne; Jeusette, Isabelle; Rothuizen, Jan; Robben, Joris H

2017-08-08

A link between lipid metabolism and disease has been recognized in cats. Since hepatic lipidosis is a frequent disorder in cats, the aim of the current study was to evaluate liver and plasma lipid dimorphism in healthy cats and the effects of gonadectomy on lipid profiling. From six female and six male cats plasma and liver lipid profiles before and after spaying/neutering were assessed and compared to five cats (three neutered male and two spayed female) diagnosed with hepatic lipidosis. Intact female cats had a significantly lower level of plasma triacylglycerides (TAG) and a higher liver level of the long chain polyunsaturated fatty acid arachidonic acid (AA) compared to their neutered state. Both male and female cats with lipidosis had a higher liver, but not plasma TAG level and an increased level of plasma and liver sphingomyelin compared to the healthy cats. Although lipid dimorphism in healthy cats resembles that of other species, intact female cats show differences in metabolic configuration that could predispose them to develop hepatic lipidosis. The increased sphingomyelin levels in cats with lipidosis could suggest a potential role in the pathogenesis of hepatic lipidosis in cats.

Structural Evidence for Regulation and Specificity of Flaviviral Proteases and Evolution of the Flaviviridae Fold

Energy Technology Data Exchange (ETDEWEB)

Aleshin,A.; Shiryaev, S.; Strongin, A.; Liddington, R.

2007-01-01

Pathogenic members of the flavivirus family, including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The two-component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication. Here, we report the crystal structure of WNV NS2B-NS3pro both in a substrate-free form and in complex with the trypsin inhibitor aprotinin/BPTI. We show that aprotinin binds in a substrate-mimetic fashion in which the productive conformation of the protease is fully formed, providing evidence for an 'induced fit' mechanism of catalysis and allowing us to rationalize the distinct substrate specificities of WNV and DV proteases. We also show that the NS2B cofactor of WNV can adopt two very distinct conformations and that this is likely to be a general feature of flaviviral proteases, providing further opportunities for regulation. Finally, by comparing the flaviviral proteases with the more distantly related Hepatitis C virus, we provide insights into the evolution of the Flaviviridae fold. Our work should expedite the design of protease inhibitors to treat a range of flaviviral infections.

Structural correlation method for model reduction and practical estimation of patient specific parameters illustrated on heart rate regulation

DEFF Research Database (Denmark)

Ottesen, Johnny T.; Mehlsen, Jesper; Olufsen, Mette

2014-01-01

We consider the inverse and patient specific problem of short term (seconds to minutes) heart rate regulation specified by a system of nonlinear ODEs and corresponding data. We show how a recent method termed the structural correlation method (SCM) can be used for model reduction and for obtaining...... a set of practically identifiable parameters. The structural correlation method includes two steps: sensitivity and correlation analysis. When combined with an optimization step, it is possible to estimate model parameters, enabling the model to fit dynamics observed in data. This method is illustrated...... in detail on a model predicting baroreflex regulation of heart rate and applied to analysis of data from a rat and healthy humans. Numerous mathematical models have been proposed for prediction of baroreflex regulation of heart rate, yet most of these have been designed to provide qualitative predictions...

Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28.

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Bonsu Ku

Full Text Available Dual-specificity phosphatases (DUSPs constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops

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Gendrault-Jacquemard A

2005-07-01

Full Text Available Abstract Background Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evolution, a task that requires reliable fine comparison data of closely related genomes. Recent analyses have shown, using pairwise whole genome alignments, that it is possible to segment bacterial genomes into a common conserved backbone and strain-specific sequences called loops. Results Here, we generalize this approach and propose a strategy that allows systematic and non-biased genome segmentation based on multiple genome alignments. Segmentation analyses, as applied to 13 different bacterial species, confirmed the feasibility of our approach to discern the 'mosaic' organization of bacterial genomes. Segmentation results are available through a Web interface permitting functional analysis, extraction and visualization of the backbone/loops structure of documented genomes. To illustrate the potential of this approach, we performed a precise analysis of the mosaic organization of three E. coli strains and functional characterization of the loops. Conclusion The segmentation results including the backbone/loops structure of 13 bacterial species genomes are new and available for use by the scientific community at the URL: http://genome.jouy.inra.fr/mosaic.

STRUCTURAL AND CONTENT-RELATED SPECIFICITY OF PROGRAMME LITERARY CRITICISM TEXTS IN THE JOURNAL

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Shilnikova Olga Gennadyevna

2015-06-01

Full Text Available The article specifies the notions of the structural, content-related, figurative, and functional characteristics of the texts which are traditionally referred to the group of informational genres of journalism. This lets us update the system of factors that influence the formation of the texts' genre specificity in the mass media. The analysis of programme literary criticism speeches published in the journals of N.M. Karamzin – Moskovsky Zhurnal, Vestnik Evropy – shows that not only rational and logical structures accomplish the constructive function in the text-formation mechanisms of such publications. The use of imaginative resources of journalistic and artistic discourses plays an important role in the implementation of the author's intentions. The supplementation of programme texts with the components non-typical of informational genres (lyrical and biographical fragments, expressive lexis, artistic and journalistic forms of the author's subjectivity expression is conditioned by organic interaction of several pragmatic goals in the texts, such as: informational, author's individual (Karamzin as a personality, and author's professional (Karamzin as an editor, writer, literary critic. These peculiarities together with a subtext contribute to the formation of new features of programme publications, which are not common for informational genres such as aesthetic function and multi-discursivity, reflected in semantic, expressive and vocabulary redundance. They also expand the range of possible effects on audience – cognitive, emotive, behavioral and communicative. As a result, a unique informational text of a programme type is formed. Therefore, a strict differentiation of genre forms of journal texts is only possible when taking into consideration all the possible text goals, as well as its role in the organization of common-journal discourse and publication policy.

Imaging specific cellular glycan structures using glycosyltransferases via click chemistry.

Science.gov (United States)

Wu, Zhengliang L; Person, Anthony D; Anderson, Matthew; Burroughs, Barbara; Tatge, Timothy; Khatri, Kshitij; Zou, Yonglong; Wang, Lianchun; Geders, Todd; Zaia, Joseph; Sackstein, Robert

2018-02-01

Heparan sulfate (HS) is a polysaccharide fundamentally important for biologically activities. T/Tn antigens are universal carbohydrate cancer markers. Here, we report the specific imaging of these carbohydrates using a mesenchymal stem cell line and human umbilical vein endothelial cells (HUVEC). The staining specificities were demonstrated by comparing imaging of different glycans and validated by either removal of target glycans, which results in loss of signal, or installation of target glycans, which results in gain of signal. As controls, representative key glycans including O-GlcNAc, lactosaminyl glycans and hyaluronan were also imaged. HS staining revealed novel architectural features of the extracellular matrix (ECM) of HUVEC cells. Results from T/Tn antigen staining suggest that O-GalNAcylation is a rate-limiting step for O-glycan synthesis. Overall, these highly specific approaches for HS and T/Tn antigen imaging should greatly facilitate the detection and functional characterization of these biologically important glycans. © The Author(s) 2017. Published by Oxford University Press.

Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment.

Science.gov (United States)

Capriles, Priscila V S Z; Guimarães, Ana C R; Otto, Thomas D; Miranda, Antonio B; Dardenne, Laurent E; Degrave, Wim M

2010-10-29

Trypanosoma cruzi is the etiological agent of Chagas' disease, an endemic infection that causes thousands of deaths every year in Latin America. Therapeutic options remain inefficient, demanding the search for new drugs and/or new molecular targets. Such efforts can focus on proteins that are specific to the parasite, but analogous enzymes and enzymes with a three-dimensional (3D) structure sufficiently different from the corresponding host proteins may represent equally interesting targets. In order to find these targets we used the workflows MHOLline and AnEnΠ obtaining 3D models from homologous, analogous and specific proteins of Trypanosoma cruzi versus Homo sapiens. We applied genome wide comparative modelling techniques to obtain 3D models for 3,286 predicted proteins of T. cruzi. In combination with comparative genome analysis to Homo sapiens, we were able to identify a subset of 397 enzyme sequences, of which 356 are homologous, 3 analogous and 38 specific to the parasite. In this work, we present a set of 397 enzyme models of T. cruzi that can constitute potential structure-based drug targets to be investigated for the development of new strategies to fight Chagas' disease. The strategies presented here support the concept of structural analysis in conjunction with protein functional analysis as an interesting computational methodology to detect potential targets for structure-based rational drug design. For example, 2,4-dienoyl-CoA reductase (EC 1.3.1.34) and triacylglycerol lipase (EC 3.1.1.3), classified as analogous proteins in relation to H. sapiens enzymes, were identified as new potential molecular targets.

Specificity in the interaction of natural products with their target proteins--a biochemical and structural insight.

Science.gov (United States)

Venkatraman, Prasanna

2010-06-01

Natural products are an abundant source of anti cancer agents. They act as cytotoxic drugs, and inhibitors of apoptosis, transcription, cell proliferation and angiogenesis. While pathways targeted by natural products have been well studied, there is paucity of information about the in vivo molecular target/s of these compounds. This review summarizes some of the natural compounds for which the molecular targets, mechanism of action and structural basis of specificity have been well documented. These examples illustrate that 'off target' binding can be explained on the basis of diversity inherent to biomolecular interactions. There is enough evidence to suggest that natural compounds are potent and versatile warheads that can be optimized for a multi targeted therapeutic intervention in cancer.

Measuring wood specific gravity, correctly

Science.gov (United States)

G. Bruce Williamson; Michael C. Wiemann

2010-01-01

The specific gravity (SG) of wood is a measure of the amount of structural material a tree species allocates to support and strength. In recent years, wood specific gravity, traditionally a forester’s variable, has become the domain of ecologists exploring the universality of plant functional traits and conservationists estimating global carbon stocks. While these...

Control over structure-specific flexibility improves anatomical accuracy for point-based deformable registration in bladder cancer radiotherapy.

Science.gov (United States)

Wognum, S; Bondar, L; Zolnay, A G; Chai, X; Hulshof, M C C M; Hoogeman, M S; Bel, A

2013-02-01

Future developments in image guided adaptive radiotherapy (IGART) for bladder cancer require accurate deformable image registration techniques for the precise assessment of tumor and bladder motion and deformation that occur as a result of large bladder volume changes during the course of radiotherapy treatment. The aim was to employ an extended version of a point-based deformable registration algorithm that allows control over tissue-specific flexibility in combination with the authors' unique patient dataset, in order to overcome two major challenges of bladder cancer registration, i.e., the difficulty in accounting for the difference in flexibility between the bladder wall and tumor and the lack of visible anatomical landmarks for validation. The registration algorithm used in the current study is an extension of the symmetric-thin plate splines-robust point matching (S-TPS-RPM) algorithm, a symmetric feature-based registration method. The S-TPS-RPM algorithm has been previously extended to allow control over the degree of flexibility of different structures via a weight parameter. The extended weighted S-TPS-RPM algorithm was tested and validated on CT data (planning- and four to five repeat-CTs) of five urinary bladder cancer patients who received lipiodol injections before radiotherapy. The performance of the weighted S-TPS-RPM method, applied to bladder and tumor structures simultaneously, was compared with a previous version of the S-TPS-RPM algorithm applied to bladder wall structure alone and with a simultaneous nonweighted S-TPS-RPM registration of the bladder and tumor structures. Performance was assessed in terms of anatomical and geometric accuracy. The anatomical accuracy was calculated as the residual distance error (RDE) of the lipiodol markers and the geometric accuracy was determined by the surface distance, surface coverage, and inverse consistency errors. Optimal parameter values for the flexibility and bladder weight parameters were determined

Control over structure-specific flexibility improves anatomical accuracy for point-based deformable registration in bladder cancer radiotherapy

International Nuclear Information System (INIS)

Wognum, S.; Chai, X.; Hulshof, M. C. C. M.; Bel, A.; Bondar, L.; Zolnay, A. G.; Hoogeman, M. S.

2013-01-01

Purpose: Future developments in image guided adaptive radiotherapy (IGART) for bladder cancer require accurate deformable image registration techniques for the precise assessment of tumor and bladder motion and deformation that occur as a result of large bladder volume changes during the course of radiotherapy treatment. The aim was to employ an extended version of a point-based deformable registration algorithm that allows control over tissue-specific flexibility in combination with the authors’ unique patient dataset, in order to overcome two major challenges of bladder cancer registration, i.e., the difficulty in accounting for the difference in flexibility between the bladder wall and tumor and the lack of visible anatomical landmarks for validation. Methods: The registration algorithm used in the current study is an extension of the symmetric-thin plate splines-robust point matching (S-TPS-RPM) algorithm, a symmetric feature-based registration method. The S-TPS-RPM algorithm has been previously extended to allow control over the degree of flexibility of different structures via a weight parameter. The extended weighted S-TPS-RPM algorithm was tested and validated on CT data (planning- and four to five repeat-CTs) of five urinary bladder cancer patients who received lipiodol injections before radiotherapy. The performance of the weighted S-TPS-RPM method, applied to bladder and tumor structures simultaneously, was compared with a previous version of the S-TPS-RPM algorithm applied to bladder wall structure alone and with a simultaneous nonweighted S-TPS-RPM registration of the bladder and tumor structures. Performance was assessed in terms of anatomical and geometric accuracy. The anatomical accuracy was calculated as the residual distance error (RDE) of the lipiodol markers and the geometric accuracy was determined by the surface distance, surface coverage, and inverse consistency errors. Optimal parameter values for the flexibility and bladder weight

Control over structure-specific flexibility improves anatomical accuracy for point-based deformable registration in bladder cancer radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Wognum, S.; Chai, X.; Hulshof, M. C. C. M.; Bel, A. [Department of Radiotherapy, Academic Medical Center, Meiberdreef 9, 1105 AZ Amsterdam (Netherlands); Bondar, L.; Zolnay, A. G.; Hoogeman, M. S. [Department of Radiation Oncology, Daniel den Hoed Cancer Center, Erasmus Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam (Netherlands)

2013-02-15

Purpose: Future developments in image guided adaptive radiotherapy (IGART) for bladder cancer require accurate deformable image registration techniques for the precise assessment of tumor and bladder motion and deformation that occur as a result of large bladder volume changes during the course of radiotherapy treatment. The aim was to employ an extended version of a point-based deformable registration algorithm that allows control over tissue-specific flexibility in combination with the authors' unique patient dataset, in order to overcome two major challenges of bladder cancer registration, i.e., the difficulty in accounting for the difference in flexibility between the bladder wall and tumor and the lack of visible anatomical landmarks for validation. Methods: The registration algorithm used in the current study is an extension of the symmetric-thin plate splines-robust point matching (S-TPS-RPM) algorithm, a symmetric feature-based registration method. The S-TPS-RPM algorithm has been previously extended to allow control over the degree of flexibility of different structures via a weight parameter. The extended weighted S-TPS-RPM algorithm was tested and validated on CT data (planning- and four to five repeat-CTs) of five urinary bladder cancer patients who received lipiodol injections before radiotherapy. The performance of the weighted S-TPS-RPM method, applied to bladder and tumor structures simultaneously, was compared with a previous version of the S-TPS-RPM algorithm applied to bladder wall structure alone and with a simultaneous nonweighted S-TPS-RPM registration of the bladder and tumor structures. Performance was assessed in terms of anatomical and geometric accuracy. The anatomical accuracy was calculated as the residual distance error (RDE) of the lipiodol markers and the geometric accuracy was determined by the surface distance, surface coverage, and inverse consistency errors. Optimal parameter values for the flexibility and bladder weight

Double-Shell Tank (DST) Utilities Specification

International Nuclear Information System (INIS)

SUSIENE, W.T.

2000-01-01

This specification establishes the performance requirements and provides the references to the requisite codes and standards to he applied during the design of the Double-Shell Tank (DST) Utilities Subsystems that support the first phase of waste feed delivery (WFD). The DST Utilities Subsystems provide electrical power, raw/potable water, and service/instrument air to the equipment and structures used to transfer low-activity waste (LAW) and high-level waste (HLW) to designated DST staging tanks. The DST Utilities Subsystems also support the equipment and structures used to deliver blended LAW and HLW feed from these staging tanks to the River Protection Project (RPP) Privatization Contractor facility where the waste will be immobilized. This specification is intended to be the basis for new projects/installations. This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program

Lack of population genetic structure and host specificity in the bat fly, Cyclopodia horsfieldi, across species of Pteropus bats in Southeast Asia.

Science.gov (United States)

Olival, Kevin J; Dick, Carl W; Simmons, Nancy B; Morales, Juan Carlos; Melnick, Don J; Dittmar, Katharina; Perkins, Susan L; Daszak, Peter; Desalle, Rob

2013-08-08

Population-level studies of parasites have the potential to elucidate patterns of host movement and cross-species interactions that are not evident from host genealogy alone. Bat flies are obligate and generally host-specific blood-feeding parasites of bats. Old-World flies in the family Nycteribiidae are entirely wingless and depend on their hosts for long-distance dispersal; their population genetics has been unstudied to date. We collected a total of 125 bat flies from three Pteropus species (Pteropus vampyrus, P. hypomelanus, and P. lylei) from eight localities in Malaysia, Cambodia, and Vietnam. We identified specimens morphologically and then sequenced three mitochondrial DNA gene fragments (CoI, CoII, cytB; 1744 basepairs total) from a subset of 45 bat flies. We measured genetic diversity, molecular variance, and population genetic subdivision (FST), and used phylogenetic and haplotype network analyses to quantify parasite genetic structure across host species and localities. All flies were identified as Cyclopodia horsfieldi with the exception of two individuals of Eucampsipoda sundaica. Low levels of population genetic structure were detected between populations of Cyclopodia horsfieldi from across a wide geographic range (~1000 km), and tests for isolation by distance were rejected. AMOVA results support a lack of geographic and host-specific population structure, with molecular variance primarily partitioned within populations. Pairwise FST values from flies collected from island populations of Pteropus hypomelanus in East and West Peninsular Malaysia supported predictions based on previous studies of host genetic structure. The lack of population genetic structure and morphological variation observed in Cyclopodia horsfieldi is most likely due to frequent contact between flying fox species and subsequent high levels of parasite gene flow. Specifically, we suggest that Pteropus vampyrus may facilitate movement of bat flies between the three Pteropus

Interplay of host specificity and biogeography in the population structure of a cosmopolitan endoparasite: microsatellite study of Ligula intestinalis (Cestoda)

Czech Academy of Sciences Publication Activity Database

Štefka, Jan; Hypša, Václav; Scholz, Tomáš

2009-01-01

Roč. 18, č. 6 (2009), s. 1187-1206 ISSN 0962-1083 R&D Projects: GA MŠk LC06073; GA ČR GA524/08/0885; GA MŠk LC522 Institutional research plan: CEZ:AV0Z60220518 Keywords : cryptic speciation * geographical isolation * host specificity * microsatellites * parasite * population structure Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 5.960, year: 2009

Structure-specificity relationships in Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus T6.

Science.gov (United States)

Lansky, Shifra; Salama, Rachel; Solomon, Hodaya V; Feinberg, Hadar; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2014-11-01

L-Arabinose sugar residues are relatively abundant in plants and are found mainly in arabinan polysaccharides and in other arabinose-containing polysaccharides such as arabinoxylans and pectic arabinogalactans. The majority of the arabinose units in plants are present in the furanose form and only a small fraction of them are present in the pyranose form. The L-arabinan-utilization system in Geobacillus stearothermophilus T6, a Gram-positive thermophilic soil bacterium, has recently been characterized, and one of the key enzymes was found to be an intracellular β-L-arabinopyranosidase (Abp). Abp, a GH27 enzyme, was shown to remove β-L-arabinopyranose residues from synthetic substrates and from the native substrates sugar beet arabinan and larch arabinogalactan. The Abp monomer is made up of 448 amino acids, and based on sequence homology it was suggested that Asp197 is the catalytic nucleophile and Asp255 is the catalytic acid/base. In the current study, the detailed three-dimensional structure of wild-type Abp (at 2.28 Å resolution) and its catalytic mutant Abp-D197A with (at 2.20 Å resolution) and without (at 2.30 Å resolution) a bound L-arabinose product are reported as determined by X-ray crystallography. These structures demonstrate that the three-dimensional structure of the Abp monomer correlates with the general fold observed for GH27 proteins, consisting of two main domains: an N-terminal TIM-barrel domain and a C-terminal all-β domain. The two catalytic residues are located in the TIM-barrel domain, such that their carboxylic functional groups are about 5.9 Å from each other, consistent with a retaining mechanism. An isoleucine residue (Ile67) located at a key position in the active site is shown to play a critical role in the substrate specificity of Abp, providing a structural basis for the high preference of the enzyme towards arabinopyranoside over galactopyranoside substrates. The crystal structure demonstrates that Abp is a tetramer

Milk whey protein modification by coffee-specific phenolics: effect on structural and functional properties.

Science.gov (United States)

Ali, Mostafa; Homann, Thomas; Khalil, Mahmoud; Kruse, Hans-Peter; Rawel, Harshadrai

2013-07-17

A suitable vehicle for integration of bioactive plant constituents is proposed. It involves modification of proteins using phenolics and applying these for protection of labile constituents. It dissects the noncovalent and covalent interactions of β-lactoglobulin with coffee-specific phenolics. Alkaline and polyphenol oxidase modulated covalent reactions were compared. Tryptic digestion combined with MALDI-TOF-MS provided tentative allocation of the modification type and site in the protein, and an in silico modeling of modified β-lactoglobulin is proposed. The modification delivers proteins with enhanced antioxidative properties. Changed structural properties and differences in solubility, surface hydrophobicity, and emulsification were observed. The polyphenol oxidase modulated reaction provides a modified β-lactoglobulin with a high antioxidative power, is thermally more stable, requires less energy to unfold, and, when emulsified with lutein esters, exhibits their higher stability against UV light. Thus, adaptation of this modification provides an innovative approach for functionalizing proteins and their uses in the food industry.

Unusual Structure of the attB Site of the Site-Specific Recombination System of Lactobacillus delbrueckii Bacteriophage mv4

Science.gov (United States)

Auvray, Frédéric; Coddeville, Michèle; Ordonez, Romy Catoira; Ritzenthaler, Paul

1999-01-01

The temperate phage mv4 integrates its genome into the chromosome of Lactobacillus delbrueckii subsp. bulgaricus by site-specific recombination within the 3′ end of a tRNASer gene. Recombination is catalyzed by the phage-encoded integrase and occurs between the phage attP site and the bacterial attB site. In this study, we show that the mv4 integrase functions in vivo in Escherichia coli and we characterize the bacterial attB site with a site-specific recombination test involving compatible plasmids carrying the recombination sites. The importance of particular nucleotides within the attB sequence was determined by site-directed mutagenesis. The structure of the attB site was found to be simple but rather unusual. A 16-bp DNA fragment was sufficient for function. Unlike most genetic elements that integrate their DNA into tRNA genes, none of the dyad symmetry elements of the tRNASer gene were present within the minimal attB site. No inverted repeats were detected within this site either, in contrast to the lambda site-specific recombination model. PMID:10572145

Pilot batch production of specific-structured lipids by lipase-catalyzed interesterification: preliminary study on incorporation and acyl migration

DEFF Research Database (Denmark)

Xu, Xuebing; Balchen, Steen; Høy, Carl-Erik

1998-01-01

Effects of water content, reaction time and their relationships in the production of two types of specific-structured lipids (sn-MLM- and sn-LML-types: L-long chain fatty acids; M-medium chain fatty acids) by lipase-catalyzed interesterification in a solvent-free system were studied...... of two totally position-opposed lipids can be observed. Presumably these are caused by the different chain length of the fatty acids. The relationships between reaction time and water content are inverse and give a quantitative prediction of incorporation and acyl migration in selected reaction...

Single event upset test structures for digital CMOS application specific integrated circuits

International Nuclear Information System (INIS)

Baze, M.P.; Bartholet, W.G.; Braatz, J.C.; Dao, T.A.

1993-01-01

An approach has been developed for the design and utilization of SEU test structures for digital CMOS ASICs. This approach minimizes the number of test structures required by categorizing ASIC library cells according to their SEU response and designing a structure to characterize each response for each category. Critical SEU response parameters extracted from these structures are used to evaluate the SEU hardness of ASIC libraries and predict the hardness of ASIC chips

Failure to replicate the internal structure of Greek-specific thalassemia quality of life instrument in adult thalassemia patients in Sabah.

Science.gov (United States)

Keowmani, Thamron; Lee, Lily Wong Lee

2016-01-01

To study the validity and reliability of the Malay version of the Specific Thalassemia Quality of Life Instrument (STQOLI) in Sabah's adult thalassemia patients. This cross-sectional study was done at Thalassemia Treatment Centre, Queen Elizabeth Hospital in Sabah, Malaysia. Eighty-two adult thalassemia patients who fulfilled the inclusion and exclusion criteria were conveniently selected for participation in the study. The English version of STQOLI was translated into Malay by using forward and back translations. The content of the questionnaire was validated by the chief hematologist of the hospital. The construct validity of the 40-item questionnaire was assessed by principal component analysis with varimax rotation and the scale reliability was assessed by Cronbach's alpha. The study failed to replicate the internal structure of the Greek STQOLI. Instead, 12 factors have been identified from the exploratory factor analysis, which accounted for 72.2% of the variance. However, only eight factors were interpretable. The factors were iron chelation pump impact, transfusion impact, time spent on treatment and its impact on work and social life, sex life, side effects of treatment, cardiovascular problems, psychology, and iron chelation pill impact. The overall scale reliability was 0.913. This study was unable to replicate the internal structure of the Greek STQOLI in Sabah's adult thalassemia patients. Instead, a new structure has emerged that can be used as a guide to develop a questionnaire specific for adult thalassemia patients in Sabah. Future research should focus on the eight factors identified from this study.

Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis.

Directory of Open Access Journals (Sweden)

Yann Reynaud

Full Text Available Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4 which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China. Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares, we distinctly identified eight tentative phylogenetic groups (T1-T8 with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages, and showed that 5 out of 8 T groups seemed phylogeographically well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequencing (WGS.

Structural basis for different phosphoinositide specificities of the PX domains of sorting nexins regulating G-protein signaling.

Science.gov (United States)

Mas, Caroline; Norwood, Suzanne J; Bugarcic, Andrea; Kinna, Genevieve; Leneva, Natalya; Kovtun, Oleksiy; Ghai, Rajesh; Ona Yanez, Lorena E; Davis, Jasmine L; Teasdale, Rohan D; Collins, Brett M

2014-10-10

Sorting nexins (SNXs) or phox homology (PX) domain containing proteins are central regulators of cell trafficking and signaling. A subfamily of PX domain proteins possesses two unique PX-associated domains, as well as a regulator of G protein-coupled receptor signaling (RGS) domain that attenuates Gαs-coupled G protein-coupled receptor signaling. Here we delineate the structural organization of these RGS-PX proteins, revealing a protein family with a modular architecture that is conserved in all eukaryotes. The one exception to this is mammalian SNX19, which lacks the typical RGS structure but preserves all other domains. The PX domain is a sensor of membrane phosphoinositide lipids and we find that specific sequence alterations in the PX domains of the mammalian RGS-PX proteins, SNX13, SNX14, SNX19, and SNX25, confer differential phosphoinositide binding preferences. Although SNX13 and SNX19 PX domains bind the early endosomal lipid phosphatidylinositol 3-phosphate, SNX14 shows no membrane binding at all. Crystal structures of the SNX19 and SNX14 PX domains reveal key differences, with alterations in SNX14 leading to closure of the binding pocket to prevent phosphoinositide association. Our findings suggest a role for alternative membrane interactions in spatial control of RGS-PX proteins in cell signaling and trafficking. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Full structure and insight into the gene cluster of the O-specific polysaccharide of Yersinia intermedia H9-36/83 (O:17).

Science.gov (United States)

Sizova, Olga V; Shashkov, Alexander S; Kondakova, Anna N; Knirel, Yuriy A; Shaikhutdinova, Rima Z; Ivanov, Sergei A; Kislichkina, Angelina A; Kadnikova, Lidia A; Bogun, Aleksandr G; Dentovskaya, Svetlana V

2018-05-02

Lipopolysaccharide was isolated from bacteria Yersinia intermedia H9-36/83 (O:17) and degraded with mild acid to give an O-specific polysaccharide, which was isolated by GPC on Sephadex G-50 and studied by sugar analysis and 1D and 2D NMR spectroscopy. The polysaccharide was found to contain 3-deoxy-3-[(R)-3-hydroxybutanoylamino]-d-fucose (d-Fuc3NR3Hb) and the following structure of the heptasaccharide repeating unit was established: The structure established is consistent with the gene content of the O-antigen gene cluster. The O-polysaccharide structure and gene cluster of Y. intermedia are related to those of Hafnia alvei 1211 and Escherichia coli O:103. Copyright © 2018 Elsevier Ltd. All rights reserved.

Discovery of core-structurally novel PTP1B inhibitors with specific selectivity containing oxindole-fused spirotetrahydrofurochroman by one-pot reaction.

Science.gov (United States)

Dong, Suzhen; Lei, Yubing; Jia, Shikun; Gao, Lixin; Li, Jia; Zhu, Tong; Liu, Shunying; Hu, Wenhao

2017-02-15

Protein tyrosine phosphatase 1B (PTP1B) has been proposed to be an ideal target for treatment of type II diabetes and obesity. However, no druggable PTP1B inhibitor has been established and there is still an urgent demand for the development of structurally novel PTPIB inhibitor. Herein, we reported core-structurally novel PTP1B inhibitors with low micromole-ranged inhibitory activity by one-pot reaction from simple starting materials. Further studies demonstrated some of these active compounds had a specific selectivity over other PTPs. The structure and activity relationship was also described. The best active and selective compound 5e inhibited PTP1B activity with an IC 50 of 4.53μM. Molecular docking analysis further demonstrated that compound 5e bound to the active pocket of PTP1B. The results might provide some insights for further development of new drugs for type II diabetes and obesity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Pellet-free isolation of human and bovine milk extracellular vesicles by size-exclusion chromatography

DEFF Research Database (Denmark)

Blans, Kristine Ingrid Marie; Hansen, Maria Stenum; Sørensen, Laila V.

2017-01-01

-marker proteins in other relevant milk fractions such as milk fat globules. Nanoparticle tracking analysis and electron microscopy reveals the presence of heterogeneous sized vesicle structures in milk EV isolates. Lipid analysis by thin layer chromatography shows that EV isolates are devoid of triacylglycerides...... accomplished in three steps based on size-exclusion chromatography (SEC) resulting in effective and reproducible EV isolation from raw milk. The approaches do not require any EV pelleting and can be applied to both human and bovine milk. We show that SEC effectively separates phospholipid membrane vesicles...... from the primary casein and whey protein components in two differently obtained casein reduced milk fractions, with one of the fractions obtained without the use of ultracentrifugation. Milk EV isolates were enriched in lactadherin, CD9, CD63 and CD81 compared to minimal levels of the EV...

Substrate specificity of low-molecular mass bacterial DD-peptidases.

Science.gov (United States)

Nemmara, Venkatesh V; Dzhekieva, Liudmila; Sarkar, Kumar Subarno; Adediran, S A; Duez, Colette; Nicholas, Robert A; Pratt, R F

2011-11-22

The bacterial DD-peptidases or penicillin-binding proteins (PBPs) catalyze the formation and regulation of cross-links in peptidoglycan biosynthesis. They are classified into two groups, the high-molecular mass (HMM) and low-molecular mass (LMM) enzymes. The latter group, which is subdivided into classes A-C (LMMA, -B, and -C, respectively), is believed to catalyze DD-carboxypeptidase and endopeptidase reactions in vivo. To date, the specificity of their reactions with particular elements of peptidoglycan structure has not, in general, been defined. This paper describes the steady-state kinetics of hydrolysis of a series of specific peptidoglycan-mimetic peptides, representing various elements of stem peptide structure, catalyzed by a range of LMM PBPs (the LMMA enzymes, Escherichia coli PBP5, Neisseria gonorrhoeae PBP4, and Streptococcus pneumoniae PBP3, and the LMMC enzymes, the Actinomadura R39 dd-peptidase, Bacillus subtilis PBP4a, and N. gonorrhoeae PBP3). The R39 enzyme (LMMC), like the previously studied Streptomyces R61 DD-peptidase (LMMB), specifically and rapidly hydrolyzes stem peptide fragments with a free N-terminus. In accord with this result, the crystal structures of the R61 and R39 enzymes display a binding site specific to the stem peptide N-terminus. These are water-soluble enzymes, however, with no known specific function in vivo. On the other hand, soluble versions of the remaining enzymes of those noted above, all of which are likely to be membrane-bound and/or associated in vivo and have been assigned particular roles in cell wall biosynthesis and maintenance, show little or no specificity for peptides containing elements of peptidoglycan structure. Peptidoglycan-mimetic boronate transition-state analogues do inhibit these enzymes but display notable specificity only for the LMMC enzymes, where, unlike peptide substrates, they may be able to effectively induce a specific active site structure. The manner in which LMMA (and HMM) DD

An integrated in silico approach to design specific inhibitors targeting human poly(a-specific ribonuclease.

Directory of Open Access Journals (Sweden)

Dimitrios Vlachakis

Full Text Available Poly(A-specific ribonuclease (PARN is an exoribonuclease/deadenylase that degrades 3'-end poly(A tails in almost all eukaryotic organisms. Much of the biochemical and structural information on PARN comes from the human enzyme. However, the existence of PARN all along the eukaryotic evolutionary ladder requires further and thorough investigation. Although the complete structure of the full-length human PARN, as well as several aspects of the catalytic mechanism still remain elusive, many previous studies indicate that PARN can be used as potent and promising anti-cancer target. In the present study, we attempt to complement the existing structural information on PARN with in-depth bioinformatics analyses, in order to get a hologram of the molecular evolution of PARNs active site. In an effort to draw an outline, which allows specific drug design targeting PARN, an unequivocally specific platform was designed for the development of selective modulators focusing on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all the publicly available genomes indicated a broad distribution for PARN across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the catalytic mechanism of PARN. Based on the above, we propose a comprehensive in silico model for the PARN's catalytic mechanism and moreover, we developed a 3D pharmacophore model, which was subsequently used for the introduction of DNP-poly(A amphipathic substrate analog as a potential inhibitor of PARN. Indeed, biochemical analysis revealed that DNP-poly(A inhibits PARN competitively. Our approach provides an efficient integrated platform for the rational design of pharmacophore models as well as novel modulators of PARN with therapeutic potential.

Structure and DNA-binding of meiosis-specific protein Hop2

Science.gov (United States)

Zhou, Donghua; Moktan, Hem; Pezza, Roberto

2014-03-01

Here we report structure elucidation of the DNA binding domain of homologous pairing protein 2 (Hop2), which is important to gene diversity when sperms and eggs are produced. Together with another protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. However, the structural and biochemical bases for the function of Hop2 and Mnd1 have not been well understood. As a first step toward such understanding, we recently solved the structure for the N-terminus of Hop2 (1-84) using solution NMR. This fragment shows a typical winged-head conformation with recognized DNA binding activity. DNA interacting sites were then investigated by chemical shift perturbations in a titration experiment. Information of these sites was used to guide protein-DNA docking with MD simulation, revealing that helix 3 is stably lodged in the DNA major groove and that wing 1 (connecting strands 2 and 3) transiently comes in contact with the minor groove in nanosecond time scale. Mutagenesis analysis further confirmed the DNA binding sites in this fragment of the protein.

Development of industrial variant specification systems

DEFF Research Database (Denmark)

Hansen, Benjamin Loer

be developed from a holistic and strategically anchored point of view. Another assumption is that this is a challenge for many industrial companies. Even though the literature presents many considerations on general issues covering new information technology, little work is found on the business perspectives...... are discussed. A list of structural variables and solution components has been created. These are related to four design aspects in the holistic system design covering the aspects of process design, selection of resources (such as hardware, software and humans), the design of information structures...... solution elements and structural variables to be used in the design of variant specification systems. The thesis presents a “top-down” procedure to be used to develop variant specification systems from a strategically anchored and holistic point of view. A methodology and related task variables...

Structure-Specific Movement Patterns in Patients With Chronic Low Back Dysfunction Using Lumbar Combined Movement Examination.

Science.gov (United States)

Monie, Aubrey P; Price, Roger I; Lind, Christopher R P; Singer, Kevin P

2017-06-01

A test-retest cohort study was conducted to assess the use of a novel computer-aided, combined movement examination (CME) to measure change in low back movement after pain management intervention in 17 cases of lumbar spondylosis. Additionally we desired to use a CME normal reference range (NRR) to compare and contrast movement patterns identified from 3 specific structural pathologic conditions: intervertebral disc, facet joint, and nerve root compression. Computer-aided CME was used before and after intervention, in a cohort study design, to record lumbar range of movement along with pain, disability, and health self-report questionnaires in 17 participants who received image-guided facet, epidural, and/or rhizotomy intervention. In the majority of cases, CME was reassessed after injection together with 2 serial self-reports after an average of 2 and 14 weeks. A minimal clinically important difference of 30% was used to interpret meaningful change in self-reports. A CME NRR (n = 159) was used for comparison with the 17 cases. Post hoc observation included subgrouping cases into 3 discrete pathologic conditions, intervertebral disc, facet dysfunction, and nerve root compression, in order to report intergroup differences in CME movement. Seven of the 17 participants stated that a "combined" movement was their most painful CME direction. Self-report outcome data indicated that 4 participants experienced significant improvement in health survey, 5 improved by ≥30% on low back function, and 8 reported that low back pain was more bothersome than stiffness, 6 of whom achieved the minimal clinically important difference for self-reported pain. Subgrouping of cases into structure-specific groups provided insight to different CME movement patterns. The use of CME assists in identifying atypical lumbar movement relative to an age and sex NRR. Data from this study, exemplified by representative case studies, provide preliminary evidence for distinct intervertebral disc

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

Energy Technology Data Exchange (ETDEWEB)

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Z.

2011-06-18

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.

Site-Specific Infrared Probes of Proteins

Science.gov (United States)

Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

2015-01-01

Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

MS/MS fragmentation-guided search of TMG-chitooligomycins and their structure-activity relationship in specific β-N-acetylglucosaminidase inhibition.

Science.gov (United States)

Usuki, Hirokazu; Yamamoto, Yukihiro; Kumagai, Yuya; Nitoda, Teruhiko; Kanzaki, Hiroshi; Hatanaka, Tadashi

2011-04-21

The reducing tetrasaccharide TMG-chitotriomycin (1) is an inhibitor of β-N-acetylglucosaminidase (GlcNAcase), produced by the actinomycete Streptomyces anulatus NBRC13369. The inhibitor shows a unique inhibitory spectrum, that is, selectivity toward enzymes from chitin-containing organisms such as insects and fungi. Nevertheless, its structure-selectivity relationship remains to be clarified. In this study, we conducted a structure-guided search of analogues of 1 in order to obtain diverse N,N,N-trimethylglucosaminium (TMG)-containing chitooligosaccharides. In this approach, the specific fragmentation profile of 1 on ESI-MS/MS analysis was used for the selective detection of desired compounds. As a result, two new analogues, named TMG-chitomonomycin (3) and TMG-chitobiomycin (2), were obtained from a culture filtrate of 1-producing Streptomyces. Their enzyme-inhibiting activity revealed that the potency and selectivity depended on the degree of polymerization of the reducing end GlcNAc units. Furthermore, a computational modeling study inspired the inhibitory mechanism of TMG-related compounds as a mimic of the substrate in the Michaelis complex of the GH20 enzyme. This study is an example of the successful application of a MS/MS experiment for structure-guided isolation of natural products.

Place-Specific Computing

DEFF Research Database (Denmark)

Messeter, Jörn

2009-01-01

An increased interest in the notion of place has evolved in interaction design based on the proliferation of wireless infrastructures, developments in digital media, and a ‘spatial turn’ in computing. In this article, place-specific computing is suggested as a genre of interaction design that add......An increased interest in the notion of place has evolved in interaction design based on the proliferation of wireless infrastructures, developments in digital media, and a ‘spatial turn’ in computing. In this article, place-specific computing is suggested as a genre of interaction design...... that addresses the shaping of interactions among people, place-specific resources and global socio-technical networks, mediated by digital technology, and influenced by the structuring conditions of place. The theoretical grounding for place-specific computing is located in the meeting between conceptions...... of place in human geography and recent research in interaction design focusing on embodied interaction. Central themes in this grounding revolve around place and its relation to embodiment and practice, as well as the social, cultural and material aspects conditioning the enactment of place. Selected...

Structural Insight into the Critical Role of the N-Terminal Region in the Catalytic Activity of Dual-Specificity Phosphatase 26.

Directory of Open Access Journals (Sweden)

Eun-Young Won

Full Text Available Human dual-specificity phosphatase 26 (DUSP26 is a novel target for anticancer therapy because its dephosphorylation of the p53 tumor suppressor regulates the apoptosis of cancer cells. DUSP26 inhibition results in neuroblastoma cell cytotoxicity through p53-mediated apoptosis. Despite the previous structural studies of DUSP26 catalytic domain (residues 61-211, DUSP26-C, the high-resolution structure of its catalytically active form has not been resolved. In this study, we determined the crystal structure of a catalytically active form of DUSP26 (residues 39-211, DUSP26-N with an additional N-terminal region at 2.0 Å resolution. Unlike the C-terminal domain-swapped dimeric structure of DUSP26-C, the DUSP26-N (C152S monomer adopts a fold-back conformation of the C-terminal α8-helix and has an additional α1-helix in the N-terminal region. Consistent with the canonically active conformation of its protein tyrosine phosphate-binding loop (PTP loop observed in the structure, the phosphatase assay results demonstrated that DUSP26-N has significantly higher catalytic activity than DUSP26-C. Furthermore, size exclusion chromatography-multiangle laser scattering (SEC-MALS measurements showed that DUSP26-N (C152S exists as a monomer in solution. Notably, the crystal structure of DUSP26-N (C152S revealed that the N-terminal region of DUSP26-N (C152S serves a scaffolding role by positioning the surrounding α7-α8 loop for interaction with the PTP-loop through formation of an extensive hydrogen bond network, which seems to be critical in making the PTP-loop conformation competent for phosphatase activity. Our study provides the first high-resolution structure of a catalytically active form of DUSP26, which will contribute to the structure-based rational design of novel DUSP26-targeting anticancer therapeutics.

The Development of Target-Specific Pose Filter Ensembles To Boost Ligand Enrichment for Structure-Based Virtual Screening.

Science.gov (United States)

Xia, Jie; Hsieh, Jui-Hua; Hu, Huabin; Wu, Song; Wang, Xiang Simon

2017-06-26

Structure-based virtual screening (SBVS) has become an indispensable technique for hit identification at the early stage of drug discovery. However, the accuracy of current scoring functions is not high enough to confer success to every target and thus remains to be improved. Previously, we had developed binary pose filters (PFs) using knowledge derived from the protein-ligand interface of a single X-ray structure of a specific target. This novel approach had been validated as an effective way to improve ligand enrichment. Continuing from it, in the present work we attempted to incorporate knowledge collected from diverse protein-ligand interfaces of multiple crystal structures of the same target to build PF ensembles (PFEs). Toward this end, we first constructed a comprehensive data set to meet the requirements of ensemble modeling and validation. This set contains 10 diverse targets, 118 well-prepared X-ray structures of protein-ligand complexes, and large benchmarking actives/decoys sets. Notably, we designed a unique workflow of two-layer classifiers based on the concept of ensemble learning and applied it to the construction of PFEs for all of the targets. Through extensive benchmarking studies, we demonstrated that (1) coupling PFE with Chemgauss4 significantly improves the early enrichment of Chemgauss4 itself and (2) PFEs show greater consistency in boosting early enrichment and larger overall enrichment than our prior PFs. In addition, we analyzed the pairwise topological similarities among cognate ligands used to construct PFEs and found that it is the higher chemical diversity of the cognate ligands that leads to the improved performance of PFEs. Taken together, the results so far prove that the incorporation of knowledge from diverse protein-ligand interfaces by ensemble modeling is able to enhance the screening competence of SBVS scoring functions.

Selecting highly structure-specific antibodies using structured synthetic mimics of the cystine knot protein sclerostin

NARCIS (Netherlands)

Back, J.W.; Frisch, C.; Van Pee, K.; Boschert, V.; van Vught, R.; Puijk, W.; Mueller, T. D.; Knappik, A.; Timmerman, P.

2012-01-01

Antibodies directed against specific regions of a protein have traditionally been raised against full proteins, protein domains or simple unstructured peptides, containing contiguous stretches of primary sequence. We have used a new approach of selecting antibodies against restrained peptides

Investigation of structure, specific heat and superconducting transition in Mg1-xAlxB2(x∼0.5)

International Nuclear Information System (INIS)

Xiang, J.Y.; Zheng, D.N.; Lang, P.L.; Zhao, Z.X.; Luo, J.L.

2004-01-01

We have carried out structure, magnetic and specific heat measurements on aluminum doped magnetism diboride samples Mg 1-x Al x B 2 in order to investigate possible superconductivity at the x=0.5 concentration. A diamagnetic signal was observed in magnetization measurements accompanied by a decrease in resistivity. However, the diamagnetic signal was extremely small as compared to what expected from full diamagnetism. Also, the transition both in magnetization and resistance was very broad. We propose that the diamagnetism is due to a very small amount of superconducting phase such as MgB 2 and the resistive transition is due to the percolation behavior. Furthermore, we performed specific heat measurements, which are considered as a tool to investigate the bulk nature of superconducting transition, on the x=0.5 sample to verify the existence of superconductivity. We observed no evident superconducting transition in the entire temperature region from 2 to 300 K. The undistinguishable data between 0 and 5 T magnetic fields also indicated the absence of bulk superconductivity in the x=0.5 sample

HTTR hydrogen production system. Structure and main specifications of mock-up test facility (Contract research)

International Nuclear Information System (INIS)

Kato, Michio; Aita, Hideki; Inagaki, Yoshiyuki; Hayashi, Koji; Ohashi, Hirofumi; Sato, Hiroyuki; Iwatsuki, Jin; Takada, Shoji; Inaba, Yoshitomo

2007-03-01

The mock-up test facility was fabricated to investigate performance of the steam generator for mitigation of the temperature fluctuation of helium gas and transient behavior of the hydrogen production system for HTTR and to obtain experimental data for verification of a dynamic analysis code. The test facility has an approximate hydrogen production capacity of 120Nm 3 /h and the steam reforming process of methane; CH 4 +H 2 O=3H 2 +CO, was used for hydrogen production of the test facility. An electric heater was used as a heat source instead of the reactor in order to heat helium gas up to 880degC (4MPa) at the chemical reactor inlet which is the same temperature as the HTTR hydrogen production system. Fabrication of the test facility was completed in February in 2002, and seven cycle operations were carried out from March in 2002 to December in 2004. This report describes the structure and main specifications of the test facility. (author)

Capital Structure around the World: The Roles of Firm- and Country-Specific Determinants

NARCIS (Netherlands)

A. de Jong (Abe); R. Kabir (Rezaul); T.T. Nguyen (Thuy Thu)

2007-01-01

textabstractWe analyze the importance of firm-specific and country-specific factors in the leverage choice of firms from 42 countries around the world. Our analysis yields two new results. First, we find that firm-specific determinants of leverage differ across countries, while prior studies

SPECIFIC PROFESSIONAL COMMUNICATION IN THE STRUCTURE OF THE PROFESSIONAL EDUCATOR

Directory of Open Access Journals (Sweden)

Olga Abramova

2012-01-01

Full Text Available The article deals with the specific characteristics of professional communication teachers in the course of his career. Characterized by the basic communication skillsfor professional communication teachers, distinguished social and psychological characteristics of professional educator.

Structural isoforms of the circadian neuropeptide PDF expressed in the optic lobes of the cricket Gryllus bimaculatus: immunocytochemical evidence from specific monoclonal antibodies.

Science.gov (United States)

Honda, Takeshi; Matsushima, Ayami; Sumida, Kazunori; Chuman, Yoshiro; Sakaguchi, Kazuyasu; Onoue, Hitoshi; Meinertzhagen, Ian A; Shimohigashi, Yasuyuki; Shimohigashi, Miki

2006-11-20

Pigment-dispersing factor (PDF) is an 18-mer peptide that acts as a principal neurotransmitter of the insect circadian clock. Our previous study, utilizing anti-Uca beta-PDH polyclonal antibody (pAb) to immunolabel the optic lobe of the cricket Gryllus bimaculatus, suggested the existence of an alternative PDF-like peptide in the outer cells of the first neuropile, or lamina (La), which were much less immunoreactive than the inner cells of the second neuropile, the medulla (Me). To obtain structural information about such a PDF-like peptide, we prepared 10 anti-Gryllus PDF monoclonal (mAb) and pAb antibodies and analyzed their detailed epitope specificities. The PDFMe and PDFLa inner cells and their axonal projections were clearly immunoreactive to all these antibodies, revealing the widespread immunocytochemical organization of the PDF system in the optic lobe, as seen previously with anti-Uca beta-PDH pAb and anti-Gryllus PDF mAb, the epitope structures of which were also clarified in this study. The lamina outer cells, which we found lacked a target pdf mRNA, displayed specific immunoreactivities, indicating that the cells contain a distinct PDF-like peptide possessing both N- and C-terminal structures. These cells were not immunolabeled by some other monoclonal antibodies, however, implying that the PDFLa outer cells have a PDF isoform peptide devoid of Asn at positions 6 and 16. This isoform was also identified in a varicose arborization in the lamina. These results suggest not only the structure of the peptide, but also the possibility of additional functions of this novel PDF isoform.

Capital structure around the world: The roles of firm- and country-specific determinants

NARCIS (Netherlands)

de Jong, Abe; Kabir, Mohammed Rezaul; Nguyen, Thuy Thu

2008-01-01

We analyze the importance of firm-specific and country-specific factors in the leverage choice of firms from 42 countries around the world. Our analysis yields two new results. First, we find that firm-specific determinants of leverage differ across countries, while prior studies implicitly assume

Failure to replicate the internal structure of Greek-specific thalassemia quality of life instrument in adult thalassemia patients in Sabah

Directory of Open Access Journals (Sweden)

Keowmani T

2016-02-01

Full Text Available Thamron Keowmani,1 Lily Wong Lee Lee21Clinical Research Centre, 2Hematology Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, MalaysiaPurpose: To study the validity and reliability of the Malay version of the Specific Thalassemia Quality of Life Instrument (STQOLI in Sabah’s adult thalassemia patients.Patients and methods: This cross-sectional study was done at Thalassemia Treatment Centre, Queen Elizabeth Hospital in Sabah, Malaysia. Eighty-two adult thalassemia patients who fulfilled the inclusion and exclusion criteria were conveniently selected for participation in the study. The English version of STQOLI was translated into Malay by using forward and back translations. The content of the questionnaire was validated by the chief hematologist of the hospital. The construct validity of the 40-item questionnaire was assessed by principal component analysis with varimax rotation and the scale reliability was assessed by Cronbach’s alpha.Results: The study failed to replicate the internal structure of the Greek STQOLI. Instead, 12 factors have been identified from the exploratory factor analysis, which accounted for 72.2% of the variance. However, only eight factors were interpretable. The factors were iron chelation pump impact, transfusion impact, time spent on treatment and its impact on work and social life, sex life, side effects of treatment, cardiovascular problems, psychology, and iron chelation pill impact. The overall scale reliability was 0.913.Conclusion: This study was unable to replicate the internal structure of the Greek STQOLI in Sabah’s adult thalassemia patients. Instead, a new structure has emerged that can be used as a guide to develop a questionnaire specific for adult thalassemia patients in Sabah. Future research should focus on the eight factors identified from this study.Keywords: STQOLI, validity, reliability, Malay, transfusion

Computational structural mechanics for engine structures

Science.gov (United States)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.

Woman's Profession and Female Role--The Development of Sex-specific Structures of Education and of the Labor Market before the First World War.

Science.gov (United States)

Klinger, Vera

1989-01-01

Examines the intrusion of female employees into the traditionally male domain of office work from 1860 to 1914. Shows that sex-specific segregation was supported by a lack of training facilities for girls and by fact that these facilities supported the dominant sex-role structure. Focuses on the development of vocational schools for girls.…

Site-Specific Pre-Swelling-Directed Morphing Structures of Patterned Hydrogels.

Science.gov (United States)

Wang, Zhi Jian; Hong, Wei; Wu, Zi Liang; Zheng, Qiang

2017-12-11

Morphing materials have promising applications in various fields, yet how to program the self-shaping process for specific configurations remains a challenge. Herein we show a versatile approach to control the buckling of individual domains and thus the outcome configurations of planar-patterned hydrogels. By photolithography, high-swelling disc gels were positioned in a non-swelling gel sheet; the swelling mismatch resulted in out-of-plain buckling of the disc gels. To locally control the buckling direction, masks with holes were used to guide site-specific swelling of the high-swelling gel under the holes, which built a transient through-thickness gradient and thus directed the buckling during the subsequent unmasked swelling process. Therefore, various configurations of an identical patterned hydrogel can be programmed by the pre-swelling step with different masks to encode the buckling directions of separate domains. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Strategy implemented through structuring and new structures

DEFF Research Database (Denmark)

Nielsen, Renate

Research objective: With the purpose of generating a new understanding of how development in organisations take place, an interpretive perspective at continuous processes in organisations will be applied: more specifically at how organisational interpretation forms an organisation's strategy...... and how the strategy is implemented through structuring, new structures and routines....

Breckinridge Project, initial effort. Report III, Volume 2. Specifications

Energy Technology Data Exchange (ETDEWEB)

None

1982-01-01

Report III, Volume 2 contains those specifications numbered K through Y, as follows: Specifications for Compressors (K); Specifications for Piping (L); Specifications for Structures (M); Specifications for Insulation (N); Specifications for Electrical (P); Specifications for Concrete (Q); Specifications for Civil (S); Specifications for Welding (W); Specifications for Painting (X); and Specifications for Special (Y). The standard specifications of Bechtel Petroleum Incorporated have been amended as necessary to reflect the specific requirements of the Breckinridge Project and the more stringent specifications of Ashland Synthetic Fuels, Inc. These standard specifications are available for the Initial Effort (Phase Zero) work performed by all contractors and subcontractors.

A rapid NMR-based method for discrimination of strain-specific cell wall teichoic acid structures reveals a third backbone type in Lactobacillus plantarum.

Science.gov (United States)

Tomita, Satoru; Tanaka, Naoto; Okada, Sanae

2017-03-01

The lactic acid bacterium Lactobacillus plantarum is capable of producing strain-specific structures of cell wall teichoic acid (WTA), an anionic polysaccharide found in the Gram-positive bacterial cell wall. In this study, we established a rapid, NMR-based procedure to discriminate WTA structures in this species, and applied it to 94 strains of L. plantarum. Six previously reported glycerol- and ribitol-containing WTA subtypes were successfully identified from 78 strains, suggesting that these were the dominant structures. However, the level of structural variety differed markedly among bacterial sources, possibly reflecting differences in strain-level microbial diversity. WTAs from eight strains were not identified based on NMR spectra and were classified into three groups. Structural analysis of a partial degradation product of an unidentified WTA produced by strain TUA 1496L revealed that the WTA was 1-O-β-d-glucosylglycerol. Two-dimensional NMR analysis of the polymer structure showed phosphodiester bonds between C-3 and C-6 of the glycerol and glucose residues, suggesting a polymer structure of 3,6΄-linked poly(1-O-β-d-glucosyl-sn-glycerol phosphate). This is the third WTA backbone structure in L. plantarum, following 3,6΄-linked poly(1-O-α-d-glucosyl-sn-glycerol phosphate) and 1,5-linked poly(ribitol phosphate). © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Gender-specific changes in laboratory indexes and structural parameters of the left ventricle myocardium in chronic heart failure on the background of diabetes mellitus type 2 and obesity

Directory of Open Access Journals (Sweden)

P. P. Bidzilya

2015-12-01

Full Text Available Modern studies have shown that the prevalence of cardiovascular disease and chronic heart failure (CHF specifically, in patients with diabetes mellitus (DM is about 50%. Aim. To study gender-specific changes in laboratory indexes and structural myocardial parameters of left ventricle (LV in CHF on the background of diabetes mellitus (DM type 2. 111 patients with I–III functional class of disease with normal, overweight and abdominal obesity I–III degree were examined. Methods and results. Clinical and biochemical blood tests? glomerular filtration rate were used. Structural parameters of the myocardium were estimated with echocardiography. It is established that in CHF on the background of DM type 2 and obesity there is a tendency to develop anemia and renal dysfunction in women. Structural changes of the myocardium is more pronounced in men and presents the prevalence ofLV hypertrophy and dilatation of the heart cavities. Conclusion. This demonstrates different ways of negative impact of gender factor on the laboratory indexes and structural myocardial parameters in CHF on the background of DM type 2 and obesity.

Rationalization of specific structure formation in electrospinning process: Study on nano-fibrous PCL- and PLGA-based scaffolds.

Science.gov (United States)

Saeed, Mahdi; Mirzadeh, Hamid; Zandi, Mojgan; Irani, Shiva; Barzin, Jalal

2015-12-01

Formation of specific structures on poly-ɛ-caprolactone (PCL) and poly lactide-co-glycolide (PLGA) based electrospun mats is rationalized and the effect of interactive parameters; high voltage and flow rate on unique surface topography is evaluated. By increasing the collecting time in electrospinning process and enhancing fiber to fiber repulsion, surface characteristics of mats changes from nano- to micro-topography. In this study surface topography of the fabricated mats based on PCL and PLGA were assessed using AFM and SEM techniques to display the distinct phenomenon occurs on collected random fibers. In this research the rationale behind the formation of bump and flower like structures on fibrous mats was discussed. Because of great potential application of the fabricated substrates in the fields of medical purposes, cell-matrix interaction was evaluated and in vitro biological test with human dermal fibroblast and mouse L929 fibroblast cells was performed to study the cell responses to different roughness of nano-fibers collected at different time intervals. Our results show that after 7 days, cell proliferation is improved on PCL collected at 40 min in the case of human fibroblast cells and on PCL collected in 70 min in the case of L929 mouse fibroblast cells. © 2015 Wiley Periodicals, Inc.

Analysis of structure and specific functional groups involved in acetylcholinesterase catalysis and inhibition. Final report, 14 June 1991-13 September 1994

Energy Technology Data Exchange (ETDEWEB)

Taylor, P.

1994-10-01

The interactions of substrates, inhibitors and antibodies with Torpedo and mammalian acetylcholinesterases and butyrylcholinesterases have been studied by enzyme kinetic analyses, site-specific mutagenesis, molecular modeling, and peptide and antibody titrations. The high yield expression systems we developed have enabled us to obtain sufficient wild-type and mutant enzymes for the kinetic and physical studies. These studies have benefited from the availability of a three-dimensional X-ray-derived structure of acetylcholinesterase which allows for interpretations at an atomic level of resolution. Three distinct regions in the enzyme appear responsible for conferring selectivity: the acyl pocket defined primarily by phenylalanines 295 and 297, the choline subsite primarily defined by tryptophan 86, tyrosine 337 and glutamate 202 and the peripheral anionic site defined by tryptophan 286, tyrosine 72, tyrosine 124 and aspartate 74. Through site-specific mutagenesis we have been able to modify acyl pocket specificity, selectivity toward neutral and charged substrates, substrate inhibition, organophosphate reactivity, organophosphate aging and oxime reactivation. These studies have important implications in developing superior antidotes for organophosphate poisoning and in using recombinant acetylcholinesterase as an antidote.

Science Student Role: Evidence of Social Structural Norms Specific to School Science

Science.gov (United States)

Shanahan, Marie-Claire; Nieswandt, Martina

2011-01-01

Sociocultural studies of science education have consistently recognized the dialectic nature of students' agency to create and author positions for themselves and the structural constraints that may influence them. This mixed-methods study explores one particular aspect of these potential constraints: the possibility of a social structure specific…

Structure-Based Analysis of Toxoplasma gondii Profilin: A Parasite-Specific Motif Is Required for Recognition by Toll-Like Receptor 11

Energy Technology Data Exchange (ETDEWEB)

K Kucera; A Koblansky; L Saunders; K Frederick; E De La Cruz; S Ghosh; Y Modis

2011-12-31

Profilins promote actin polymerization by exchanging ADP for ATP on monomeric actin and delivering ATP-actin to growing filament barbed ends. Apicomplexan protozoa such as Toxoplasma gondii invade host cells using an actin-dependent gliding motility. Toll-like receptor (TLR) 11 generates an innate immune response upon sensing T. gondii profilin (TgPRF). The crystal structure of TgPRF reveals a parasite-specific surface motif consisting of an acidic loop, followed by a long {beta}-hairpin. A series of structure-based profilin mutants show that TLR11 recognition of the acidic loop is responsible for most of the interleukin (IL)-12 secretion response to TgPRF in peritoneal macrophages. Deletion of both the acidic loop and the {beta}-hairpin completely abrogates IL-12 secretion. Insertion of the T. gondii acidic loop and {beta}-hairpin into yeast profilin is sufficient to generate TLR11-dependent signaling. Substitution of the acidic loop in TgPRF with the homologous loop from the apicomplexan parasite Cryptosporidium parvum does not affect TLR11-dependent IL-12 secretion, while substitution with the acidic loop from Plasmodium falciparum results in reduced but significant IL-12 secretion. We conclude that the parasite-specific motif in TgPRF is the key molecular pattern recognized by TLR11. Unlike other profilins, TgPRF slows nucleotide exchange on monomeric rabbit actin and binds rabbit actin weakly. The putative TgPRF actin-binding surface includes the {beta}-hairpin and diverges widely from the actin-binding surfaces of vertebrate profilins.

Antigenic polysaccharides of bacteria. 14. Structure of the O-specific polysaccharide chain of the lipopolysaccharide of pseudomonas aeruginosa O12 (Lanyi)

International Nuclear Information System (INIS)

Knirel', Y.A.; Shashkov, A.S.; Dmitriev, B.A.; Kochetkov, N.K.; Stanislavskii, E.S.; Mashilova, G.M.

1986-01-01

The mild-alkaline hydrolysis of the lipopolysaccharide of Pseudomonas aeruginosa O12 (Lanyi classification) has given the O-specific polysaccharide, which is constructed of D-ribose and N-acetyl-D-galactosamine residues. The disaccharide structure for the repeating unit of this polysaccharide has been established by a nondestructive method as the result of the complete deciphering of its 1 H and 13 C NMR spectra using homonuclear and selective heteronuclear 13 C { 1 H} double resonance

Evaluation of acute toxicity of babassu mesocarp in mice

Directory of Open Access Journals (Sweden)

Elizabeth S. B. Barroqueiro

2011-07-01

Full Text Available The safety of babassu mesocarp (Orbignya phalerata Mart., Arecaceae, which exhibited anti-inflammatory and antithrombotic activities, was evaluated by determining the potential acute toxicity in mice. A lyophilized ethanol extract of babassu mesocarp (BME was administered to C3H/HePas mice (10/group in a single dose of 1000, 3000 and 5000 mg/kg, by gavage. General behavior adverse effects and mortality were determined for up to fourteen days. Selected biochemical parameters including glucose, triacylglyceride, cholesterol, urea, alkaline phosphatase and creatinine were determined by colorimetric assay. The heart, liver, spleen, kidneys and brain were weighted and evaluated macro and microscopically. The median lethal dose (LD50 of BME was greater than 5000 mg/kg. No behavior or body weight alterations were detected after the treatment. The acute treatment with BME has no effect on macroscopic and microscopic aspect of examined organs. Instead, BME increased the alkaline phosphatase and reduced the urea concentration in all groups. A significant increase on triacylglyceride was detected in the group BME1000. In conclusion, the acute treatment with high doses of BME can affect some biochemical parameters with a long lasting effect, although any change was detected at tissue level or body and organ weight.

Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

Science.gov (United States)

Fazelinia, Hossein; Xu, Ming; Cheng, Hong; Roder, Heinrich

2014-01-15

Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.

On the specification of structural equation models for ecological systems

NARCIS (Netherlands)

Grace, James B.; Anderson, T. Michael; Olff, Han; Scheiner, Samuel M.

The use of structural equation modeling (SEM) is often motivated by its utility for investigating complex networks of relationships, but also because of its promise as a means of representing theoretical Concepts using latent variables. In this paper, we discuss characteristics of ecological theory

Specific patterns of whole-brain structural covariance of the anterior and posterior hippocampus in young APOE ε4 carriers.

Science.gov (United States)

Stening, Eva; Persson, Jonas; Eriksson, Elias; Wahlund, Lars-Olof; Zetterberg, Henrik; Söderlund, Hedvig

2017-05-30

Apolipoprotein E (APOE) ε4 has been associated with smaller hippocampal volumes in healthy aging, while findings in young adults are inconclusive. Previous studies have mostly used univariate methods, and without considering potential anterior/posterior differences. Here, we used a multivariate method, partial least squares, and assessed whole-brain structural covariance of the anterior (aHC) and posterior (pHC) hippocampus in young adults (n=97) as a function of APOE ε4 status and sex. Two significant patterns emerged: (1) specific structural covariance of the aHC with frontal regions, temporal and occipital areas in APOE ε4 women, whereas the volume of both the aHC and pHC in all other groups co-varied with frontal, parietal and cerebellar areas; and (2) opposite structural covariance of the pHC in ε4 carriers compared to the aHC in non-carriers, with the pHC of ε4 carriers covarying with parietal and frontal areas, and the aHC of ε4 non-carriers covarying with motor areas and the middle frontal gyrus. APOE ε4 has in young adults been associated with better episodic and spatial memory, functions involving the aHC and pHC, respectively. We found no associations between structural covariance and performance, suggesting that other factors underlie the performance differences seen between carriers and non-carriers. Our findings indicate that APOE ε4 carriers and non-carriers differ in hippocampal organization and that there are differences as a function of sex and hippocampal segment. They stress the need to consider the hippocampus as a heterogeneous structure, and highlight the benefits of multivariate methods in assessing group differences in the brain. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.

Science.gov (United States)

Lin, Lianyun; Liu, Chen; Qin, Juan; Wang, Jie; Dong, Shengjie; Chen, Wei; He, Weiyi; Gao, Qingzhi; You, Minsheng; Yuchi, Zhiguang

2018-01-01

Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide. Copyright © 2017 Elsevier Ltd. All rights reserved.

Specification styles in distributed systems design and verification

NARCIS (Netherlands)

Vissers, C.A.; Scollo, Giuseppe; van Sinderen, Marten J.; Brinksma, Hendrik

1991-01-01

Substantial experience with the use of formal specification languages in the design of distributed systems has shown that finding appropriate structures for formal specifications presents a serious, and often underestimated problem. Its solutions are of great importance for ensuring the quality of

Pose Estimation using Local Structure-Specific Shape and Appearance Context

DEFF Research Database (Denmark)

Buch, Anders Glent; Kraft, Dirk; Kämäräinen, Joni-Kristian

2013-01-01

information for both edge and texture structures. This is achieved by defining feature space relations which describe the neighborhood of a descriptor. By quantitative evaluations, we show that our descriptors provide high discriminative power compared to state of the art approaches. In addition, we show how...

Map Specifications and Exchange of Geographical Information

DEFF Research Database (Denmark)

Frederiksen, Poul

1999-01-01

Specifications for Technical Maps 1993 – 99 are described giving an overview of the specification structure including the object description of the latest version: TK99.The technical map specifications are related to the standards for topographical maps - especially the TOP10DK standard. Common...... object definitions are essential for the standards. Technical as well as topographical map information is exchangeable through the Danish developed “Standard for Exchange of Digital Map Information”, known as the DSFL-format....

Disease-Specific Care: Spine Surgery Program Development.

Science.gov (United States)

Koerner, Katie; Franker, Lauren; Douglas, Barbara; Medero, Edgardo; Bromeland, Jennifer

2017-10-01

Minimal literature exists describing the process for development of a Joint Commission comprehensive spine surgery program within a community hospital health system. Components of a comprehensive program include structured communication across care settings, preoperative education, quality outcomes tracking, and patient follow-up. Organizations obtaining disease-specific certification must have clear knowledge of the planning, time, and overall commitment, essential to developing a successful program. Health systems benefit from disease-specific certification because of their commitment to a higher standard of service. Certification standards establish a framework for organizational structure and management and provide institutions a competitive edge in the marketplace. A framework for the development of a spine surgery program is described to help guide organizations seeking disease-specific certification. In developing a comprehensive program, it is critical to define the program's mission and vision, identify key stakeholders, implement clinical practice guidelines, and evaluate program outcomes.

Structural specificity of chloroquine-hematin binding related to inhibition of hematin polymerization and parasite growth.

Science.gov (United States)

Vippagunta, S R; Dorn, A; Matile, H; Bhattacharjee, A K; Karle, J M; Ellis, W Y; Ridley, R G; Vennerstrom, J L

1999-11-04

Considerable data now support the hypothesis that chloroquine (CQ)-hematin binding in the parasite food vacuole leads to inhibition of hematin polymerization and parasite death by hematin poisoning. To better understand the structural specificity of CQ-hematin binding, 13 CQ analogues were chosen and their hematin binding affinity, inhibition of hematin polymerization, and inhibition of parasite growth were measured. As determined by isothermal titration calorimetry (ITC), the stoichiometry data and exothermic binding enthalpies indicated that, like CQ, these analogues bind to two or more hematin mu-oxo dimers in a cofacial pi-pi sandwich-type complex. Association constants (K(a)'s) ranged from 0.46 to 2.9 x 10(5) M(-1) compared to 4.0 x 10(5) M(-1) for CQ. Remarkably, we were not able to measure any significant interaction between hematin mu-oxo dimer and 11, the 6-chloro analogue of CQ. This result indicates that the 7-chloro substituent in CQ is a critical structural determinant in its binding affinity to hematin mu-oxo dimer. Molecular modeling experiments reinforce the view that the enthalpically favorable pi-pi interaction observed in the CQ-hematin mu-oxo dimer complex derives from a favorable alignment of the out-of-plane pi-electron density in CQ and hematin mu-oxo dimer at the points of intermolecular contact. For 4-aminoquinolines related to CQ, our data suggest that electron-withdrawing functional groups at the 7-position of the quinoline ring are required for activity against both hematin polymerization and parasite growth and that chlorine substitution at position 7 is optimal. Our results also confirm that the CQ diaminoalkyl side chain, especially the aliphatic tertiary nitrogen atom, is an important structural determinant in CQ drug resistance. For CQ analogues 1-13, the lack of correlation between K(a) and hematin polymerization IC(50) values suggests that other properties of the CQ-hematin mu-oxo dimer complex, rather than its association

Combining specificity determining and conserved residues improves functional site prediction

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Gelfand Mikhail S

2009-06-01

Full Text Available Abstract Background Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core. Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities. Results Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs, as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples. Conclusion The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.

Specificity and affinity quantification of protein-protein interactions.

Science.gov (United States)

Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

2013-05-01

Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

Fluid-Structure Simulations of a Ruptured Intracranial Aneurysm: Constant versus Patient-Specific Wall Thickness

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S. Voß

2016-01-01

Full Text Available Computational Fluid Dynamics is intensively used to deepen the understanding of aneurysm growth and rupture in order to support physicians during therapy planning. However, numerous studies considering only the hemodynamics within the vessel lumen found no satisfactory criteria for rupture risk assessment. To improve available simulation models, the rigid vessel wall assumption has been discarded in this work and patient-specific wall thickness is considered within the simulation. For this purpose, a ruptured intracranial aneurysm was prepared ex vivo, followed by the acquisition of local wall thickness using μCT. The segmented inner and outer vessel surfaces served as solid domain for the fluid-structure interaction (FSI simulation. To compare wall stress distributions within the aneurysm wall and at the rupture site, FSI computations are repeated in a virtual model using a constant wall thickness approach. Although the wall stresses obtained by the two approaches—when averaged over the complete aneurysm sac—are in very good agreement, strong differences occur in their distribution. Accounting for the real wall thickness distribution, the rupture site exhibits much higher stress values compared to the configuration with constant wall thickness. The study reveals the importance of geometry reconstruction and accurate description of wall thickness in FSI simulations.

Structural analysis of the evolution of steroid specificity in the mineralocorticoid and glucocorticoid receptors

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Ollikainen Noah

2007-02-01

Full Text Available Abstract Background The glucocorticoid receptor (GR and mineralocorticoid receptor (MR evolved from a common ancestor. Still not completely understood is how specificity for glucocorticoids (e.g. cortisol and mineralocorticoids (e.g. aldosterone evolved in these receptors. Results Our analysis of several vertebrate GRs and MRs in the context of 3D structures of human GR and MR indicates that with the exception of skate GR, a cartilaginous fish, there is a deletion in all GRs, at the position corresponding to Ser-949 in human MR. This deletion occurs in a loop before helix 12, which contains the activation function 2 (AF2 domain, which binds coactivator proteins and influences transcriptional activity of steroids. Unexpectedly, we find that His-950 in human MR, which is conserved in the MR in chimpanzee, orangutan and macaque, is glutamine in all teleost and land vertebrate MRs, including New World monkeys and prosimians. Conclusion Evolution of differences in the responses of the GR and MR to corticosteroids involved deletion in the GR of a residue corresponding to Ser-949 in human MR. A mutation corresponding to His-950 in human MR may have been important in physiological changes associated with emergence of Old World monkeys from prosimians.

Adenovirus structural protein IIIa is involved in the serotype specificity of viral DNA packaging.

Science.gov (United States)

Ma, Hsin-Chieh; Hearing, Patrick

2011-08-01

The packaging of the adenovirus (Ad) genome into a capsid displays serotype specificity. This specificity has been attributed to viral packaging proteins, the IVa2 protein and the L1-52/55K protein. We previously found that the Ad17 L1-52/55K protein was not able to complement the growth of an Ad5 L1-52/55K mutant virus, whereas two other Ad17 packaging proteins, IVa2 and L4-22K, could complement the growth of Ad5 viruses with mutations in the respective genes. In this report, we investigated why the Ad17 L1-52/55K protein was not able to complement the Ad5 L1-52/55K mutant virus. We demonstrate that the Ad17 L1-52/55K protein binds to the Ad5 IVa2 protein in vitro and the Ad5 packaging domain in vivo, activities previously associated with packaging function. The Ad17 L1-52/55K protein also associates with empty Ad5 capsids. Interestingly, we find that the Ad17 L1-52/55K protein is able to complement the growth of an Ad5 L1-52/55K mutant virus in conjunction with the Ad17 structural protein IIIa. The same result was found with the L1-52/55K and IIIa proteins of several other Ad serotypes, including Ad3 and Ad4. The Ad17 IIIa protein associates with empty Ad5 capsids. Consistent with the complementation results, we find that the IIIa protein interacts with the L1-52/55K protein in vitro and associates with the viral packaging domain in vivo. These results underscore the complex nature of virus assembly and genome encapsidation and provide a new model for how the viral genome may tether to the empty capsid during the encapsidation process.

Attribution of global foodborne disease to specific foods: Findings from a World Health Organization structured expert elicitation.

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Sandra Hoffmann

Full Text Available Recently the World Health Organization, Foodborne Disease Burden Epidemiology Reference Group (FERG estimated that 31 foodborne diseases (FBDs resulted in over 600 million illnesses and 420,000 deaths worldwide in 2010. Knowing the relative role importance of different foods as exposure routes for key hazards is critical to preventing illness. This study reports the findings of a structured expert elicitation providing globally comparable food source attribution estimates for 11 major FBDs in each of 14 world subregions.We used Cooke's Classical Model to elicit and aggregate judgments of 73 international experts. Judgments were elicited from each expert individually and aggregated using both equal and performance weights. Performance weighted results are reported as they increased the informativeness of estimates, while retaining accuracy. We report measures of central tendency and uncertainty bounds on food source attribution estimate. For some pathogens we see relatively consistent food source attribution estimates across subregions of the world; for others there is substantial regional variation. For example, for non-typhoidal salmonellosis, pork was of minor importance compared to eggs and poultry meat in the American and African subregions, whereas in the European and Western Pacific subregions the importance of these three food sources were quite similar. Our regional results broadly agree with estimates from earlier European and North American food source attribution research. As in prior food source attribution research, we find relatively wide uncertainty bounds around our median estimates.We present the first worldwide estimates of the proportion of specific foodborne diseases attributable to specific food exposure routes. While we find substantial uncertainty around central tendency estimates, we believe these estimates provide the best currently available basis on which to link FBDs and specific foods in many parts of the world

Attribution of global foodborne disease to specific foods: Findings from a World Health Organization structured expert elicitation.

Science.gov (United States)

Hoffmann, Sandra; Devleesschauwer, Brecht; Aspinall, Willy; Cooke, Roger; Corrigan, Tim; Havelaar, Arie; Angulo, Frederick; Gibb, Herman; Kirk, Martyn; Lake, Robin; Speybroeck, Niko; Torgerson, Paul; Hald, Tine

2017-01-01

Recently the World Health Organization, Foodborne Disease Burden Epidemiology Reference Group (FERG) estimated that 31 foodborne diseases (FBDs) resulted in over 600 million illnesses and 420,000 deaths worldwide in 2010. Knowing the relative role importance of different foods as exposure routes for key hazards is critical to preventing illness. This study reports the findings of a structured expert elicitation providing globally comparable food source attribution estimates for 11 major FBDs in each of 14 world subregions. We used Cooke's Classical Model to elicit and aggregate judgments of 73 international experts. Judgments were elicited from each expert individually and aggregated using both equal and performance weights. Performance weighted results are reported as they increased the informativeness of estimates, while retaining accuracy. We report measures of central tendency and uncertainty bounds on food source attribution estimate. For some pathogens we see relatively consistent food source attribution estimates across subregions of the world; for others there is substantial regional variation. For example, for non-typhoidal salmonellosis, pork was of minor importance compared to eggs and poultry meat in the American and African subregions, whereas in the European and Western Pacific subregions the importance of these three food sources were quite similar. Our regional results broadly agree with estimates from earlier European and North American food source attribution research. As in prior food source attribution research, we find relatively wide uncertainty bounds around our median estimates. We present the first worldwide estimates of the proportion of specific foodborne diseases attributable to specific food exposure routes. While we find substantial uncertainty around central tendency estimates, we believe these estimates provide the best currently available basis on which to link FBDs and specific foods in many parts of the world, providing guidance

pH-Specific structural speciation of the ternary V(V)-peroxido-betaine system: a chemical reactivity-structure correlation.

Science.gov (United States)

Gabriel, C; Kioseoglou, E; Venetis, J; Psycharis, V; Raptopoulou, C P; Terzis, A; Voyiatzis, G; Bertmer, M; Mateescu, C; Salifoglou, A

2012-06-04

Vanadium involvement in cellular processes requires deep understanding of the nature and properties of its soluble and bioavailable forms arising in aqueous speciations of binary and ternary systems. In an effort to understand the ternary vanadium-H(2)O(2)-ligand interactions relevant to that metal ion's biological role, synthetic efforts were launched involving the physiological ligands betaine (Me(3)N(+)CH(2)CO(2)(-)) and H(2)O(2). In a pH-specific fashion, V(2)O(5), betaine, and H(2)O(2) reacted and afforded three new, unusual, and unique compounds, consistent with the molecular formulation K(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}]·H(2)O (1), (NH(4))(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}]·0.75H(2)O (2), and {Na(2)[V(2)O(2)(O(2))(4){(CH(3))(3)NCH(2)CO(2))}(2)]}(n)·4nH(2)O (3). All complexes 1-3 were characterized by elemental analysis; UV/visible, FT-IR, Raman, and NMR spectroscopy in solution and the solid state; cyclic voltammetry; TGA-DTG; and X-ray crystallography. The structures of 1 and 2 reveal the presence of unusual ternary dinuclear vanadium-tetraperoxido-betaine complexes containing [(V(V)═O)(O(2))(2)] units interacting through long V-O bonds. The two V(V) ions are bridged through the oxygen terminal of one of the peroxide groups bound to the vanadium centers. The betaine ligand binds only one of the two V(V) ions. In the case of the third complex 3, the two vanadium centers are not immediate neighbors, with Na(+) ions (a) acting as efficient oxygen anchors and through Na-O bonds holding the two vanadium ions in place and (b) providing for oxygen-containing ligand binding leading to a polymeric lattice. In 1 and 3, interesting 2D (honeycomb) and 1D (zigzag chains) topologies of potassium nine-coordinate polyhedra (1) and sodium octahedra (3), respectively, form. The collective physicochemical properties of the three ternary species 1-3 project the chemical role of the low molecular mass biosubstrate betaine in binding V

Structural and functional conservation of CLEC-2 with the species-specific regulation of transcript expression in evolution.

Science.gov (United States)

Wang, Lan; Ren, Shifang; Zhu, Haiyan; Zhang, Dongmei; Hao, Yuqing; Ruan, Yuanyuan; Zhou, Lei; Lee, Chiayu; Qiu, Lin; Yun, Xiaojing; Xie, Jianhui

2012-08-01

CLEC-2 was first identified by sequence similarity to C-type lectin-like molecules with immune functions and has been reported as a receptor for the platelet-aggregating snake venom toxin rhodocytin and the endogenous sialoglycoprotein podoplanin. Recent researches indicate that CLEC-2-deficient mice were lethal at the embryonic stage associated with disorganized and blood-filled lymphatic vessels and severe edema. In view of a necessary role of CLEC-2 in the individual development, it is of interest to investigate its phylogenetic homology and highly conserved functional regions. In this work, we reported that CLEC-2 from different species holds with an extraordinary conservation by sequence alignment and phylogenetic tree analysis. The functional structures including N-linked oligosaccharide sites and ligand-binding domain implement a structural and functional conservation in a variety of species. The glycosylation sites (N120 and N134) are necessary for the surface expression CLEC-2. CLEC-2 from different species possesses the binding activity of mouse podoplanin. Nevertheless, the expression of CLEC-2 is regulated with a species-specific manner. The alternative splicing of pre-mRNA, a regulatory mechanism of gene expression, and the binding sites on promoter for several key transcription factors vary between different species. Therefore, CLEC-2 shares high sequence homology and functional identity. However the transcript expression might be tightly regulated by different mechanisms in evolution.

An approach for activity-based DEVS model specification

DEFF Research Database (Denmark)

Alshareef, Abdurrahman; Sarjoughian, Hessam S.; Zarrin, Bahram

2016-01-01

Creation of DEVS models has been advanced through Model Driven Architecture and its frameworks. The overarching role of the frameworks has been to help develop model specifications in a disciplined fashion. Frameworks can provide intermediary layers between the higher level mathematical models...... and their corresponding software specifications from both structural and behavioral aspects. Unlike structural modeling, developing models to specify behavior of systems is known to be harder and more complex, particularly when operations with non-trivial control schemes are required. In this paper, we propose specifying...... activity-based behavior modeling of parallel DEVS atomic models. We consider UML activities and actions as fundamental units of behavior modeling, especially in the presence of recent advances in the UML 2.5 specifications. We describe in detail how to approach activity modeling with a set of elemental...

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.

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Tomáš Kovaľ

Full Text Available The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.

Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails

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Wu Jihui

2007-09-01

Full Text Available Abstract Background Brd2 is a transcriptional regulator and belongs to BET family, a less characterized novel class of bromodomain-containing proteins. Brd2 contains two tandem bromodomains (BD1 and BD2, 46% sequence identity in the N-terminus and a conserved motif named ET (extra C-terminal domain at the C-terminus that is also present in some other bromodomain proteins. The two bromodomains have been shown to bind the acetylated histone H4 and to be responsible for mitotic retention on chromosomes, which is probably a distinctive feature of BET family proteins. Although the crystal structure of Brd2 BD1 is reported, no structure features have been characterized for Brd2 BD2 and its interaction with acetylated histones. Results Here we report the solution structure of human Brd2 BD2 determined by NMR. Although the overall fold resembles the bromodomains from other proteins, significant differences can be found in loop regions, especially in the ZA loop in which a two amino acids insertion is involved in an uncommon π-helix, termed πD. The helix πD forms a portion of the acetyl-lysine binding site, which could be a structural characteristic of Brd2 BD2 and other BET bromodomains. Unlike Brd2 BD1, BD2 is monomeric in solution. With NMR perturbation studies, we have mapped the H4-AcK12 peptide binding interface on Brd2 BD2 and shown that the binding was with low affinity (2.9 mM and in fast exchange. Using NMR and mutational analysis, we identified several residues important for the Brd2 BD2-H4-AcK12 peptide interaction and probed the potential mechanism for the specific recognition of acetylated histone codes by Brd2 BD2. Conclusion Brd2 BD2 is monomeric in solution and dynamically interacts with H4-AcK12. The additional secondary elements in the long ZA loop may be a common characteristic of BET bromodomains. Surrounding the ligand-binding cavity, five aspartate residues form a negatively charged collar that serves as a secondary binding site

Local structure and structural signature underlying properties in metallic glasses and supercooled liquids

Science.gov (United States)

Ding, Jun

Metallic glasses (MGs), discovered five decades ago as a newcomer in the family of glasses, are of current interest because of their unique structures and properties. There are also many fundamental materials science issues that remain unresolved for metallic glasses, as well as their predecessor above glass transition temperature, the supercooled liquids. In particular, it is a major challenge to characterize the local structure and unveil the structure-property relationship for these amorphous materials. This thesis presents a systematic study of the local structure of metallic glasses as well as supercooled liquids via classical and ab initio molecular dynamics simulations. Three typical MG models are chosen as representative candidate, Cu64 Zr36, Pd82Si18 and Mg65Cu 25Y10 systems, while the former is dominant with full icosahedra short-range order and the prism-type short-range order dominate for latter two. Furthermore, we move to unravel the underlying structural signature among several properties in metallic glasses. Firstly, the temperature dependence of specific heat and liquid fragility between Cu-Zr and Mg-Cu-Y (also Pd-Si) in supercooled liquids are quite distinct: gradual versus fast evolution of specific heat and viscosity/relaxation time with undercooling. Their local structural ordering are found to relate with the temperature dependence of specific heat and relaxation time. Then elastic heterogeneity has been studied to correlate with local structure in Cu-Zr MGs. Specifically, this part covers how the degree of elastic deformation correlates with the internal structure at the atomic level, how to quantitatively evaluate the local solidity/liquidity in MGs and how the network of interpenetrating connection of icosahedra determine the corresponding shear modulus. Finally, we have illustrated the structure signature of quasi-localized low-frequency vibrational normal modes, which resides the intriguing vibrational properties in MGs. Specifically, the

Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.

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Zhiqiang Yan

Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.

Combinatorics of γ-Structures

DEFF Research Database (Denmark)

Han, Hillary Siwei; Li, Thomas Jiaxian; reidys, Christian

2014-01-01

In this paper we study canonical $\\gamma$-structures, a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A $\\gamma$-structure is composed by specific building blocks, that have topological genus less than or equal...

Crystal Structures of the Helicobacter pylori MTAN Enzyme Reveal Specific Interactions between S-Adenosylhomocysteine and the 5'-Alkylthio Binding Subsite

Energy Technology Data Exchange (ETDEWEB)

Mishra, Vidhi [Univ. of Toledo, OH (United States); Ronning, Donald R. [Univ. of Toledo, OH (United States)

2012-11-13

The bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzyme is a multifunctional enzyme that catalyzes the hydrolysis of the N-ribosidic bond of at least four different adenosine-based metabolites: S-adenosylhomocysteine (SAH), 5'-methylthioadenosine (MTA), 5'-deoxyadenosine (5'-DOA), and 6-amino-6-deoxyfutalosine. These activities place the enzyme at the hub of seven fundamental bacterial metabolic pathways: S-adenosylmethionine (SAM) utilization, polyamine biosynthesis, the purine salvage pathway, the methionine salvage pathway, the SAM radical pathways, autoinducer-2 biosynthesis, and menaquinone biosynthesis. The last pathway makes MTAN essential for Helicobacter pylori viability. Although structures of various bacterial and plant MTANs have been described, the interactions between the homocysteine moiety of SAH and the 5'-alkylthiol binding site of MTAN have never been resolved. We have determined crystal structures of an inactive mutant form of H. pylori MTAN bound to MTA and SAH to 1.63 and 1.20 Å, respectively. The active form of MTAN was also crystallized in the presence of SAH, allowing the determination of the structure of a ternary enzyme–product complex resolved at 1.50 Å. These structures identify interactions between the homocysteine moiety and the 5'-alkylthiol binding site of the enzyme. This information can be leveraged for the development of species-specific MTAN inhibitors that prevent the growth of H. pylori.

A Structure-Function Study of RecA: The Structural Basis for ATP Specificity in the Strand Exchange Reaction

Science.gov (United States)

Gegner, Julie; Spruill, Natalie; Plesniak, Leigh A.

1999-11-01

The terms "structure" and "function" can assume a variety of meanings. In biochemistry, the "structure" of a protein can refer to its sequence of amino acids, the three-dimensional arrangement of atoms within a subunit, or the arrangement of subunits into a larger oligomeric or filamentous state. Likewise, the function of biological macromolecules can be examined at many levels. The function of a protein can be described by its role in an organism's survival or by a chemical reaction that it promotes. We have designed a three-part biochemical laboratory experiment that characterizes the structure and function of the Escherichia coli RecA protein. The first part examines the importance of RecA in the survival of bacteria that have been exposed to UV light. This is the broadest view of function of the enzyme. Second, the students use an in vitro assay of RecA whereby the protein promotes homologous recombination. Because RecA functions not catalytically, but rather stoichiometrically, in this recombination reaction, the oligomeric state of RecA in complex with DNA must also be discussed. Finally, through molecular modeling of X-ray crystallographic structures, students identify functionally important features of the ATP cofactor binding site of RecA.

Salt bridges: geometrically specific, designable interactions.

Science.gov (United States)

Donald, Jason E; Kulp, Daniel W; DeGrado, William F

2011-03-01

Salt bridges occur frequently in proteins, providing conformational specificity and contributing to molecular recognition and catalysis. We present a comprehensive analysis of these interactions in protein structures by surveying a large database of protein structures. Salt bridges between Asp or Glu and His, Arg, or Lys display extremely well-defined geometric preferences. Several previously observed preferences are confirmed, and others that were previously unrecognized are discovered. Salt bridges are explored for their preferences for different separations in sequence and in space, geometric preferences within proteins and at protein-protein interfaces, co-operativity in networked salt bridges, inclusion within metal-binding sites, preference for acidic electrons, apparent conformational side chain entropy reduction on formation, and degree of burial. Salt bridges occur far more frequently between residues at close than distant sequence separations, but, at close distances, there remain strong preferences for salt bridges at specific separations. Specific types of complex salt bridges, involving three or more members, are also discovered. As we observe a strong relationship between the propensity to form a salt bridge and the placement of salt-bridging residues in protein sequences, we discuss the role that salt bridges might play in kinetically influencing protein folding and thermodynamically stabilizing the native conformation. We also develop a quantitative method to select appropriate crystal structure resolution and B-factor cutoffs. Detailed knowledge of these geometric and sequence dependences should aid de novo design and prediction algorithms. Copyright © 2010 Wiley-Liss, Inc.

Structural basis for sequence-specific recognition of DNA by TAL effectors

KAUST Repository

Deng, Dong; Yan, Chuangye; Pan, Xiaojing; Mahfouz, Magdy M.; Wang, Jiawei; Zhu, Jiankang; Shi, Yi Gong; Yan, Nieng

2012-01-01

TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair

Estimating inverse probability weights using super learner when weight-model specification is unknown in a marginal structural Cox model context.

Science.gov (United States)

Karim, Mohammad Ehsanul; Platt, Robert W

2017-06-15

Correct specification of the inverse probability weighting (IPW) model is necessary for consistent inference from a marginal structural Cox model (MSCM). In practical applications, researchers are typically unaware of the true specification of the weight model. Nonetheless, IPWs are commonly estimated using parametric models, such as the main-effects logistic regression model. In practice, assumptions underlying such models may not hold and data-adaptive statistical learning methods may provide an alternative. Many candidate statistical learning approaches are available in the literature. However, the optimal approach for a given dataset is impossible to predict. Super learner (SL) has been proposed as a tool for selecting an optimal learner from a set of candidates using cross-validation. In this study, we evaluate the usefulness of a SL in estimating IPW in four different MSCM simulation scenarios, in which we varied the specification of the true weight model specification (linear and/or additive). Our simulations show that, in the presence of weight model misspecification, with a rich and diverse set of candidate algorithms, SL can generally offer a better alternative to the commonly used statistical learning approaches in terms of MSE as well as the coverage probabilities of the estimated effect in an MSCM. The findings from the simulation studies guided the application of the MSCM in a multiple sclerosis cohort from British Columbia, Canada (1995-2008), to estimate the impact of beta-interferon treatment in delaying disability progression. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Standardized Technical Specifications for Westinghouse PWRs

International Nuclear Information System (INIS)

1978-01-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Westinghouse plants currently being reviewed for an Operating License. Accordingly, the document contains specifications applicable to plants (1) with either 3 or 4 loops and (2) with and without loop stop valves. In addition, four separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric, Ice Condenser, Sub-Atmospheric, and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. The format of the STS addresses the categories required by 10 CFR 50 and consists of six sections covering the areas of: Definitions, Safety Limits and Limiting Safety System Settings, Limiting Conditions for Operation, Surveillance Requirements, Design Features, and Administrative Controls

Food choice effects on herbivory: Intra-specific seagrass palatability and inter-specific macrophyte palatability in seagrass communities

Science.gov (United States)

Jiménez-Ramos, Rocío; Brun, Fernando G.; Egea, Luis G.; Vergara, Juan J.

2018-05-01

Interactions between the palatability and abundance of different food sources may influence herbivory patterns in seagrass-dominated communities. In addition, intra-specific differences in nutrient and structural quality of leaves may also alter seagrass palatability and generate different rates of consumption within these communities. We offered two temperate seagrasses species, (Cymodocea nodosa and Zostera noltei) from two different locations to look at intraspecific differences, and two other macrophytes, both of which occur at the same location as seagrasses but represent the extremes of palatability, to a generalist herbivore Paracentrotus lividus (purple sea urchin). Using feeding assays, we compared the consumption rates in individual (single plant species) and combined diets at different food availabilities. Intra-specific differences between seagrass species growing at different locations (inner and outer bay) were indeed found to significantly modify the consumption rate for one species. Structural traits such as carbon content were linked to the low consumption found in Cymodocea nodosa from the inner bay location. In addition, we found that the co-occurrence of different macrophyte species can result in preferential consumption of the more palatable macrophyte with high nutritional content and low structural defence over seagrasses, especially when P. lividus has an abundant food supply. Overall, our findings suggest that intra- and inter-specific differences in seagrass traits and the relative abundance of other macrophytes may explain the variability in patterns of herbivory found within seagrass communities.

Analysis of Primary Structural Determinants That Distinguish the Centromere-Specific Function of Histone Variant Cse4p from Histone H3

OpenAIRE

Keith, Kevin C.; Baker, Richard E.; Chen, Yinhuai; Harris, Kendra; Stoler, Sam; Fitzgerald-Hayes, Molly

1999-01-01

Cse4p is a variant of histone H3 that has an essential role in chromosome segregation and centromere chromatin structure in budding yeast. Cse4p has a unique 135-amino-acid N terminus and a C-terminal histone-fold domain that is more than 60% identical to histone H3 and the mammalian centromere protein CENP-A. Cse4p and CENP-A have biochemical properties similar to H3 and probably replace H3 in centromere-specific nucleosomes in yeasts and mammals, respectively. In order to identify regions o...

Serotype-specific Differences in Dengue Virus Non-structural Protein 5 Nuclear Localization*

Science.gov (United States)

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D.

2013-01-01

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes. PMID:23770669

Serotype-specific differences in dengue virus non-structural protein 5 nuclear localization.

Science.gov (United States)

Hannemann, Holger; Sung, Po-Yu; Chiu, Han-Chen; Yousuf, Amjad; Bird, Jim; Lim, Siew Pheng; Davidson, Andrew D

2013-08-02

The four serotypes of dengue virus (DENV-1 to -4) cause the most important arthropod-borne viral disease of humans. DENV non-structural protein 5 (NS5) contains enzymatic activities required for capping and replication of the viral RNA genome that occurs in the host cytoplasm. However, previous studies have shown that DENV-2 NS5 accumulates in the nucleus during infection. In this study, we examined the nuclear localization of NS5 for all four DENV serotypes. We demonstrate for the first time that there are serotypic differences in NS5 nuclear localization. Whereas the DENV-2 and -3 proteins accumulate in the nucleus, DENV-1 and -4 NS5 are predominantly if not exclusively localized to the cytoplasm. Comparative studies on the DENV-2 and -4 NS5 proteins revealed that the difference in DENV-4 NS5 nuclear localization was not due to rapid nuclear export but rather the lack of a functional nuclear localization sequence. Interaction studies using DENV-2 and -4 NS5 and human importin-α isoforms failed to identify an interaction that supported the differential nuclear localization of NS5. siRNA knockdown of the human importin-α isoform KPNA2, corresponding to the murine importin-α isoform previously shown to bind to DENV-2 NS5, did not substantially affect DENV-2 NS5 nuclear localization, whereas knockdown of importin-β did. The serotypic differences in NS5 nuclear localization did not correlate with differences in IL-8 gene expression. The results show that NS5 nuclear localization is not strictly required for virus replication but is more likely to have an auxiliary function in the life cycle of specific DENV serotypes.

Social-psychological specific of individual adaptation

OpenAIRE

Ovsyanik, Olga

2012-01-01

There is analyzing of specific of social-psychological adaptation person by model of adaptation. Structure model of adaptation of women of our age group, which was named “adaptation complex” was made by theoretic analyzes of problem of adaptation adult.

Dynamic Recruitment of Cdc2 to Specific Microtubule Structures during Mitosis

Czech Academy of Sciences Publication Activity Database

Weingartner, M.; Binarová, Pavla; Dryková, Denisa; Achweighofer, A.; David, P.; Heberle, E.; Doonan, J.; Bogre, L.

2001-01-01

Roč. 13, - (2001), s. 1929-1943 ISSN 1040-4651 R&D Projects: GA AV ČR IAA5020803 Grant - others:XE(XC) GA QLRT-00454 Keywords : dynamic * recruitment * specific Subject RIV: EE - Microbiology, Virology Impact factor: 11.081, year: 2001

U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.

Science.gov (United States)

Gürel, Güliz; Blaha, Gregor; Moore, Peter B; Steitz, Thomas A

2009-05-29

Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 A. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: The Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome

Energy Technology Data Exchange (ETDEWEB)

Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.; Yale

2009-06-30

Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the Asite cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

Lipidomic and Transcriptomic Basis of Lysosomal Dysfunction in Progranulin Deficiency

Directory of Open Access Journals (Sweden)

Bret M. Evers

2017-09-01

Full Text Available Defective lysosomal function defines many neurodegenerative diseases, such as neuronal ceroid lipofuscinoses (NCL and Niemann-Pick type C (NPC, and is implicated in Alzheimer’s disease (AD and frontotemporal lobar degeneration (FTLD-TDP with progranulin (PGRN deficiency. Here, we show that PGRN is involved in lysosomal homeostasis and lipid metabolism. PGRN deficiency alters lysosome abundance and morphology in mouse neurons. Using an unbiased lipidomic approach, we found that brain lipid composition in humans and mice with PGRN deficiency shows disease-specific differences that distinguish them from normal and other pathologic groups. PGRN loss leads to an accumulation of polyunsaturated triacylglycerides, as well as a reduction of diacylglycerides and phosphatidylserines in fibroblast and enriched lysosome lipidomes. Transcriptomic analysis of PGRN-deficient mouse brains revealed distinct expression patterns of lysosomal, immune-related, and lipid metabolic genes. These findings have implications for the pathogenesis of FTLD-TDP due to PGRN deficiency and suggest lysosomal dysfunction as an underlying mechanism.

Instantaneous Characterization Of Vegetable Oils Via Tag And Ffa Profiles By Easy Ambient Sonic-spray Ionization Mass Spectrometry.

OpenAIRE

Simas, Rosineide C; Catharino, Rodrigo R; Cunha, Ildenize B S; Cabral, Elaine C; Barrera-Arellano, Daniel; Eberlin, Marcos N; Alberici, Rosana M

2015-01-01

A fast and reliable method is presented for the analysis of vegetable oils. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to efficiently desorb and ionize the main oil constituents from an inert surface under ambient conditions and to provide comprehensive triacylglyceride (TAG) and free fatty acid (FFA) profiles detected mainly as either [TAG + Na](+) or [FFA-H](-) ions. EASI(+/-)-MS analysis is simple, easily implemented, requires just a tiny droplet of the oil an...

General and specific lipid-protein interactions in Na,K-ATPase.

Science.gov (United States)

Cornelius, F; Habeck, M; Kanai, R; Toyoshima, C; Karlish, S J D

2015-09-01

The molecular activity of Na,K-ATPase and other P2 ATPases like Ca(2+)-ATPase is influenced by the lipid environment via both general (physical) and specific (chemical) interactions. Whereas the general effects of bilayer structure on membrane protein function are fairly well described and understood, the importance of the specific interactions has only been realized within the last decade due particularly to the growing field of membrane protein crystallization, which has shed new light on the molecular details of specific lipid-protein interactions. It is a remarkable observation that specific lipid-protein interactions seem to be evolutionarily conserved, and conformations of specifically bound lipids at the lipid-protein surface within the membrane are similar in crystal structures determined with different techniques and sources of the protein, despite the rather weak lipid-protein interaction energy. Studies of purified detergent-soluble recombinant αβ or αβFXYD Na,K-ATPase complexes reveal three separate functional effects of phospholipids and cholesterol with characteristic structural selectivity. The observations suggest that these three effects are exerted at separate binding sites for phophatidylserine/cholesterol (stabilizing), polyunsaturated phosphatidylethanolamine (stimulatory), and saturated PC or sphingomyelin/cholesterol (inhibitory), which may be located within three lipid-binding pockets identified in recent crystal structures of Na,K-ATPase. The findings point to a central role of direct and specific interactions of different phospholipids and cholesterol in determining both stability and molecular activity of Na,K-ATPase and possible implications for physiological regulation by membrane lipid composition. This article is part of a special issue titled "Lipid-Protein Interactions." Copyright © 2015 Elsevier B.V. All rights reserved.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

Science.gov (United States)

Uroz, S; Oger, P; Tisserand, E; Cébron, A; Turpault, M-P; Buée, M; De Boer, W; Leveau, J H J; Frey-Klett, P

2016-06-15

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Specifications in early conceptual design work

DEFF Research Database (Denmark)

Hansen, Claus Thorp; Andreasen, Mogens Myrup

2007-01-01

In early conceptual design the design team is working in an uncertain situation, where the understanding of a need is limited and not much is known about the solution space. In this situation the design team has to both analyse need and explore solution space. Thus, the team has to formulate design...... specifications, which express attractive product goals, and has to synthesise the product idea. The authors of this paper see a challenge to enhance and improve our understanding of the nature of design specifications as a means to support the synthesis of a product idea. In this empirical study we analyse...... the structure and content of design specifications during early ideation activities, where initial design specifications are formulated and a product idea is synthesised. We have analysed specification documents of 19 teams of novice designers. Our analysis indicates that a productive product design...

Deconstructing thermodynamic parameters of a coupled system from site-specific observables.

Science.gov (United States)

Chowdhury, Sandipan; Chanda, Baron

2010-11-02

Cooperative interactions mediate information transfer between structural domains of a protein molecule and are major determinants of protein function and modulation. The prevalent theories to understand the thermodynamic origins of cooperativity have been developed to reproduce the complex behavior of a global thermodynamic observable such as ligand binding or enzyme activity. However, in most cases the measurement of a single global observable cannot uniquely define all the terms that fully describe the energetics of the system. Here we establish a theoretical groundwork for analyzing protein thermodynamics using site-specific information. Our treatment involves extracting a site-specific parameter (defined as χ value) associated with a structural unit. We demonstrate that, under limiting conditions, the χ value is related to the direct interaction terms associated with the structural unit under observation and its intrinsic activation energy. We also introduce a site-specific interaction energy term (χ(diff)) that is a function of the direct interaction energy of that site with every other site in the system. When combined with site-directed mutagenesis and other molecular level perturbations, analyses of χ values of site-specific observables may provide valuable insights into protein thermodynamics and structure.

Crystal Structure of the Homo sapiens Kynureninase-3-Hydroxyhippuric Acid Inhibitor Complex: Insights into the Molecular Basis Of Kynureninase Substrate Specificity

Energy Technology Data Exchange (ETDEWEB)

Lima,Santiago; Kumar,Sunil; Gawandi,Vijay; Momany,Cory; Phillips,Robert S.; (Georgia)

2009-02-23

Homo sapiens kynureninase is a pyridoxal-5'-phosphate dependent enzyme that catalyzes the hydrolytic cleavage of 3-hydroxykynurenine to yield 3-hydroxyanthranilate and L-alanine as part of the tryptophan catabolic pathway leading to the de novo biosynthesis of NAD{sup +}. This pathway results in quinolinate, an excitotoxin that is an NMDA receptor agonist. High levels of quinolinate have been correlated with the etiology of neurodegenerative disorders such as AIDS-related dementia and Alzheimer's disease. We have synthesized a novel kynureninase inhibitor, 3-hydroxyhippurate, cocrystallized it with human kynureninase, and solved the atomic structure. On the basis of an analysis of the complex, we designed a series of His-102, Ser-332, and Asn-333 mutants. The H102W/N333T and H102W/S332G/N333T mutants showed complete reversal of substrate specificity between 3-hydroxykynurenine and L-kynurenine, thus defining the primary residues contributing to substrate specificity in kynureninases.

Disease-specific structural changes in thalamus and dentatorubrothalamic tract in progressive supranuclear palsy

Energy Technology Data Exchange (ETDEWEB)

Surova, Yulia; Hall, Sara; Widner, Haakan [Lund University, Department of Clinical Sciences, Lund (Sweden); Skaane University Hospital, Department of Neurology, Lund (Sweden); Nilsson, Markus [Lund University, Lund University Bioimaging Center, Lund (Sweden); Laett, Jimmy [Skaane University Hospital, Center for Medical Imaging and Physiology, Lund (Sweden); Lampinen, Bjoern [Lund University, Department of Medical Radiation Physics, Lund (Sweden); Lindberg, Olof [Malmoe, Lund University, Department of Clinical Sciences, Malmoe (Sweden); Nilsson, Christer [Skaane University Hospital, Department of Neurology, Lund (Sweden); Malmoe, Lund University, Department of Clinical Sciences, Malmoe (Sweden); Westen, Danielle van [Lund University, Department of Clinical Sciences, Lund (Sweden); Skaane University Hospital, Center for Medical Imaging and Physiology, Lund (Sweden); Hansson, Oskar [Malmoe, Lund University, Department of Clinical Sciences, Malmoe (Sweden); Skaane University Hospital, Memory Clinic, Lund (Sweden)

2015-11-15

The aim of this study is to identify disease-specific changes of the thalamus, basal ganglia, pons, and midbrain in patients with progressive supranuclear palsy (PSP), Parkinson's disease (PD), and multiple system atrophy with predominant parkinsonism (MSA-P) using diffusion tensor imaging and volumetric analysis. MRI diffusion and volumetric data were acquired in a derivation of 30 controls and 8 patients with PSP and a validation cohort comprised of controls (n = 21) and patients with PSP (n = 27), PD (n = 10), and MSA-P (n = 11). Analysis was performed using regions of interest (ROI), tract-based spatial statistic (TBSS), and tractography and results compared between diagnostic groups. In the derivation cohort, we observed increased mean diffusivity (MD) in the thalamus, superior cerebellar peduncle, and the midbrain in PSP compared to controls. Furthermore, volumetric analysis showed reduced thalamic volumes in PSP. In the validation cohort, the observations of increased MD were replicated by ROI-based analysis and in the thalamus by TBSS-based analysis. Such differences were not found for patients with PD in any of the cohorts. Tractography of the dentatorubrothalamic tract (DRTT) showed increased MD in PSP patients from both cohorts compared to controls and in the validation cohort in PSP compared to PD and MSA patients. Increased MD in the thalamus and along the DRTT correlated with disease stage and motor function in PSP. Patients with PSP, but not PD or MSA-P, exhibit signs of structural abnormalities in the thalamus and in the DRTT. These changes are associated with disease stage and impaired motor function. (orig.)

Disease-specific structural changes in thalamus and dentatorubrothalamic tract in progressive supranuclear palsy

International Nuclear Information System (INIS)

Surova, Yulia; Hall, Sara; Widner, Haakan; Nilsson, Markus; Laett, Jimmy; Lampinen, Bjoern; Lindberg, Olof; Nilsson, Christer; Westen, Danielle van; Hansson, Oskar

2015-01-01

The aim of this study is to identify disease-specific changes of the thalamus, basal ganglia, pons, and midbrain in patients with progressive supranuclear palsy (PSP), Parkinson's disease (PD), and multiple system atrophy with predominant parkinsonism (MSA-P) using diffusion tensor imaging and volumetric analysis. MRI diffusion and volumetric data were acquired in a derivation of 30 controls and 8 patients with PSP and a validation cohort comprised of controls (n = 21) and patients with PSP (n = 27), PD (n = 10), and MSA-P (n = 11). Analysis was performed using regions of interest (ROI), tract-based spatial statistic (TBSS), and tractography and results compared between diagnostic groups. In the derivation cohort, we observed increased mean diffusivity (MD) in the thalamus, superior cerebellar peduncle, and the midbrain in PSP compared to controls. Furthermore, volumetric analysis showed reduced thalamic volumes in PSP. In the validation cohort, the observations of increased MD were replicated by ROI-based analysis and in the thalamus by TBSS-based analysis. Such differences were not found for patients with PD in any of the cohorts. Tractography of the dentatorubrothalamic tract (DRTT) showed increased MD in PSP patients from both cohorts compared to controls and in the validation cohort in PSP compared to PD and MSA patients. Increased MD in the thalamus and along the DRTT correlated with disease stage and motor function in PSP. Patients with PSP, but not PD or MSA-P, exhibit signs of structural abnormalities in the thalamus and in the DRTT. These changes are associated with disease stage and impaired motor function. (orig.)

Anthropometric assessment of cervical neurovascular structures using CTA to determine zone-specific vulnerability to penetrating fragmentation injuries

International Nuclear Information System (INIS)

Breeze, J.; West, A.; Clasper, J.

2013-01-01

Aim: To determine military-specific cervical neurovascular and external anthropometric data to scale future numerical injury models of the neck and improve body armour design with a view to prevention or mitigation of combat neck injury. Materials and methods: Contrast-enhanced computed tomography (CT) angiograms of 50 UK servicemen were analysed. Mean diameters and distances from the skin surface were determined for the carotid artery (CA), internal jugular vein (IJV), vertebral artery (VA) and spinal cord (SC) at the three surgical neck zones. Horizontal neck circumference at C6 and three potential vertical cervical anthropometric measurements were analysed to determine which had the least variability between subjects. Results: The diameters of cervical vascular structures are greater and the vessels more superficial as the anatomical plane moves caudally. The SC and VA are better protected than the IJV and CA due to their greater depth and bony coverage, except for the VA in zone 1. Conclusion: Future cervical anthropometric assessments should use the vertical angle of mandible to mid-claviclular distance in combination with the horizontal neck circumference as these demonstrated the least variability. Cervical neurovascular structures are least vulnerable posterosuperiorly and therefore extending the posterior aspect of a ballistic helmet inferiorly or adding a nape protector would appear to be less justified. Cervical vessels are most vulnerable in zone 1 and a circumferential collar of ballistic material at least 75 mm high would cover this area in 95% of this population.

Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces

KAUST Repository

Cui, Xuefeng; Naveed, Hammad; Gao, Xin

2015-01-01

that are not limited to backbone fragments, and by employing a maximum weighted bipartite matching solver from the beginning of the alignment process. In addition, our methods incorporate similarities of sequentially and structurally remote residues that potentially

Specific heat and magnetization of RMn2(H,D)2

International Nuclear Information System (INIS)

Tarnawski, Z.; Kolwicz-Chodak, L.; Figiel, H.; Kim-Ngan, N.-T.H.; Havela, L.; Miliyanchuk, K.; Sechovsky, V.; Santava, E.; Sebek, J.

2007-01-01

The effect of hydrogen absorption on magnetic and thermodynamic properties of hydrides compounds RMn 2 (H,D) 2 (R = Y, Nd, Tb, Ho, and Er) have been investigated by performing specific heat and magnetization measurements in the temperature range of 2-320 K and in magnetic fields up to 9 T. The phase transition to the antiferromagnetic order accompanying a crystal structure transformation have been revealed by complicated-structure anomalies in specific heat and weak anomalies in magnetization

Gender specific pattern of left ventricular cardiac adaptation to ...

African Journals Online (AJOL)

EB

2013-09-03

Sep 3, 2013 ... Some gender specific associations with left ventricular structure and function have been described ... used for analysis. ... risk due to LVH and that cardiac adaptation to ... had history taking, physical examination and ..... between the gender specific differences in cardiac ... A metaanalysis of individual.

Gender specific pattern of left ventricular cardiac adaptation to ...

African Journals Online (AJOL)

Background: Cardiac adaptation to hypertension and obesity may be related to many factors such as race, gender and haemodynamic status. Some gender specific associations with left ventricular structure and function have been described among Caucasians. Objectives: To describe the sex specific pattern of left ...

Professional masters in science education: structure, specificity, effectivity and teaching professional development

Directory of Open Access Journals (Sweden)

Alberto Villani

2017-04-01

Full Text Available Historically teacher education constituted an important object of study and actions in the field of Science education. Between these actions, the professional masters (PM in Science education represent one of the most challenging and broader movements in teacher training up to this moment. However, the literature in the field is still rare and dispersed. Considering the complexity of this project and its singularity as a case of teacher training, due to its standard orientations, its large volume of people and institutions involved, it is important and necessary to produce a wider view of this initiative that has a history of 15 years and was characterized by many disagreements and changes. One of the possibilities to produce this wider view is through a state of art that organize and analyse the actual production in this field. In order to monitor these contributions we conducted a study such as “State of Art” based on the meta analysis guidance, thus, though a critical analysis we faced the challenge to discuss the scientific production on this theme. Therefore, we searched in all journals of education and science education, evaluated as A1 to B4 at Qualis/Capes published from 2000 to 2015, for articles published on this theme and selected 26 to analyse. Based on the empirical analysis of this corpus two categories were defined a-posteriori, representing the main themes whereupon the articles aimed to contribute: the wider nature of PM courses – structure, specificity and efectivity; and the Professional Master in Science Teaching (PMST and the professional development. The first category allowed us to identify the characteristics of the PM courses based on their curricular structure, faculty and educational projects. We highlight the fact that, since its creation, the PMST carry controversies about its singular characteristics. The opposition between its goals and the academic master in science teaching are constantly being used to find

Structure-specific endonucleases

DEFF Research Database (Denmark)

Minocherhomji, Sheroy; Hickson, Ian D

2014-01-01

Fragile sites are conserved loci predisposed to form breaks in metaphase chromosomes. The inherent instability of these loci is associated with chromosomal rearrangements in cancers and is a feature of cells from patients with chromosomal instability syndromes. One class of fragile sites, the com...

Structural basis of glycan specificity of P[19] VP8*: Implications for rotavirus zoonosis and evolution.

Science.gov (United States)

Liu, Yang; Xu, Shenyuan; Woodruff, Andrew L; Xia, Ming; Tan, Ming; Kennedy, Michael A; Jiang, Xi

2017-11-01

Recognition of specific cell surface glycans, mediated by the VP8* domain of the spike protein VP4, is the essential first step in rotavirus (RV) infection. Due to lack of direct structural information of virus-ligand interactions, the molecular basis of ligand-controlled host ranges of the major human RVs (P[8] and P[4]) in P[II] genogroup remains unknown. Here, through characterization of a minor P[II] RV (P[19]) that can infect both animals (pigs) and humans, we made an important advance to fill this knowledge gap by solving the crystal structures of the P[19] VP8* in complex with its ligands. Our data showed that P[19] RVs use a novel binding site that differs from the known ones of other genotypes/genogroups. This binding site is capable of interacting with two types of glycans, the mucin core and type 1 histo-blood group antigens (HBGAs) with a common GlcNAc as the central binding saccharide. The binding site is apparently shared by other P[II] RVs and possibly two genotypes (P[10] and P[12]) in P[I] as shown by their highly conserved GlcNAc-interacting residues. These data provide strong evidence of evolutionary connections among these human and animal RVs, pointing to a common ancestor in P[I] with a possible animal host origin. While the binding properties to GlcNAc-containing saccharides are maintained, changes in binding to additional residues, such as those in the polymorphic type 1 HBGAs may occur in the course of RV evolution, explaining the complex P[II] genogroup that mainly causes diseases in humans but also in some animals.

Automated effect-specific mammographic pattern measures

DEFF Research Database (Denmark)

Raundahl, Jakob; Loog, Marco; Pettersen, Paola

2008-01-01

We investigate the possibility to develop methodologies for assessing effect specific structural changes of the breast tissue using a general statistical machine learning framework. We present an approach of obtaining objective mammographic pattern measures quantifying a specific biological effect......, such as hormone replacement therapy (HRT). We compare results using this approach to using standard density measures. We show that the proposed method can quantify both age related effects and effects caused by HRT. Age effects are significantly detected by our method where standard methodologies fail...

QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity

Energy Technology Data Exchange (ETDEWEB)

Yao, Jianzhuang [University of Tennessee, Knoxville (UTK); Xu, Qin [University of Tennessee, Knoxville (UTK); Chen, Feng [University of Tennessee, Knoxville (UTK); Guo, Hong [University of Tennessee, Knoxville (UTK)

2010-01-01

Salicylic acid methyltransferases (SAMTs) synthesize methyl salicylate (MeSA) using salicylate as the substrate. MeSA synthesized in plants may function as an airborne signal to activate the expression of defense-related genes and could also be a critical mobile signaling molecule that travels from the site of plant infection to establish systemic immunity in the induction of disease resistance. Here the results of QM/MM free energy simulations for the methyl transfer process in Clarkia breweri SAMT (CbSAMT) are reported to determine the origin of the substrate specificity of SAMTs. The free energy barrier for the methyl transfer from S-adenosyl-l-methionine (AdoMet) to 4-hydroxybenzoate in CbSAMT is found to be about 5 kcal/mol higher than that from AdoMet to salicylate, consistent with the experimental observations. It is suggested that the relatively high efficiency for the methylation of salicylate compared to 4-hydroxybenzoate is due, at least in part, to the reason that a part of the stabilization of the transition state (TS) configuration is already reflected in the reactant complex, presumably, through the binding. The results seem to indicate that the creation of the substrate complex (e.g., through mutagenesis and substrate modifications) with its structure closely resembling TS might be fruitful for improving the catalytic efficiency for some enzymes. The results show that the computer simulations may provide important insights into the origin of the substrate specificity for the SABATH family and could be used to help experimental efforts in generating engineered enzymes with altered substrate specificity.

Mycobacterium tuberculosis DinG is a structure-specific helicase that unwinds G4 DNA: implications for targeting G4 DNA as a novel therapeutic approach.

Science.gov (United States)

Thakur, Roshan Singh; Desingu, Ambika; Basavaraju, Shivakumar; Subramanya, Shreelakshmi; Rao, Desirazu N; Nagaraju, Ganesh

2014-09-05

The significance of G-quadruplexes and the helicases that resolve G4 structures in prokaryotes is poorly understood. The Mycobacterium tuberculosis genome is GC-rich and contains >10,000 sequences that have the potential to form G4 structures. In Escherichia coli, RecQ helicase unwinds G4 structures. However, RecQ is absent in M. tuberculosis, and the helicase that participates in G4 resolution in M. tuberculosis is obscure. Here, we show that M. tuberculosis DinG (MtDinG) exhibits high affinity for ssDNA and ssDNA translocation with a 5' → 3' polarity. Interestingly, MtDinG unwinds overhangs, flap structures, and forked duplexes but fails to unwind linear duplex DNA. Our data with DNase I footprinting provide mechanistic insights and suggest that MtDinG is a 5' → 3' polarity helicase. Notably, in contrast to E. coli DinG, MtDinG catalyzes unwinding of replication fork and Holliday junction structures. Strikingly, we find that MtDinG resolves intermolecular G4 structures. These data suggest that MtDinG is a multifunctional structure-specific helicase that unwinds model structures of DNA replication, repair, and recombination as well as G4 structures. We finally demonstrate that promoter sequences of M. tuberculosis PE_PGRS2, mce1R, and moeB1 genes contain G4 structures, implying that G4 structures may regulate gene expression in M. tuberculosis. We discuss these data and implicate targeting G4 structures and DinG helicase in M. tuberculosis could be a novel therapeutic strategy for culminating the infection with this pathogen. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Structural and enzymatic characterization of a host-specificity determinant from Salmonella

Energy Technology Data Exchange (ETDEWEB)

Kohler, Amanda C. [Rockefeller University, New York, NY 10065 (United States); Spanò, Stefania; Galán, Jorge E. [Yale University School of Medicine, New Haven, CT 06536 (United States); Stebbins, C. Erec, E-mail: stebbins@rockefeller.edu [Rockefeller University, New York, NY 10065 (United States)

2014-02-01

The Salmonella effector protein GtgE functions as a cysteine protease to cleave a subset of the Rab-family GTPases and to prevent delivery of antimicrobial agents to the Salmonella-containing vacuole. GtgE is an effector protein from Salmonella Typhimurium that modulates trafficking of the Salmonella-containing vacuole. It exerts its function by cleaving the Rab-family GTPases Rab29, Rab32 and Rab38, thereby preventing the delivery of antimicrobial factors to the bacteria-containing vacuole. Here, the crystal structure of GtgE at 1.65 Å resolution is presented, and structure-based mutagenesis and in vivo infection assays are used to identify its catalytic triad. A panel of cysteine protease inhibitors were examined and it was determined that N-ethylmaleimide, antipain and chymostatin inhibit GtgE activity in vitro. These findings provide the basis for the development of novel therapeutic strategies to combat Salmonella infections.

Lipidomic and Antioxidant Response to Grape Seed, Corn and Coconut Oils in Healthy Wistar Rats

Directory of Open Access Journals (Sweden)

Abraham Wall-Medrano

2017-01-01

Full Text Available Specialty oils differ in fatty acid, phytosterol and antioxidant content, impacting their benefits for cardiovascular health. The lipid (fatty acid, phytosterol and antioxidant (total phenolics, radical scavenging capacity profiles of grapeseed (GSO, corn (CO and coconut (CNO oils and their physiological (triacylglycerides, total and HDL-cholesterol and antioxidant capacity (FRAP in serum and fatty acid and phytosterol hepatic deposition and genomic (HL, LCAT, ApoA-1 and SR-BP1 mRNA hepatic levels responses after their sub-chronic intake (10% diet for 28 days was examined in healthy albino rats. Fatty acid, phytosterol and antioxidant profiles differed between oils (p ≤ 0.01. Serum and hepatic triacylglycerides and total cholesterol increased (p ≤ 0.01; serum HDL-Cholesterol decreased (p < 0.05; but serum FRAP did not differ (p > 0.05 in CNO-fed rats as compared to CO or GSO groups. Hepatic phytosterol deposition was higher (+2.2 mg/g; p ≤ 0.001 in CO- than GSO-fed rats, but their fatty acid deposition was similar. All but ApoA-1 mRNA level increased in GSO-fed rats as compared to other groups (p ≤ 0.01. Hepatic fatty acid handling, but not antioxidant response, nor hepatic phytosterol deposition, could be related to a more efficient reverse-cholesterol transport in GSO-fed rats as compared to CO or CNO.

Prevalence and Associated Factors of Insulin Resistance in Adults from Maracaibo City, Venezuela

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Valmore Bermudez

2016-01-01

Full Text Available Background and Aim. Insulin resistance (IR is a prominent pathophysiologic component in a myriad of metabolic disorders, including obesity, prediabetes, and type 2 diabetes mellitus, which are common in our locality. The objective of this study was to determine the prevalence of IR and factors associated with this condition in an adult population from Maracaibo city, Venezuela. Methodology. A cross-sectional, descriptive study with multistaged randomized sampling was carried out in 2026 adults. IR was defined as HOMA2-IR ≥ 2. A multiple logistic regression model was constructed in order to evaluate factors associated with IR. Results. The prevalence of IR was 46.5% (n=943, with 46.7% (n=450 in the general population, 46.4% (n=493 in females, and 47.90% (n=970 in males (p=0.895. IR prevalence tended to increase with age and was significantly greater in subjects aged ≥30 years (χ2=16.726; p=2.33×10-4. Employment, alcohol consumption, obesity, high triacylglycerides, low HDL-C, and dysglycemia were associated with greater odds of IR, whereas a high level of physical activity appeared to be weak protective factor against IR. Conclusions. The prevalence of IR is elevated in our locality. The main determinants of this condition appear to be the presence of obesity, high triacylglycerides, low HDL-C, dysglycemia, and alcohol intake.

U2504 Determines the Species Specificity of the A-site Cleft Antibiotics. The Structures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

Science.gov (United States)

Gürel, Güliz; Blaha, Gregor; Moore, Peter B.; Steitz, Thomas A.

2009-01-01

Structures have been obtained for the complexes tiamulin, homoharringtonine and bruceatin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.8 to 3.2 Å. They show that these inhibitors all block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl transferase center, which is universally conserved. In addition these structures support the hypothesis that the species-specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (E. coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms. PMID:19362093

Target specific proteochemometric model development for BACE1 - protein flexibility and structural water are critical in virtual screening.

Science.gov (United States)

Manoharan, Prabu; Chennoju, Kiranmai; Ghoshal, Nanda

2015-07-01

BACE1 is an attractive target in Alzheimer's disease (AD) treatment. A rational drug design effort for the inhibition of BACE1 is actively pursued by researchers in both academic and pharmaceutical industries. This continued effort led to the steady accumulation of BACE1 crystal structures, co-complexed with different classes of inhibitors. This wealth of information is used in this study to develop target specific proteochemometric models and these models are exploited for predicting the prospective BACE1 inhibitors. The models developed in this study have performed excellently in predicting the computationally generated poses, separately obtained from single and ensemble docking approaches. The simple protein-ligand contact (SPLC) model outperforms other sophisticated high end models, in virtual screening performance, developed during this study. In an attempt to account for BACE1 protein active site flexibility information in predictive models, we included the change in the area of solvent accessible surface and the change in the volume of solvent accessible surface in our models. The ensemble and single receptor docking results obtained from this study indicate that the structural water mediated interactions improve the virtual screening results. Also, these waters are essential for recapitulating bioactive conformation during docking study. The proteochemometric models developed in this study can be used for the prediction of BACE1 inhibitors, during the early stage of AD drug discovery.

XML for data representation and model specification in neuroscience.

Science.gov (United States)

Crook, Sharon M; Howell, Fred W

2007-01-01

EXtensible Markup Language (XML) technology provides an ideal representation for the complex structure of models and neuroscience data, as it is an open file format and provides a language-independent method for storing arbitrarily complex structured information. XML is composed of text and tags that explicitly describe the structure and semantics of the content of the document. In this chapter, we describe some of the common uses of XML in neuroscience, with case studies in representing neuroscience data and defining model descriptions based on examples from NeuroML. The specific methods that we discuss include (1) reading and writing XML from applications, (2) exporting XML from databases, (3) using XML standards to represent neuronal morphology data, (4) using XML to represent experimental metadata, and (5) creating new XML specifications for models.

Determining the depth of certain gravity sources without a priori specification of their structural index

Science.gov (United States)

Zhou, Shuai; Huang, Danian

2015-11-01

We have developed a new method for the interpretation of gravity tensor data based on the generalized Tilt-depth method. Cooper (2011, 2012) extended the magnetic Tilt-depth method to gravity data. We take the gradient-ratio method of Cooper (2011, 2012) and modify it so that the source type does not need to be specified a priori. We develop the new method by generalizing the Tilt-depth method for depth estimation for different types of source bodies. The new technique uses only the three vertical tensor components of the full gravity tensor data observed or calculated at different height plane to estimate the depth of the buried bodies without a priori specification of their structural index. For severely noise-corrupted data, our method utilizes different upward continuation height data, which can effectively reduce the influence of noise. Theoretical simulations of the gravity source model with and without noise illustrate the ability of the method to provide source depth information. Additionally, the simulations demonstrate that the new method is simple, computationally fast and accurate. Finally, we apply the method using the gravity data acquired over the Humble Salt Dome in the USA as an example. The results show a good correspondence to the previous drilling and seismic interpretation results.

The use of PROLOG for computerized Technical Specifications

International Nuclear Information System (INIS)

Lidsky, L.M.; Lanning, D.D.; Dobrzeniecki, A.B.; Meyers, K.; Reese, T.G.

1987-01-01

The task of deciding whether a particular nuclear plant condition is in compliance with its Technical Specifications is, in principle, algorithmic. However, the implicit algorithm is so complex and the required level of confidence in code validity is so high that traditional methods of computerized analysis have proven unsatisfactory. PROLOG provides a close match to the explicit semantic structure of the written specifications, a good tool for analysis of the implicit subsystem operability trees and, by virtue of its declarative style and imbedded logical structure, greatly simplifies the problem of code validation. LCOM, a PROLOG representation of a subset of BWR Technical Specifications, was developed to explore the applicability of PROLOG in this problem domain and to provide benchmark data for full-scale implementations. The declarative style and built-in unification mechanism of PROLOG does substantially simplify the process of program construction and validation. Extrapolations indicate processing times for a complete Tech Spec implementation of ≤ 1 minute in systems capable of ≥ 20 KLIPS

Structure, specific surface area and thermal conductivity of the snowpack around Barrow, Alaska

Science.gov (United States)

Domine, Florent; Gallet, Jean-Charles; Bock, Josué; Morin, Samuel

2012-07-01

The structure of the snowpack near Barrow was studied in March-April 2009. Vertical profiles of density, specific surface area (SSA) and thermal conductivity were measured on tundra, lakes and landfast ice. The average thickness was 41 cm on tundra and 21 cm on fast ice. Layers observed were diamond dust or recent wind drifts on top, overlaying wind slabs, occasional faceted crystals and melt-freeze crusts, and basal depth hoar layers. The top layer had a SSA between 45 and 224 m2 kg-1. All layers at Barrow had SSAs higher than at many other places because of the geographical and climatic characteristics of Barrow. In particular, a given snow layer was remobilized several times by frequent winds, which resulted in SSA increases each time. The average snow area index (SAI, the dimensionless vertically integrated SSA) on tundra was 3260, higher than in the Canadian High Arctic or in the Alaskan taiga. This high SAI, combined with low snow temperatures, imply that the Barrow snowpack efficiently traps persistent organic pollutants, as illustrated with simple calculations for PCB 28 and PCB 180. The average thermal conductivity was 0.21 Wm-1 K-1, and the average thermal resistance on tundra was 3.25 m2 K W-1. This low value partly explains why the snow-ground interface was cold, around -19°C. The high SAI and low thermal resistance values illustrate the interplay between climate, snow physical properties, and their potential impact on atmospheric chemistry, and the need to describe these relationships in models of polar climate and atmospheric chemistry, especially in a climate change context.

Structure-specific selection of earthquake ground motions for the reliable design and assessment of structures

DEFF Research Database (Denmark)

Katsanos, E. I.; Sextos, A. G.

2018-01-01

A decision support process is presented to accommodate selecting and scaling of earthquake motions as required for the time domain analysis of structures. Code-compatible suites of seismic motions are provided being, at the same time, prequalified through a multi-criterion approach to induce...... was subjected to numerous suites of motions that were highly ranked according to both the proposed approach (δsv–sc) and the conventional one (δconv), that is commonly used for earthquake records selection and scaling. The findings from numerous linear response history analyses reveal the superiority...

U2504 Determines the Species Specificity of the A-site Cleft Antibiotics: The sStructures of Tiamulin, Homoharringtonine and Bruceantin Bound to the Ribosome

Energy Technology Data Exchange (ETDEWEB)

Gurel, G.; Blaha, G; Moore, P; Steitz,

2009-01-01

Structures have been obtained for the complexes that tiamulin, homoharringtonine, and bruceantin form with the large ribosomal subunit of Haloarcula marismortui at resolutions ranging from 2.65 to 3.2 {angstrom}. They show that all these inhibitors block protein synthesis by competing with the amino acid side chains of incoming aminoacyl-tRNAs for binding in the A-site cleft in the peptidyl-transferase center, which is universally conserved. In addition, these structures support the hypothesis that the species specificity exhibited by the A-site cleft inhibitors is determined by the interactions they make, or fail to make, with a single nucleotide, U2504 (Escherichia coli). In the ribosome, the position of U2504 is controlled by its interactions with neighboring nucleotides, whose identities vary among kingdoms.

The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

Science.gov (United States)

Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

2017-01-15

During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1

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Ismaila Yada Sudi

2012-11-01

Full Text Available Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD simulation and docking of D-2-chloropropionate (D-2CP, D-2-bromopropionate (D-2BP, monochloroacetate (MCA, monobromoacetate (MBA, 2,2-dichloropropionate (2,2-DCP, d,l-2,3-dichloropropionate (d,l-2,3-DCP, and 3-chloropropionate (3-CP into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials.

Technical specifications requirements: Automated reasoning applications

International Nuclear Information System (INIS)

Lidsky, L.M.; Dobrzeniecki, A.B.

1990-03-01

Several software systems were developed and tested to determine what advantages could be gained from explicitly translating complicated regulatory requirements into computerized relationships. The Technical Specifications for US nuclear power plants were chosen as the test-bed application domain, and two analysis systems were developed to monitor plant compliance with operational limits, and track and schedule equipment test and maintenance activities mandated by Technical Specifications. Choosing PROLOG as the computer language to represent these regulatory requirements resulted in a natural match between the semantic structure of the written specifications and the corollary coded rules. Additional research results affirmed the utility of declarative programming styles, explicit management of problem complexity, and attention to the robustness and flexibility of the overall software systems. 5 refs., 2 figs

Are Autonomous and Controlled Motivations School-Subjects-Specific?

Science.gov (United States)

Chanal, Julien; Guay, Frédéric

2015-01-01

This research sought to test whether autonomous and controlled motivations are specific to school subjects or more general to the school context. In two cross-sectional studies, 252 elementary school children (43.7% male; mean age = 10.7 years, SD = 1.3 years) and 334 junior high school children (49.7% male, mean age = 14.07 years, SD = 1.01 years) were administered a questionnaire assessing their motivation for various school subjects. Results based on structural equation modeling using the correlated trait-correlated method minus one model (CTCM-1) showed that autonomous and controlled motivations assessed at the school subject level are not equally school-subject-specific. We found larger specificity effects for autonomous (intrinsic and identified) than for controlled (introjected and external) motivation. In both studies, results of factor loadings and the correlations with self-concept and achievement demonstrated that more evidence of specificity was obtained for autonomous regulations than for controlled ones. These findings suggest a new understanding of the hierarchical and multidimensional academic structure of autonomous and controlled motivations and of the mechanisms involved in the development of types of regulations for school subjects. PMID:26247788

Specificity determinants for lysine incorporation in Staphylococcus aureus peptidoglycan as revealed by the structure of a MurE enzyme ternary complex.

Science.gov (United States)

Ruane, Karen M; Lloyd, Adrian J; Fülöp, Vilmos; Dowson, Christopher G; Barreteau, Hélène; Boniface, Audrey; Dementin, Sébastien; Blanot, Didier; Mengin-Lecreulx, Dominique; Gobec, Stanislav; Dessen, Andréa; Roper, David I

2013-11-15

Formation of the peptidoglycan stem pentapeptide requires the insertion of both L and D amino acids by the ATP-dependent ligase enzymes MurC, -D, -E, and -F. The stereochemical control of the third position amino acid in the pentapeptide is crucial to maintain the fidelity of later biosynthetic steps contributing to cell morphology, antibiotic resistance, and pathogenesis. Here we determined the x-ray crystal structure of Staphylococcus aureus MurE UDP-N-acetylmuramoyl-L-alanyl-D-glutamate:meso-2,6-diaminopimelate ligase (MurE) (E.C. 6.3.2.7) at 1.8 Å resolution in the presence of ADP and the reaction product, UDP-MurNAc-L-Ala-γ-D-Glu-L-Lys. This structure provides for the first time a molecular understanding of how this Gram-positive enzyme discriminates between L-lysine and D,L-diaminopimelic acid, the predominant amino acid that replaces L-lysine in Gram-negative peptidoglycan. Despite the presence of a consensus sequence previously implicated in the selection of the third position residue in the stem pentapeptide in S. aureus MurE, the structure shows that only part of this sequence is involved in the selection of L-lysine. Instead, other parts of the protein contribute substrate-selecting residues, resulting in a lysine-binding pocket based on charge characteristics. Despite the absolute specificity for L-lysine, S. aureus MurE binds this substrate relatively poorly. In vivo analysis and metabolomic data reveal that this is compensated for by high cytoplasmic L-lysine concentrations. Therefore, both metabolic and structural constraints maintain the structural integrity of the staphylococcal peptidoglycan. This study provides a novel focus for S. aureus-directed antimicrobials based on dual targeting of essential amino acid biogenesis and its linkage to cell wall assembly.

GirlPOWER! Strengthening Mentoring Relationships through a Structured, Gender-Specific Program

Science.gov (United States)

Pryce, Julia M.; Silverthorn, Naida; Sanchez, Bernadette; DuBois, David L.

2010-01-01

The authors examine GirlPOWER! an innovative program that uses structure and group-based activities to enhance one-to-one mentoring relationships for young adolescent girls from the perspective of the focus, purpose, and authorship dimensions of mentoring relationships that Karcher and Nakkula described. The discussion draws on several sources of…

Is a matrix exponential specification suitable for the modeling of spatial correlation structures?

Science.gov (United States)

Strauß, Magdalena E; Mezzetti, Maura; Leorato, Samantha

2017-05-01

This paper investigates the adequacy of the matrix exponential spatial specifications (MESS) as an alternative to the widely used spatial autoregressive models (SAR). To provide as complete a picture as possible, we extend the analysis to all the main spatial models governed by matrix exponentials comparing them with their spatial autoregressive counterparts. We propose a new implementation of Bayesian parameter estimation for the MESS model with vague prior distributions, which is shown to be precise and computationally efficient. Our implementations also account for spatially lagged regressors. We further allow for location-specific heterogeneity, which we model by including spatial splines. We conclude by comparing the performances of the different model specifications in applications to a real data set and by running simulations. Both the applications and the simulations suggest that the spatial splines are a flexible and efficient way to account for spatial heterogeneities governed by unknown mechanisms.

Temporal changes of CB1 cannabinoid receptor in the basal ganglia as a possible structure-specific plasticity process in 6-OHDA lesioned rats.

Directory of Open Access Journals (Sweden)

Gabriela P Chaves-Kirsten

Full Text Available The endocannabinoid system has been implicated in several neurobiological processes, including neurodegeneration, neuroprotection and neuronal plasticity. The CB1 cannabinoid receptors are abundantly expressed in the basal ganglia, the circuitry that is mostly affected in Parkinson's Disease (PD. Some studies show variation of CB1 expression in basal ganglia in different animal models of PD, however the results are quite controversial, due to the differences in the procedures employed to induce the parkinsonism and the periods analyzed after the lesion. The present study evaluated the CB1 expression in four basal ganglia structures, namely striatum, external globus pallidus (EGP, internal globus pallidus (IGP and substantia nigra pars reticulata (SNpr of rats 1, 5, 10, 20, and 60 days after unilateral intrastriatal 6-hydroxydopamine injections, that causes retrograde dopaminergic degeneration. We also investigated tyrosine hydroxylase (TH, parvalbumin, calbindin and glutamic acid decarboxylase (GAD expression to verify the status of dopaminergic and GABAergic systems. We observed a structure-specific modulation of CB1 expression at different periods after lesions. In general, there were no changes in the striatum, decreased CB1 in IGP and SNpr and increased CB1 in EGP, but this increase was not sustained over time. No changes in GAD and parvalbumin expression were observed in basal ganglia, whereas TH levels were decreased and the calbindin increased in striatum in short periods after lesion. We believe that the structure-specific variation of CB1 in basal ganglia in the 6-hydroxydopamine PD model could be related to a compensatory process involving the GABAergic transmission, which is impaired due to the lack of dopamine. Our data, therefore, suggest that the changes of CB1 and calbindin expression may represent a plasticity process in this PD model.

Protein Stabilization and Enzyme Activation in Ionic Liquids: Specific Ion Effects

Science.gov (United States)

Zhao, Hua

2015-01-01

There are still debates on whether the hydration of ions perturbs the water structure, and what is the degree of such disturbance; therefore, the origin of Hofmeister effect on protein stabilization continues being questioned. For this reason, it is suggested to use the ‘specific ion effect’ instead of other misleading terms such as Hofmeister effect, Hofmeister series, lyotropic effect, and lyotropic series. In this review, we firstly discuss the controversial aspect of inorganic ion effects on water structures, and several possible contributors to the specific ion effect of protein stability. Due to recent overwhelming attraction of ionic liquids (ILs) as benign solvents in many enzymatic reactions, we further evaluate the structural properties and molecular-level interactions in neat ILs and their aqueous solutions. Next, we systematically compare the specific ion effects of ILs on enzyme stability and activity, and conclude that (a) the specificity of many enzymatic systems in diluted aqueous IL solutions is roughly in line with the traditional Hofmeister series albeit some exceptions; (b) however, the specificity follows a different track in concentrated or neat ILs because other factors (such as hydrogen-bond basicity, nucelophilicity, and hydrophobicity, etc) are playing leading roles. In addition, we demonstrate some examples of biocatalytic reactions in IL systems that are guided by the empirical specificity rule. PMID:26949281

Family Structure and Home-Leaving: A Further Specification of the Relationship.

Science.gov (United States)

Aquilino, William S.

1991-01-01

Investigated impact of childhood family structure on timing of home-leaving. Data from 1988 National Survey of Families and Households suggest that exposure to nonintact family living during childhood raises likelihood of home-leaving prior to age 19. Adopted children and children who lived in nonparental situations were most likely to leave…

A modal specification theory for components with data

DEFF Research Database (Denmark)

Bauer, Sebastian S.; Larsen, Kim G.; Legay, Axel

2014-01-01

of transitions allows for developing a unique approach for both logical and structural compositions, and eases the step-wise refine- ment process for building implementations. We propose Modal Specifications with Data (MSDs), the first modal specification theory with explicit representation of data. Our new...... theory includes the most commonly seen ingredients of a specification the- ory; that is parallel composition, conjunction and quotient. As MSDs are by nature potentially infinite-state systems, we propose symbolic representations based on effec- tive predicates. Our theory serves as a new abstraction...

Determination of the structure of thiol-specific antioxidant (Tsa 2) of Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Breyer, C.A.; Oliveira, M.A.

2012-01-01

Full text: The peroxiredoxin (Prx), is a group of antioxidant proteins that have been widely studied for its role in the decomposition of several species of peroxides such as hydrogen peroxide, peroxynitrite and organic hydroperoxides using two highly reactive cysteines, named cysteine peroxidatic (Cys P ) and resolve cysteine (Cys R ), present in the active site. In Saccharomyces cerevisiae were identified five Prx isoforms, three cytosolic (Tsa1, Tsa2 and Ahp1), a mitochondrial (mTPx) and a nu- clear one (nTPx). Tsa1 and Tsa2 are homodimers that in heat shock or oxidative stress form complex structures of high molecular-weight with chaperone function. These proteins are very similar (86% identity and 96% similarity) but despite this structural similarity it has been shown that they present different functions: Tsa1 is mainly involved in the response to oxidative stress while Tsa2 is involved in signal transduction. Tsa1 was already crystallized and a structural model was generated, but Tsa2 structural studies were not performed. The research goal is the determination of the structure of Tsa2. The initial screening experiments of crystallization using the kits CS1 and CS2 (Hampton Research) showed favorable results when the conditions were 0,1M sodium acetate trihydrate pH 4.6 and 8% polyethylene glycol 4000. To improve our results the crystallization condition is been refined using variations of pH and concentration of polyethylene glycol 4000. We believe that the results of this study may contribute significantly to the understanding of the formation of over oxidized forms and cellular functions of Tsa2. (author)

Contact networks structured by sex underpin sex-specific epidemiology of infection.

Science.gov (United States)

Silk, Matthew J; Weber, Nicola L; Steward, Lucy C; Hodgson, David J; Boots, Mike; Croft, Darren P; Delahay, Richard J; McDonald, Robbie A

2018-02-01

Contact networks are fundamental to the transmission of infection and host sex often affects the acquisition and progression of infection. However, the epidemiological impacts of sex-related variation in animal contact networks have rarely been investigated. We test the hypothesis that sex-biases in infection are related to variation in multilayer contact networks structured by sex in a population of European badgers Meles meles naturally infected with Mycobacterium bovis. Our key results are that male-male and between-sex networks are structured at broader spatial scales than female-female networks and that in male-male and between-sex contact networks, but not female-female networks, there is a significant relationship between infection and contacts with individuals in other groups. These sex differences in social behaviour may underpin male-biased acquisition of infection and may result in males being responsible for more between-group transmission. This highlights the importance of sex-related variation in host behaviour when managing animal diseases. © 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

Structure, processing, and properties of potatoes

Science.gov (United States)

Lloyd, Isabel K.; Kolos, Kimberly R.; Menegaux, Edmond C.; Luo, Huy; McCuen, Richard H.; Regan, Thomas M.

1992-06-01

The objective of this experiment and lesson intended for high school students in an engineering or materials science course or college freshmen is to demonstrate the relation between processing, structure, and thermodynamic and physical properties. The specific objectives are to show the effect of structure and structural changes on thermodynamic properties (specific heat) and physical properties (compressive strength); to illustrate the first law of thermodynamics; to compare boiling a potato in water with cooking it in a microwave in terms of the rate of structural change and the energy consumed to 'process' the potato; and to demonstrate compression testing.

Structure, processing, and properties of potatoes

Science.gov (United States)

Lloyd, Isabel K.; Kolos, Kimberly R.; Menegaux, Edmond C.; Luo, Huy; Mccuen, Richard H.; Regan, Thomas M.

1992-01-01

The objective of this experiment and lesson intended for high school students in an engineering or materials science course or college freshmen is to demonstrate the relation between processing, structure, and thermodynamic and physical properties. The specific objectives are to show the effect of structure and structural changes on thermodynamic properties (specific heat) and physical properties (compressive strength); to illustrate the first law of thermodynamics; to compare boiling a potato in water with cooking it in a microwave in terms of the rate of structural change and the energy consumed to 'process' the potato; and to demonstrate compression testing.

Structured triglyceride emulsions in parenteral nutrition.

Science.gov (United States)

Chambrier, C; Lauverjat, M; Bouletreau, P

2006-08-01

Over the past 3 decades, various concepts for IV fat emulsions (IVFE) have been developed. A randomized, structured-lipid emulsion based on an old technology has recently become available. This structured-lipid emulsion is produced by mixing medium-chain triglycerides and long-chain triglycerides, then allowing hydrolysis to form free fatty acids, followed by random transesterification of the fatty acids into mixed triglyceride molecules. Studies in animals have shown an improvement in nitrogen balance with the use of these lipid emulsions. Only 8 human clinical studies with these products have been performed. The results of these human clinical studies have been less promising than the animal studies; however, an improvement in nitrogen balance and lipid metabolism exceeds results associated with infusion of long-chain triglycerides (LCT) or a physical mixture of long-chain triglycerides and medium-chain triglycerides (LCT-MCT). Structured-lipid emulsion seems to induce less elevation in serum liver function values compared with standard IVFEs. In addition, structured-lipid emulsions have no detrimental effect on the reticuloendothelial system. Further studies are necessary in order to recommend the use of structured-lipid emulsions. The clinical community hopes that chemically defined structured triglycerides will make it possible to determine the distribution of specific fatty acids on a specific position on the glycerol core and therefore obtain specific activity for a specific clinical situation.

Functional and structural analysis of yeast trx system reveals structural elements of substrate specificity

International Nuclear Information System (INIS)

Oliveira, Marcos Antonio; Discola, Karen Fulan; Alves, Simone Vidigal; Netto, Luis Eduardo Soares; Amorim, Gisele Cardoso; Pinheiro, Anderson Sa; Valente, Ana Paula; Almeida, Fabio Ceneviva Lacerda; Medrano, Francisco Javier; Guimaraes, Beatriz Gomes

2006-01-01

Thioredoxin reductases (Trr) are members of the nucleotide pyridine disulfide oxide reductase family, which includes glutathione reductase (Gr), alkyl hydroperoxide reductase F (AhpF) and lipoamide dehydrogenase (Lpd). Constituents of this family are homodimeric flavoproteins containing one redoxactive disulfide and one tightly bound flavin adenine dinucleotide (FAD) per subunit. Trr catalyzes the disulfide reduction of oxidized Thioredoxin (Trx) using nicotinamide adenine dinucleotide phosphate (NADPH) via a FAD molecule and a redox-active cysteine motif. In this context, FAD transfers the reducing equivalents from NADPH molecule to the reactive cysteines and then to the Trx. Trx, Trr and NADPH comprise the Trx system. Trx are low molecular weight proteins (∼12 KDa) which are involved in several thiol-dependent cellular reactions such as synthesis of deoxyribonucleotides, sulphur metabolism, regulation of the gene expression and oxidative stress defenses. Remarkably, Trr - Trx interactions presents high species and organelle specificities. (author)

Residual Structures in Latent Growth Curve Modeling

Science.gov (United States)

Grimm, Kevin J.; Widaman, Keith F.

2010-01-01

Several alternatives are available for specifying the residual structure in latent growth curve modeling. Two specifications involve uncorrelated residuals and represent the most commonly used residual structures. The first, building on repeated measures analysis of variance and common specifications in multilevel models, forces residual variances…

Finding Specification Pages from the Web

Science.gov (United States)

Yoshinaga, Naoki; Torisawa, Kentaro

This paper presents a method of finding a specification page on the Web for a given object (e.g., ``Ch. d'Yquem'') and its class label (e.g., ``wine''). A specification page for an object is a Web page which gives concise attribute-value information about the object (e.g., ``county''-``Sauternes'') in well formatted structures. A simple unsupervised method using layout and symbolic decoration cues was applied to a large number of the Web pages to acquire candidate attributes for each class (e.g., ``county'' for a class ``wine''). We then filter out irrelevant words from the putative attributes through an author-aware scoring function that we called site frequency. We used the acquired attributes to select a representative specification page for a given object from the Web pages retrieved by a normal search engine. Experimental results revealed that our system greatly outperformed the normal search engine in terms of this specification retrieval.

Specification of primordial germ cells in medaka (Oryzias latipes

Directory of Open Access Journals (Sweden)

Raz Erez

2007-01-01

Full Text Available Abstract Background Primordial germ cells (PGCs give rise to gametes that are responsible for the development of a new organism in the next generation. Two modes of germ line specification have been described: the inheritance of asymmetrically-localized maternally provided cytoplasmic determinants and the induction of the PGC fate by other cell types. PGCs specification in zebrafish appears to depend on inheritance of germ plasm in which several RNA molecules such as vasa and nanos reside. Whether the specification mode of PGCs found in zebrafish is general for other fish species was brought into question upon analysis of olvas expression – the vasa homologue in another teleost, medaka (Oryzias latipes. Here, in contrast to the findings in zebrafish, the PGCs are found in a predictable position relative to a somatic structure, the embryonic shield. This finding, coupled with the fact that vasa mRNA, which is localized to the germ plasm of zebrafish but does not label a similar structure in medaka opened the possibility of fundamentally different mechanisms governing PGC specification in these two fish species. Results In this study we addressed the question concerning the mode of PGC specification in medaka using embryological experiments, analysis of RNA stability in the PGCs and electron microscopy observations. Dramatic alterations in the somatic environment, i.e. induction of a secondary axis or mesoderm formation alteration, did not affect the PGC number. Furthermore, the PGCs of medaka are capable of protecting specific RNA molecules from degradation and could therefore exhibit a specific mRNA expression pattern controlled by posttrancriptional mechanisms. Subsequent analysis of 4-cell stage medaka embryos using electron microscopy revealed germ plasm-like structures located at a region corresponding to that of zebrafish germ plasm. Conclusion Taken together, these results are consistent with the idea that in medaka the inheritance of

Relative Expression Levels Rather Than Specific Activity Plays the Major Role in Determining In Vivo AKT Isoform Substrate Specificity

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Rachel S. Lee

2011-01-01

Full Text Available The AKT protooncogene mediates many cellular processes involved in normal development and disease states such as cancer. The three structurally similar isoforms: AKT1, AKT2, and AKT3 exhibit both functional redundancy and isoform-specific functions; however the basis for their differential signalling remains unclear. Here we show that in vitro, purified AKT3 is ∼47-fold more active than AKT1 at phosphorylating peptide and protein substrates. Despite these marked variations in specific activity between the individual isoforms, a comprehensive analysis of phosphorylation of validated AKT substrates indicated only subtle differences in signalling via individual isoforms in vivo. Therefore, we hypothesise, at least in this model system, that relative tissue/cellular abundance, rather than specific activity, plays the dominant role in determining AKT substrate specificity in situ.

The topological filtration of gamma-structures

DEFF Research Database (Denmark)

Li, Thomas; Reidys, Christian

2013-01-01

In this paper we study gamma-structures filtered by topological genus. gamma-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A gamma-structure is composed by specific building blocks, that have...... topological genus less than or equal to gamma, where composition means concatenation and nesting of such blocks. Our main results are the derivation of a new bivariate generating function for gamma-structures via symbolic methods, the singularity analysis of the solutions and a central limit theorem...... for the distribution of topological genus in gamma-structures of given length. In our derivation specific bivariate polynomials play a central role. Their coefficients count particular motifs of fixed topological genus and they are of relevance in the context of genus recursion and novel folding algorithms....

Machine tool structures

CERN Document Server

Koenigsberger, F

1970-01-01

Machine Tool Structures, Volume 1 deals with fundamental theories and calculation methods for machine tool structures. Experimental investigations into stiffness are discussed, along with the application of the results to the design of machine tool structures. Topics covered range from static and dynamic stiffness to chatter in metal cutting, stability in machine tools, and deformations of machine tool structures. This volume is divided into three sections and opens with a discussion on stiffness specifications and the effect of stiffness on the behavior of the machine under forced vibration c

A Dual-Specific Targeting Approach Based on the Simultaneous Recognition of Duplex and Quadruplex Motifs.

Science.gov (United States)

Nguyen, Thi Quynh Ngoc; Lim, Kah Wai; Phan, Anh Tuân

2017-09-20

Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements. Such a dual-specific targeting strategy would combine the sequence specificity of duplex-binders and the strong binding affinity of quadruplex-binders, potentially allowing the specific targeting of unique quadruplex structures. Future research can be directed towards the development of conjugated compounds targeting specific genomic quadruplex-duplex sites, for which the linker would be highly context-dependent in terms of length and flexibility, as well as the attachment points onto both ligands.

Structural Alterations of the Language Connectome in Children with Specific Language Impairment

Czech Academy of Sciences Publication Activity Database

Vydrová, R.; Komárek, V.; Šanda, J.; Štěrbová, K.; Jahodová, A.; Maulisová, A.; Žáčková, J.; Reissigová, Jindra; Kršek, P.; Kyncl, M.

2015-01-01

Roč. 151, December (2015), s. 35-41 ISSN 0093-934X Institutional support: RVO:67985807 Keywords : Specific language disorder * DTI * Arcuate fascicle * IFOF * Ventral stream Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 3.038, year: 2015

A specific interdomain interaction preserves the structural and binding properties of the ModA protein from the phytopathogen Xanthomonas citri domain interaction and transport in ModA.

Science.gov (United States)

Santacruz-Perez, Carolina; Pegos, Vanessa Rodrigues; Honorato, Rodrigo V; Verli, Hugo; Lindahl, Erik; Barbosa, João Alexandre Ribeiro Gonçalves; Balan, Andrea

2013-11-01

The periplasmic-binding proteins in ATP-binding cassette systems (ABC Transporters) are responsible for the capture and delivery of ligands to their specific transporters, triggering a series of ATP-driven conformational changes that leads to the transport of the ligand. Structurally consisting of two lobes, the proteins change conformation after interaction with the ligand. The structure of the molybdate-binding protein (ModA) from Xanthomonas citri, bound to molybdate, was previously solved by our group and an interdomain interaction, mediated by a salt bridge between K127 and D59, apparently supports the binding properties and keeps the domains closed. To determinate the importance of this interaction, we built two ModA mutants, K127S and D59A, and analysed their functional and structural properties. Based on a set of spectroscopic experiments, crystallisation trials, structure determination and molecular dynamics (MD) simulations, we showed that the salt bridge is essential to maintain the structure and binding properties. Additionally, the MD simulations revealed that this mutant adopted a more compact structure that packed down the ligand-binding pocket. From the closed bound to open structure, the positioning of the helices forming the dipole and the salt bridge are essential to induce an intermediate state. Copyright © 2013 Elsevier Inc. All rights reserved.

Human-Specific Endogenous Retroviruses

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Anton Buzdin

2007-01-01

Full Text Available This review focuses on a small family of human-specific genomic repetitive elements, presented by 134 members that shaped ~330 kb of the human DNA. Although modest in terms of its copy number, this group appeared to modify the human genome activity by endogenizing ~50 functional copies of viral genes that may have important implications in the immune response, cancer progression, and antiretroviral host defense. A total of 134 potential promoters and enhancers have been added to the human DNA, about 50% of them in the close gene vicinity and 22% in gene introns. For 60 such human-specific promoters, their activity was confirmed by in vivo assays, with the transcriptional level varying ~1000-fold from hardly detectable to as high as ~3% of β-actin transcript level. New polyadenylation signals have been provided to four human RNAs, and a number of potential antisense regulators of known human genes appeared due to human-specific retroviral insertional activity. This information is given here in the context of other major genomic changes underlining differences between human and chimpanzee DNAs. Finally, a comprehensive database, is available for download, of human-specific and polymorphic endogenous retroviruses is presented, which encompasses the data on their genomic localization, primary structure, encoded viral genes, human gene neighborhood, transcriptional activity, and methylation status.

Lattice cluster theory for polymer melts with specific interactions

International Nuclear Information System (INIS)

Xu, Wen-Sheng; Freed, Karl F.

2014-01-01

Despite the long-recognized fact that chemical structure and specific interactions greatly influence the thermodynamic properties of polymer systems, a predictive molecular theory that enables systematically addressing the role of chemical structure and specific interactions has been slow to develop even for polymer melts. While the lattice cluster theory (LCT) provides a powerful vehicle for understanding the influence of various molecular factors, such as monomer structure, on the thermodynamic properties of polymer melts and blends, the application of the LCT has heretofore been limited to the use of the simplest polymer model in which all united atom groups within the monomers of a species interact with a common monomer averaged van der Waals energy. Thus, the description of a compressible polymer melt involves a single van der Waals energy. As a first step towards developing more realistic descriptions to aid in the analysis of experimental data and the design of new materials, the LCT is extended here to treat models of polymer melts in which the backbone and side groups have different interaction strengths, so three energy parameters are present, namely, backbone-backbone, side group-side group, and backbone-side group interaction energies. Because of the great algebraic complexity of this extension, we retain maximal simplicity within this class of models by further specializing this initial study to models of polymer melts comprising chains with poly(n-α-olefin) structures where only the end segments on the side chains may have different, specific van der Waals interaction energies with the other united atom groups. An analytical expression for the LCT Helmholtz free energy is derived for the new model. Illustrative calculations are presented to demonstrate the degree to which the thermodynamic properties of polymer melts can be controlled by specific interactions

Gene structure of CYP3A4, an adult-specific form of cytochrome P450 in human livers, and its transcriptional control.

Science.gov (United States)

Hashimoto, H; Toide, K; Kitamura, R; Fujita, M; Tagawa, S; Itoh, S; Kamataki, T

1993-12-01

CYP3 A4 is the adult-specific form of cytochrome P450 in human livers [Komori, M., Nishio, K., Kitada, M., Shiramatsu, K., Muroya, K., Soma, M., Nagashima, K. & Kamataki, T. (1990) Biochemistry 29, 4430-4433]. The sequences of three genomic clones for CYP3A4 were analyzed for all exons, exon-intron junctions and the 5'-flanking region from the major transcription site to nucleotide position -1105, and compared with those of the CYP3A7 gene, a fetal-specific form of cytochrome P450 in humans. The results showed that the identity of 5'-flanking sequences between CYP3A4 and CYP3A7 genes was 91%, and that each 5'-flanking region had characteristic sequences termed as NFSE (P450NF-specific element) and HFLaSE (P450HFLa specific element), respectively. A basic transcription element (BTE) also lay in the 5'-flanking region of the CYP3A4 gene as seen in many CYP genes [Yanagida, A., Sogawa, K., Yasumoto, K. & Fujii-Kuriyama, Y. (1990) Mol. Cell. Biol. 10, 1470-1475]. The BTE binding factor (BTEB) was present in both adult and fetal human livers. To examine the transcriptional activity of the CYP3A4 gene, DNA fragments in the 5'-flanking region of the gene were inserted in front of the simian virus 40 promoter and the chloramphenicol acetyltransferase structural gene, and the constructs were transfected in HepG2 cells. The analysis of the chloramphenicol acetyltransferase activity indicated that (a) specific element(s) which could bind with a factor(s) in livers was present in the 5'-flanking region of the CYP3A4 gene to show the transcriptional activity.

Kernel structures for Clouds

Science.gov (United States)

Spafford, Eugene H.; Mckendry, Martin S.

1986-01-01

An overview of the internal structure of the Clouds kernel was presented. An indication of how these structures will interact in the prototype Clouds implementation is given. Many specific details have yet to be determined and await experimentation with an actual working system.

Current Methods for the Analysis of Selected Novel Nutrients in Infant Formulas and Adult Nutritionals.

Science.gov (United States)

Gill, Brendon D; Indyk, Harvey E; Woollard, David C

2016-01-01

Infant formula is designed to provide the human infant with a sole source of nutrition and it is intended to imitate breast milk. In recent years, advances in the science of infant nutrition have led to an increasing number of novel ingredients that are supplemented into infant formula. As the list of these nutritionally important nutrients is lengthy, this review summarizes contemporary analytical methods that have been applied to a representative selection (lutein, carnitine, choline, nucleotides, inositol, taurine, sialic acid, gangliosides, triacylglycerides, oligosaccharides, α-lactalbumin, and lactoferrin).

Thermodynamic and structural properties of the specific binding between Ag⁺ ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair.

Science.gov (United States)

Torigoe, Hidetaka; Okamoto, Itaru; Dairaku, Takenori; Tanaka, Yoshiyuki; Ono, Akira; Kozasa, Tetsuo

2012-11-01

Metal ion-nucleic acid interactions have attracted considerable interest for their involvement in structure formation and catalytic activity of nucleic acids. Although interactions between metal ion and mismatched base pair duplex are important to understand mechanism of gene mutations related to heavy metal ions, they have not been well-characterized. We recently found that the Ag(+) ion stabilized a C:C mismatched base pair duplex DNA. A C-Ag-C metal-mediated base pair was supposed to be formed by the binding between the Ag(+) ion and the C:C mismatched base pair to stabilize the duplex. Here, we examined specificity, thermodynamics and structure of possible C-Ag-C metal-mediated base pair. UV melting indicated that only the duplex with the C:C mismatched base pair, and not of the duplexes with the perfectly matched and other mismatched base pairs, was specifically stabilized on adding the Ag(+) ion. Isothermal titration calorimetry demonstrated that the Ag(+) ion specifically bound with the C:C base pair at 1:1 molar ratio with a binding constant of 10(6) M(-1), which was significantly larger than those for nonspecific metal ion-DNA interactions. Electrospray ionization mass spectrometry also supported the specific 1:1 binding between the Ag(+) ion and the C:C base pair. Circular dichroism spectroscopy and NMR revealed that the Ag(+) ion may bind with the N3 positions of the C:C base pair without distorting the higher-order structure of the duplex. We conclude that the specific formation of C-Ag-C base pair with large binding affinity would provide a binding mode of metal ion-DNA interactions, similar to that of the previously reported T-Hg-T base pair. The C-Ag-C base pair may be useful not only for understanding of molecular mechanism of gene mutations related to heavy metal ions but also for wide variety of potential applications of metal-mediated base pairs in various fields, such as material, life and environmental sciences. Copyright © 2012 Elsevier

Analysis of owner design specifications for snubbers. Report 2

Energy Technology Data Exchange (ETDEWEB)

Butler, J.H.

1977-08-05

The report discusses and evaluates the adequacy of buyer specifications for snubbers. Technical specifications for snubbers (hydraulic and mechanical) were studied in detail in an effort to define the ''fundamental needs'' of the industry with respect to characteristics of snubbers during operation. In the course of this study, it was determined that there is insufficient consensus among users to make such a definition. Authorities in the fields of structural dynamics, structural systems design, and snubber design were also consulted for additional information. Information from these sources is incorporated to identify the fundamental areas of concern, areas where consensus is lacking, and problems to be resolved in order to establish meaningful standards for this equipment.

Analysis of owner design specifications for snubbers. Report 2

International Nuclear Information System (INIS)

Butler, J.H.

1977-01-01

The report discusses and evaluates the adequacy of buyer specifications for snubbers. Technical specifications for snubbers (hydraulic and mechanical) were studied in detail in an effort to define the ''fundamental needs'' of the industry with respect to characteristics of snubbers during operation. In the course of this study, it was determined that there is insufficient consensus among users to make such a definition. Authorities in the fields of structural dynamics, structural systems design, and snubber design were also consulted for additional information. Information from these sources is incorporated to identify the fundamental areas of concern, areas where consensus is lacking, and problems to be resolved in order to establish meaningful standards for this equipment

TAL effectors specificity stems from negative discrimination.

Directory of Open Access Journals (Sweden)

Basile I M Wicky

Full Text Available Transcription Activator-Like (TAL effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats with almost identical sequences. Most of the polymorphism is located at two consecutive amino acids termed Repeat Variable Diresidue (RVD. The discovery of a direct link between the RVD composition and the targeted nucleotide allowed the design of TAL-derived DNA-binding tools with programmable specificities that revolutionized the field of genome engineering. Despite structural data, the molecular origins of this specificity as well as the recognition mechanism have remained unclear. Molecular simulations of the recent crystal structures suggest that most of the protein-DNA binding energy originates from non-specific interactions between the DNA backbone and non-variable residues, while RVDs contributions are negligible. Based on dynamical and energetic considerations we postulate that, while the first RVD residue promotes helix breaks--allowing folding of TAL as a DNA-wrapping super-helix--the second provides specificity through a negative discrimination of matches. Furthermore, we propose a simple pharmacophore-like model for the rationalization of RVD-DNA interactions and the interpretation of experimental findings concerning shared affinities and binding efficiencies. The explanatory paradigm presented herein provides a better comprehension of this elegant architecture and we hope will allow for improved designs of TAL-derived biotechnological tools.

On the Evolution of Specificity in Members of the Yeast Amino Acid Transporter Family as Parts of Specific Metabolic Pathways

Directory of Open Access Journals (Sweden)

Christos Gournas

2018-05-01

Full Text Available In the recent years, molecular modeling and substrate docking, coupled with biochemical and genetic analyses have identified the substrate-binding residues of several amino acid transporters of the yeast amino acid transporter (YAT family. These consist of (a residues conserved across YATs that interact with the invariable part of amino acid substrates and (b variable residues that interact with the side chain of the amino acid substrate and thus define specificity. Secondary structure sequence alignments showed that the positions of these residues are conserved across YATs and could thus be used to predict the specificity of YATs. Here, we discuss the potential of combining molecular modeling and structural alignments with intra-species phylogenetic comparisons of transporters, in order to predict the function of uncharacterized members of the family. We additionally define some orphan branches which include transporters with potentially novel, and to be characterized specificities. In addition, we discuss the particular case of the highly specific l-proline transporter, PrnB, of Aspergillus nidulans, whose gene is part of a cluster of genes required for the utilization of proline as a carbon and/or nitrogen source. This clustering correlates with transcriptional regulation of these genes, potentially leading to the efficient coordination of the uptake of externally provided l-Pro via PrnB and its enzymatic degradation in the cell.

Actinide-specific complexing agents: their structural and solution chemistry

International Nuclear Information System (INIS)

Raymond, K.N.; Freeman, G.E.; Kappel, M.J.

1983-07-01

The synthesis of a series of tetracatecholate ligands designed to be specific for Pu(IV) and other actinide(IV) ions has been achieved. Although these compounds are very effective as in vivo plutonium removal agents, potentiometric and voltammetric data indicate that at neutral pH full complexation of the Pu(IV) ion by all four catecholate groups does not occur. Spectroscopic results indicate that the tetracatecholates, 3,4,3-LICAMS and 3,4,3-LICAMC, complex Am(III). The Am(IV)/(III)-catecholate couple (where catecholate = 3,4,3-LICAMS or 3,4,3-LICAMC) is not observed, but may not be observable due to the large currents associated with ligand oxidation. However, within the potential range where ligand oxidation does not occur, these experiments indicate that the reduction potential of free Am(IV)/(III) is probably greater than or equal to + 2.6 V vs NHE or higher. Proof of the complexation of americium in the trivalent oxidation state by 3,4,3-LICAMS and 3,4,3-LICAMC elimates the possibility of tetracatholates stabilizing Am(IV) in vivo

Dual host specificity of phage SP6 is facilitated by tailspike rotation

Energy Technology Data Exchange (ETDEWEB)

Tu, Jiagang [Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030 (United States); Park, Taehyun [Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712 (United States); Morado, Dustin R. [Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030 (United States); Hughes, Kelly T. [Department of Biology, University of Utah, Salt Lake City, UT 84112 (United States); Molineux, Ian J., E-mail: molineux@austin.utexas.edu [Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712 (United States); Liu, Jun, E-mail: Jun.Liu.1@uth.tmc.edu [Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030 (United States)

2017-07-15

Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspike orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection. - Highlights: •Cryo-electron tomography reveals the structural basis for dual host specificity. •Sub-tomogram classification reveals distinct orientations of the tailspikes during infection of different hosts. •Tailspike-adaptor modules rotate as they bind different O antigens. •In the absence of any O antigen, tailspikes bind weakly and without specificity to LPS. •Interaction of the phage tail with LPS is essential for infection.

Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations.

Science.gov (United States)

Song, Wei; Guo, Jun-Tao

2015-01-01

Transcription factors regulate gene expression through binding to specific DNA sequences. How transcription factors achieve high binding specificity is still not well understood. In this paper, we investigated the role of protein flexibility in protein-DNA-binding specificity by comparative molecular dynamics (MD) simulations. Protein flexibility has been considered as a key factor in molecular recognition, which is intrinsically a dynamic process involving fine structural fitting between binding components. In this study, we performed comparative MD simulations on wild-type and F10V mutant P22 Arc repressor in both free and complex conformations. The F10V mutant has lower DNA-binding specificity though both the bound and unbound main-chain structures between the wild-type and F10V mutant Arc are highly similar. We found that the DNA-binding motif of wild-type Arc is structurally more flexible than the F10V mutant in the unbound state, especially for the six DNA base-contacting residues in each dimer. We demonstrated that the flexible side chains of wild-type Arc lead to a higher DNA-binding specificity through forming more hydrogen bonds with DNA bases upon binding. Our simulations also showed a possible conformational selection mechanism for Arc-DNA binding. These results indicate the important roles of protein flexibility and dynamic properties in protein-DNA-binding specificity.

Inhibition of DD-peptidases by a specific trifluoroketone: crystal structure of a complex with the Actinomadura R39 DD-peptidase.

Science.gov (United States)

Dzhekieva, Liudmila; Adediran, S A; Herman, Raphael; Kerff, Frédéric; Duez, Colette; Charlier, Paulette; Sauvage, Eric; Pratt, R F

2013-03-26

Inhibitors of bacterial DD-peptidases represent potential antibiotics. In the search for alternatives to β-lactams, we have investigated a series of compounds designed to generate transition state analogue structures upon reaction with DD-peptidases. The compounds contain a combination of a peptidoglycan-mimetic specificity handle and a warhead capable of delivering a tetrahedral anion to the enzyme active site. The latter includes a boronic acid, two alcohols, an aldehyde, and a trifluoroketone. The compounds were tested against two low-molecular mass class C DD-peptidases. As expected from previous observations, the boronic acid was a potent inhibitor, but rather unexpectedly from precedent, the trifluoroketone [D-α-aminopimelyl(1,1,1-trifluoro-3-amino)butan-2-one] was also very effective. Taking into account competing hydration, we found the trifluoroketone was the strongest inhibitor of the Actinomadura R39 DD-peptidase, with a subnanomolar (free ketone) inhibition constant. A crystal structure of the complex between the trifluoroketone and the R39 enzyme showed that a tetrahedral adduct had indeed formed with the active site serine nucleophile. The trifluoroketone moiety, therefore, should be considered along with boronic acids and phosphonates as a warhead that can be incorporated into new and effective DD-peptidase inhibitors and therefore, perhaps, antibiotics.

Electrochemical Label-Free Aptasensor for Specific Analysis of Dopamine in Serum in the Presence of Structurally Related Neurotransmitters.

Science.gov (United States)

Álvarez-Martos, Isabel; Ferapontova, Elena E

2016-04-05

Cellular and brain metabolism of dopamine can be correlated with a number of neurodegenerative disorders, and as such, in vivo analysis of dopamine in the presence of structurally related neurotransmitters (NT) represents a holy grail of neuroscience. Interference from those NTs generally does not allow selective electroanalysis of dopamine, which redox transformation overlaps with those of other catecholamines. In our previous work, we reported an electrochemical RNA-aptamer-based biosensor for specific analysis of dopamine (Analytical Chemistry, 2013; Vol. 85, p 121). However, the overall design of the biosensor restricted its stability and impeded its operation in serum. Here, we show that specific biorecognition and electroanalysis of dopamine in serum can be performed by the RNA aptamer tethered to cysteamine-modified gold electrodes via the alkanethiol linker. The stabilized dopamine aptasensor allowed continuous 20 h amperometric analysis of dopamine in 10% serum within the physiologically important 0.1-1 μM range and in the presence of catechol and such dopamine precursors and metabolites as norepinephrine and l-DOPA. In a flow-injection mode, the aptasensor response to dopamine was ∼1 s, the sensitivity of analysis, optimized by adjusting the aptamer surface coverage, was 67 ± 1 nA μM(-1) cm(-2), and the dopamine LOD was 62 nM. The proposed design of the aptasensor, exploiting both the aptamer alkanethiol tethering to the electrode and screening of the catecholamine-aptamer electrostatic interactions, allows direct monitoring of dopamine levels in biological fluids in the presence of competitive NT and thus may be further applicable in biomedical research.

Electronic specific heat of transition metal carbides

International Nuclear Information System (INIS)

Conte, R.

1964-07-01

The experimental results that make it possible to define the band structure of transition metal carbides having an NaCI structure are still very few. We have measured the electronic specific heat of some of these carbides of varying electronic concentration (TiC, either stoichiometric or non-stoichiometric, TaC and mixed (Ti, Ta) - C). We give the main characteristics (metallography, resistivity, X-rays) of our samples and we describe the low temperature specific heat apparatus which has been built. In one of these we use helium as the exchange gas. The other is set up with a mechanical contact. The two use a germanium probe for thermometer. The measurement of the temperature using this probe is described, as well as the various measurement devices. The results are presented in the form of a rigid band model and show that the density of the states at the Fermi level has a minimum in the neighbourhood of the group IV carbides. (author) [fr

Flow stagnation volume and abdominal aortic aneurysm growth: Insights from patient-specific computational flow dynamics of Lagrangian-coherent structures.

Science.gov (United States)

Joly, Florian; Soulez, Gilles; Garcia, Damien; Lessard, Simon; Kauffmann, Claude

2018-01-01

Abdominal aortic aneurysms (AAA) are localized, commonly-occurring dilations of the aorta. When equilibrium between blood pressure (loading) and wall mechanical resistance is lost, rupture ensues, and patient death follows, if not treated immediately. Experimental and numerical analyses of flow patterns in arteries show direct correlations between wall shear stress and wall mechano-adaptation with the development of zones prone to thrombus formation. For further insights into AAA flow topology/growth interaction, a workout of patient-specific computational flow dynamics (CFD) is proposed to compute finite-time Lyapunov exponents and extract Lagrangian-coherent structures (LCS). This computational model was first compared with 4-D phase-contrast magnetic resonance imaging (MRI) in 5 patients. To better understand the impact of flow topology and transport on AAA growth, hyperbolic, repelling LCS were computed in 1 patient during 8-year follow-up, including 9 volumetric morphologic AAA measures by computed tomography-angiography (CTA). LCS defined barriers to Lagrangian jet cores entering AAA. Domains enclosed between LCS and the aortic wall were considered to be stagnation zones. Their evolution was studied during AAA growth. Good correlation - 2-D cross-correlation coefficients of 0.65, 0.86 and 0.082 (min, max, SD) - was obtained between numerical simulations and 4-D MRI acquisitions in 6 specific cross-sections from 4 patients. In follow-up study, LCS divided AAA lumens into 3 dynamically-isolated zones: 2 stagnation volumes lying in dilated portions of the AAA, and circulating volume connecting the inlet to the outlet. The volume of each zone was tracked over time. Although circulating volume remained unchanged during 8-year follow-up, the AAA lumen and main stagnation zones grew significantly (8 cm 3 /year and 6 cm 3 /year, respectively). This study reveals that transient transport topology can be quantified in patient-specific AAA during disease progression

Influence of specific amino acid side-chains on the antimicrobial activity and structure of bovine lactoferrampin.

Science.gov (United States)

Haney, Evan F; Nazmi, Kamran; Bolscher, Jan G M; Vogel, Hans J

2012-06-01

Lactoferrin is an 80 kDa iron binding protein found in the secretory fluids of mammals and it plays a major role in host defence. An antimicrobial peptide, lactoferrampin, was identified through sequence analysis of bovine lactoferrin and its antimicrobial activity against a wide range of bacteria and yeast species is well documented. In the present work, the contribution of specific amino acid residues of lactoferrampin was examined to evaluate the role that they play in membrane binding and bilayer disruption. The structures of all the bovine lactoferrampin derivatives were examined with circular dichroism and nuclear magnetic resonance spectroscopy, and their interactions with phospholipids were evaluated with differential scanning calorimetry and isothermal titration calorimetry techniques. From our results it is apparent that the amphipathic N-terminal helix anchors the peptide to membranes with Trp 268 and Phe 278 playing important roles in determining the strength of the interaction and for inducing peptide folding. In addition, the N-terminal helix capping residues (DLI) increase the affinity for negatively charged vesicles and they mediate the depth of membrane insertion. Finally, the unique flexibility in the cationic C-terminal region of bovine lactoferrampin does not appear to be essential for the antimicrobial activity of the peptide.

Sleep loss and structural plasticity.

Science.gov (United States)

Areal, Cassandra C; Warby, Simon C; Mongrain, Valérie

2017-06-01

Wakefulness and sleep are dynamic states during which brain functioning is modified and shaped. Sleep loss is detrimental to many brain functions and results in structural changes localized at synapses in the nervous system. In this review, we present and discuss some of the latest observations of structural changes following sleep loss in some vertebrates and insects. We also emphasize that these changes are region-specific and cell type-specific and that, most importantly, these structural modifications have functional roles in sleep regulation and brain functions. Selected mechanisms driving structural modifications occurring with sleep loss are also discussed. Overall, recent research highlights that extending wakefulness impacts synapse number and shape, which in turn regulate sleep need and sleep-dependent learning/memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Capital Structure Determinants and Governance Structure Variety in Franchising

OpenAIRE

Jiang, Tao

2009-01-01

textabstractThis thesis investigates two questions: the determinants of capital structure in franchising and its subsequent impact on the franchise financing decisions; and the efficient governance structure choice in franchising. We posit that firms franchise in order to benefit from the reduced franchisees’ operational risks by limiting the debt level, such that the franchisor can bear more debt and gain tax-deduction benefits. Specific hypotheses are based on various theories like resource...

Towards performance requirements for structural connections

NARCIS (Netherlands)

Stark, J.W.B.

1999-01-01

There is a tendency in the Construction Industry to move from solution driven specifications towards performance specifications. Traditionally structural specifications including those for steel construction used to be mainly solution driven. In this paper the position of the draft European

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

Energy Technology Data Exchange (ETDEWEB)

Prokofev, I. I.; Lashkov, A. A., E-mail: alashkov83@gmail.com; Gabdulkhakov, A. G.; Balaev, V. V.; Seregina, T. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation); Mironov, A. S. [State Research Institute of Genetics and Selection of Industrial Microorganisms (Russian Federation); Betzel, C. [University of Hamburg (Germany); Mikhailov, A. M. [Russian Academy of Sciences, Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” (Russian Federation)

2016-11-15

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2′-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation.

X-ray structures of uridine phosphorylase from Vibrio cholerae in complexes with uridine, thymidine, uracil, thymine, and phosphate anion: Substrate specificity of bacterial uridine phosphorylases

Science.gov (United States)

Prokofev, I. I.; Lashkov, A. A.; Gabdulkhakov, A. G.; Balaev, V. V.; Seregina, T. A.; Mironov, A. S.; Betzel, C.; Mikhailov, A. M.

2016-11-01

In many types of human tumor cells and infectious agents, the demand for pyrimidine nitrogen bases increases during the development of the disease, thus increasing the role of the enzyme uridine phosphorylase in metabolic processes. The rational use of uridine phosphorylase and its ligands in pharmaceutical and biotechnology industries requires knowledge of the structural basis for the substrate specificity of the target enzyme. This paper summarizes the results of the systematic study of the three-dimensional structure of uridine phosphorylase from the pathogenic bacterium Vibrio cholerae in complexes with substrates of enzymatic reactions—uridine, phosphate anion, thymidine, uracil, and thymine. These data, supplemented with the results of molecular modeling, were used to consider in detail the structural basis for the substrate specificity of uridine phosphorylases. It was shown for the first time that the formation of a hydrogen-bond network between the 2'-hydroxy group of uridine and atoms of the active-site residues of uridine phosphorylase leads to conformational changes of the ribose moiety of uridine, resulting in an increase in the reactivity of uridine compared to thymidine. Since the binding of thymidine to residues of uridine phosphorylase causes a smaller local strain of the β-N1-glycosidic bond in this the substrate compared to the uridine molecule, the β-N1-glycosidic bond in thymidine is more stable and less reactive than that in uridine. It was shown for the first time that the phosphate anion, which is the second substrate bound at the active site, interacts simultaneously with the residues of the β5-strand and the β1-strand through hydrogen bonding, thus securing the gate loop in a conformation

Double Shell Tank (DST) Transfer Piping Subsystem Specification

International Nuclear Information System (INIS)

GRAVES, C.E.

2000-01-01

This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Piping Subsystem that supports the first phase of Waste Feed Delivery. This specification establishes the performance requirements and provides references to the requisite codes and standards to be applied during design of the Double-Shell Tank (DST) Transfer Piping Subsystem that supports the first phase of waste feed delivery. This subsystem transfers waste between transfer-associated structures (pits) and to the River Protection Project (RPP) Privatization Contractor Facility where it will be processed into an immobilized waste form. This specification is intended to be the basis for new projects/installations (W-521, etc.). This specification is not intended to retroactively affect previously established project design criteria without specific direction by the program

Significance of sterol structural specificity : desmosterol cannot replace cholesterol in lipid rafts

NARCIS (Netherlands)

Vainio, S.; Jansen, Maurice; Koivusalo, M.; Róg, T.; Karttunen, M.E.J.; Vattulainen, I.; Ikonen, E.

2006-01-01

Desmosterol is an immediate precursor of cholesterol in the Bloch pathway of sterol synthesis and an abundant membrane lipid in specific cell types. The significance of the difference between the two sterols, an additional double bond at position C24 in the tail of desmosterol, is not known. Here,

Friendship networks and psychological well-being from late adolescence to young adulthood: a gender-specific structural equation modeling approach.

Science.gov (United States)

Miething, Alexander; Almquist, Ylva B; Östberg, Viveca; Rostila, Mikael; Edling, Christofer; Rydgren, Jens

2016-07-11

The importance of supportive social relationships for psychological well-being has been previously recognized, but the direction of associations between both dimensions and how they evolve when adolescents enter adulthood have scarcely been addressed. The present study aims to examine the gender-specific associations between self-reported friendship network quality and psychological well-being of young people during the transition from late adolescence to young adulthood by taking into account the direction of association. A random sample of Swedes born in 1990 were surveyed at age 19 and again at age 23 regarding their own health and their relationships with a maximum of five self-nominated friends. The response rate was 55.3 % at baseline and 43.7 % at follow-up, resulting in 772 cases eligible for analysis. Gender-specific structural equation modeling was conducted to explore the associations between network quality and well-being. The measurement part included a latent measure of well-being, whereas the structural part accounted for autocorrelation for network quality and for well-being over time and further examined the cross-lagged associations. The results show that network quality increased while well-being decreased from age 19 to age 23. Females reported worse well-being at both time points, whereas no gender differences were found for network quality. Network quality at age 19 predicted network quality at age 23, and well-being at age 19 predicted well-being at age 23. The results further show positive correlations between network quality and well-being for males and females alike. The strength of the correlations diminished over time but remained significant at age 23. Simultaneously testing social causation and social selection in a series of competing models indicates that while there were no cross-lagged associations among males, there was a weak reverse association between well-being at age 19 and network quality at age 23 among females. The study

A fluid-structure interaction study using patient-specific ruptured and unruptured aneurysm: the effect of aneurysm morphology, hypertension and elasticity.

Science.gov (United States)

Lee, C J; Zhang, Y; Takao, H; Murayama, Y; Qian, Y

2013-09-27

Fluid-structure interaction (FSI) simulations using five patient-specific aneurysm geometries are carried out to investigate the difference between ruptured and unruptured aneurysms. Two different blood pressure conditions (normal and hypertension, for all cases), and two different values of elastic modulus (1 and 2MPa, for two cases) are tested. Ruptured aneurysms (RA) generally displayed larger displacement at the dome, lower area-average WSS and higher von Mises stress than unruptured aneurysms (URA) regardless of elasticity or blood pressure condition. RAs had a longitudinal expansion whereas URAs had a radial expansion, which was the key difference between the two types. The difference in expansion pattern may be one of the keys to explaining aneurysm rupture, and further analysis is required in the future to confirm this theory. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sequence-specific activation of the DNA sensor cGAS by Y-form DNA structures as found in primary HIV-1 cDNA.

Science.gov (United States)

Herzner, Anna-Maria; Hagmann, Cristina Amparo; Goldeck, Marion; Wolter, Steven; Kübler, Kirsten; Wittmann, Sabine; Gramberg, Thomas; Andreeva, Liudmila; Hopfner, Karl-Peter; Mertens, Christina; Zillinger, Thomas; Jin, Tengchuan; Xiao, Tsan Sam; Bartok, Eva; Coch, Christoph; Ackermann, Damian; Hornung, Veit; Ludwig, Janos; Barchet, Winfried; Hartmann, Gunther; Schlee, Martin

2015-10-01

Cytosolic DNA that emerges during infection with a retrovirus or DNA virus triggers antiviral type I interferon responses. So far, only double-stranded DNA (dsDNA) over 40 base pairs (bp) in length has been considered immunostimulatory. Here we found that unpaired DNA nucleotides flanking short base-paired DNA stretches, as in stem-loop structures of single-stranded DNA (ssDNA) derived from human immunodeficiency virus type 1 (HIV-1), activated the type I interferon-inducing DNA sensor cGAS in a sequence-dependent manner. DNA structures containing unpaired guanosines flanking short (12- to 20-bp) dsDNA (Y-form DNA) were highly stimulatory and specifically enhanced the enzymatic activity of cGAS. Furthermore, we found that primary HIV-1 reverse transcripts represented the predominant viral cytosolic DNA species during early infection of macrophages and that these ssDNAs were highly immunostimulatory. Collectively, our study identifies unpaired guanosines in Y-form DNA as a highly active, minimal cGAS recognition motif that enables detection of HIV-1 ssDNA.

Serum concentrations of lipids, vitamin d metabolites, retinol, retinyl esters, tocopherols and selected carotenoids in twelve captive wild felid species at four zoos.

Science.gov (United States)

Crissey, Susan D; Ange, Kimberly D; Jacobsen, Krista L; Slifka, Kerri A; Bowen, Phyllis E; Stacewicz-Sapuntzakis, Maria; Langman, Craig B; Sadler, William; Kahn, Stephen; Ward, Ann

2003-01-01

Serum concentrations of several nutrients were measured in 12 captive wild felid species including caracal (Felis caracal), cheetah (Acinonyx jubatus), cougar (Felis concolor), fishing cat (Felis viverrinus), leopard (Panthera pardus), lion (Panthera leo), ocelot (Felis pardalis), pallas cat (Felis manul), sand cat (Felis margarita), serval (Felis serval), snow leopard (Panthera uncia) and tiger (Panthera tigris). Diet information was collected for these animals from each participating zoo (Brookfield Zoo, Fort Worth Zoo, Lincoln Park Zoological Gardens and North Carolina Zoological Park). The nutritional composition of the diets at each institution met the probable dietary requirements for each species except for the pallas cat. Blood samples were collected from each animal (n = 69) and analyzed for lipids (total cholesterol, triacylglycerides, HDL cholesterol and LDL cholesterol), vitamin D metabolites [25-hydroxycholecalciferol (25(OH)D) and 1,25-dihydroxycholecalciferol (1,25(OH)(2)D)], vitamin A (retinol, retinyl stearate and retinyl palmitate), vitamin E (alpha- and gamma-tocopherol) and selected carotenoids. Species differences were found for all except triacylglycerides and 1,25(OH)(2)D. Genus differences were found for retinol, retinyl palmitate, retinyl stearate, gamma-tocopherol and beta-carotene. Circulating nutrient concentrations for many of the species in this study have not been reported previously and most have not been compared with the animals' dietary intakes. The large number of animals analyzed provides a substantial base for comparing the serum nutrient concentrations of healthy animals, for both wild and captive exotic species.

The Okhansk Meteorite: Specifics of Composition, Structure, and Genesis

Directory of Open Access Journals (Sweden)

A.I. Bakhtin

2016-12-01

Full Text Available The Okhansk meteorite fell on August 18, 1887 near the village of Tabor, about 15 km away from the town of Okhansk in Perm province and weighed 186.5 kg (the total weight of collected fragments, according to P.I. Krotov, was more than 245 kg. The shock wave from the meteorite entry knocked down animals and riders on horses. Despite the fact that it was significantly stronger than that caused by the Chelyabinsk meteorite of 2013, all information about this meteorite has completely erased from people's memory. It has been shown that the meteorite is an ordinary olivine-bronzite chondrite. Its main silicate minerals are olivine, bronzite, plagioclase, and diopside. The main ore minerals are kamacite and troilite. The meteorite contains silicate glass in large amounts. The analysis of the composition and structure of the Okhansk meteorite has demonstrated that it was formed at the early stages of accretion of the melted substance of the protosolar nebula without undergoing endogenous, temperature, or pressure changes.

Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes.

Science.gov (United States)

Martin, Juliette; Regad, Leslie; Etchebest, Catherine; Camproux, Anne-Claude

2008-11-15

Interresidue protein contacts in proteins structures and at protein-protein interface are classically described by the amino acid types of interacting residues and the local structural context of the contact, if any, is described using secondary structures. In this study, we present an alternate analysis of interresidue contact using local structures defined by the structural alphabet introduced by Camproux et al. This structural alphabet allows to describe a 3D structure as a sequence of prototype fragments called structural letters, of 27 different types. Each residue can then be assigned to a particular local structure, even in loop regions. The analysis of interresidue contacts within protein structures defined using Voronoï tessellations reveals that pairwise contact specificity is greater in terms of structural letters than amino acids. Using a simple heuristic based on specificity score comparison, we find that 74% of the long-range contacts within protein structures are better described using structural letters than amino acid types. The investigation is extended to a set of protein-protein complexes, showing that the similar global rules apply as for intraprotein contacts, with 64% of the interprotein contacts best described by local structures. We then present an evaluation of pairing functions integrating structural letters to decoy scoring and show that some complexes could benefit from the use of structural letter-based pairing functions.

Structure of Sphingolipids From Sea Cucumber Cucumaria frondosa and Structure-Specific Cytotoxicity Against Human HepG2 Cells.

Science.gov (United States)

Jia, Zicai; Song, Yu; Tao, Suyuan; Cong, Peixu; Wang, Xiaoxu; Xue, Changhu; Xu, Jie

2016-03-01

To investigate the relationship between structure and activity, three glucocerebroside series (CFC-1, CFC-2 and CFC-3), ceramides (CF-Cer) and long-chain bases (CF-LCB) of sea cucumber Cucumaria frondosa (C. frondosa) were isolated and evaluated in HepG2 cells. The molecular species of CFC-1, CFC-2 and CFC-3 and CF-Cer were identified using reversed-phase liquid chromatography with heated electrospray ionization coupled to high-resolution mass spectrometry (RPLC-HESI-HRMS), and determined on the basis of chemical and spectroscopic evidence: For the three glucocerebroside series, fatty acids (FA) were mainly saturated (18:0 and 22:0), monounsaturated (22:1, 23:1 and 24:1) and 2-hydroxyl FA (2-HFA) (23:1 h and 24:1 h), the structure of long-chain bases (LCB) were dihydroxy (d17:1, d18:1 and d18:2) and trihydroxy (t16:0 and t17:0), and the glycosylation was glucose; For CF-Cer, FA were primarily saturated (17:0) and monounsaturated (16:1 and 19:1), the structure of LCB were dihydroxy (d17:1 and d18:1), and trihydroxy (t16:0). The results of cell experiment indicated that all of three glucocerebroside series, CF-Cer and CF-LCB exhibited an inhibitory effects on cell proliferation. Moreover, CFC-3 was most effective in three glucocerebrosides to HepG-2 cell viability. The inhibition effect of CF-LCB was the strongest, and the inhibition effect of CF-Cer was much stronger than glucocerebrosides.

Structural and functional studies on the pituitary-specific transcription factor Pit-1

NARCIS (Netherlands)

Augustijn, K.D.

2002-01-01

Pit-1 is a pituitary specific transcription factor that plays a central role in the development and maintenance of a number of cell lineages in the anterior pituitary gland. In these cell lineages, Pit-1 is required for the selective expression of the growth hormone (GH), prolactin (PRL) and the

Seismic characteristics and identification of negative flower structures, positive flower structures, and positive structural inversion

Energy Technology Data Exchange (ETDEWEB)

Harding, T.P.

1985-04-01

Negative and positive flower structures and positive inverted structures imply specific modes of formation, and their distinctive characteristics make them important criteria for the identification of certain structural styles. A negative flower structure from the Andaman Sea consists of a shallow synform bounded by upward-spreading strands of a wrench fault that have mostly normal separations. Paralleling monoclines and oblique, en echelon normal faults flank the divergent wrench fault. A positive flower structure from the Ardmore basin, Oklahoma, consists of a shallow antiform displaced by the upward diverging strands of a wrench fault that have mostly reverse separations. En echelon folds are present on either side of this convergent wrench fault. Positive structural inversion at the Rambutan oil field, South Sumatra basin, has formed a shallow anticlinorium and has partly uplifted the underlying graben. Deeper fault segments bounding the graben have retained their normal fault profiles, but at shallow levels some of these faults have reverse separations.

Standard technical specifications for Westinghouse pressurized water reactors

International Nuclear Information System (INIS)

Wagner, P.C.

1979-07-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Westinghouse plants currently being reviewed for an Operating License. Accordingly, the document contains specifications applicable to plants with (1) either 3 or 4 loops and (2) with and without loop stop valves. In addition, four separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric, Ice Condenser, Sub-Atmospheric, and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. This revision of the STS does not typically include requirements which may be added or revised as a result of the NRC staff's further review of the Three Mile Island incident

Describing migration spatial structure

NARCIS (Netherlands)

Rogers, A; Willekens, F; Little, J; Raymer, J

The age structure of a population is a fundamental concept in demography and is generally depicted in the form of an age pyramid. The spatial structure of an interregional system of origin-destination-specific migration streams is, however, a notion lacking a widely accepted definition. We offer a

Dynamic term structure models

DEFF Research Database (Denmark)

Andreasen, Martin Møller; Meldrum, Andrew

This paper studies whether dynamic term structure models for US nominal bond yields should enforce the zero lower bound by a quadratic policy rate or a shadow rate specification. We address the question by estimating quadratic term structure models (QTSMs) and shadow rate models with at most four...

Perturbation of N-linked oligosaccharide structure results in an altered incorporation of [3H]palmitate into specific proteins in Chinese hamster ovary cells

International Nuclear Information System (INIS)

Wellner, R.B.; Ghosh, P.C.; Roecklein, B.; Wu, H.C.

1987-01-01

Increased [ 3 H]palmitate incorporation into specific cellular proteins has been reported to occur in Chinese hamster ovary and yeast mutant cells. In this paper we report studies concerning the relationship between N-linked oligosaccharide structure and [ 3 H]palmitate incorporation into proteins of Chinese hamster ovary (CHO) cells. We have compared the incorporation of [ 3 H]palmitate into proteins of wild-type and four different mutant CHO cell lines defective in various steps of N-linked protein glycosylation. Sodium dodecyl sulfate-gel electrophoretic analysis showed that three of the mutants exhibited increased [ 3 H]palmitate incorporation into several CHO cellular proteins (approximately 30,000-38,000 molecular weight) as compared to the wild-type cells. One of the affected mutants which accumulates the Man5Gn2Asn intermediate structure was examined in detail. In agreement with earlier reports, virtually all of the [ 3 H] palmitate-labeled proteins of both wild-type and mutant cell lines are membrane-bound. Pretreatment of the mutant cell line with tunicamycin blocked the increased [ 3 H]palmitate incorporation into the two specific proteins (both of approximately 30,000 molecular weight) observed in untreated cells; the decreased incorporation of [ 3 H]palmitate into the 30,000 molecular weight species was accompanied by a concomitant increase in the incorporation of [ 3 H]palmitate into two proteins of approximately 20,000 molecular weight. Pretreatment of wild-type cells with tunicamycin also caused increased [ 3 H]palmitate incorporation into the 20,000 molecular weight species

Standard technical specifications for combustion engineering pressurized water reactors

International Nuclear Information System (INIS)

1979-08-01

This Standard Technical Specification (STS) has been structured for the broadest possible use on Combustion Engineering plants currently being reviewed for an Operating License. Two separate and discrete containment specification sections are provided for each of the following containment types: Atmospheric and Dual. Optional specifications are provided for those features and systems which may be included in individual plant designs but are not generic in their scope of application. Alternate specifications are provided in a limited number of cases to cover situations where alternate specification requirements are necessary on a generic basis because of design differences. This revision of STS does not typically include requirements which may be added or revised as a result of the NRC staff's further review of the Three Mile Island incident

SU-F-T-227: A Comprehensive Patient Specific, Structure Specific, Pre-Treatment 3D QA Protocol for IMRT, SBRT and VMAT - Clinical Experience

Energy Technology Data Exchange (ETDEWEB)

Gueorguiev, G; Cotter, C; Young, M; Toomeh, D [Massachusetts General Hospital Boston MA (United States); University of Massachusetts Lowell Lowell, MA (United States); Khan, F; Crawford, B; Turcotte, J; Sharp, G [Massachusetts General Hospital Boston MA (United States); Mah’D, M [University of Massachusetts Lowell Lowell, MA (United States)

2016-06-15

Purpose: To present a 3D QA method and clinical results for 550 patients. Methods: Five hundred and fifty patient treatment deliveries (400 IMRT, 75 SBRT and 75 VMAT) from various treatment sites, planned on Raystation treatment planning system (TPS), were measured on three beam-matched Elekta linear accelerators using IBA’s COMPASS system. The difference between TPS computed and delivered dose was evaluated in 3D by applying three statistical parameters to each structure of interest: absolute average dose difference (AADD, 6% allowed difference), absolute dose difference greater than 6% (ADD6, 4% structure volume allowed to fail) and 3D gamma test (3%/3mm DTA, 4% structure volume allowed to fail). If the allowed value was not met for a given structure, manual review was performed. The review consisted of overlaying dose difference or gamma results with the patient CT, scrolling through the slices. For QA to pass, areas of high dose difference or gamma must be small and not on consecutive slices. For AADD to manually pass QA, the average dose difference in cGy must be less than 50cGy. The QA protocol also includes DVH analysis based on QUANTEC and TG-101 recommended dose constraints. Results: Figures 1–3 show the results for the three parameters per treatment modality. Manual review was performed on 67 deliveries (27 IMRT, 22 SBRT and 18 VMAT), for which all passed QA. Results show that statistical parameter AADD may be overly sensitive for structures receiving low dose, especially for the SBRT deliveries (Fig.1). The TPS computed and measured DVH values were in excellent agreement and with minimum difference. Conclusion: Applying DVH analysis and different statistical parameters to any structure of interest, as part of the 3D QA protocol, provides a comprehensive treatment plan evaluation. Author G. Gueorguiev discloses receiving travel and research funding from IBA for unrelated to this project work. Author B. Crawford discloses receiving travel funding from

Antibody structural modeling with prediction of immunoglobulin structure (PIGS)

DEFF Research Database (Denmark)

Marcatili, Paolo; Olimpieri, Pier Paolo; Chailyan, Anna

2014-01-01

Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful...... applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (∼10 min...... on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together....

Target-specific delivery of doxorubicin to human glioblastoma cell ...

Indian Academy of Sciences (India)

Abdullah Tahir Bayraç

2018-01-29

Jan 29, 2018 ... was previously selected for specific recognition of glioblastoma and represented many advantageous ... antigens, receptors or any 3-D structure on the target cells ..... both PSMA (?) and PSMA (-) prostate cancers.

Structural health monitoring for ship structures

Energy Technology Data Exchange (ETDEWEB)

Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Angel, Marian [Los Alamos National Laboratory; Bement, Matthew [Los Alamos National Laboratory; Salvino, Liming [NSWC, CADEROCK

2009-01-01

Currently the Office of Naval Research is supporting the development of structural health monitoring (SHM) technology for U.S. Navy ship structures. This application is particularly challenging because of the physical size of these structures, the widely varying and often extreme operational and environmental conditions associated with these ships missions, lack of data from known damage conditions, limited sensing that was not designed specifically for SHM, and the management of the vast amounts of data that can be collected during a mission. This paper will first define a statistical pattern recognition paradigm for SHM by describing the four steps of (1) Operational Evaluation, (2) Data Acquisition, (3) Feature Extraction, and (4) Statistical Classification of Features as they apply to ship structures. Note that inherent in the last three steps of this process are additional tasks of data cleansing, compression, normalization and fusion. The presentation will discuss ship structure SHM challenges in the context of applying various SHM approaches to sea trials data measured on an aluminum multi-hull high-speed ship, the HSV-2 Swift. To conclude, the paper will discuss several outstanding issues that need to be addressed before SHM can make the transition from a research topic to actual field applications on ship structures and suggest approaches for addressing these issues.

Modeling age-specific mortality for countries with generalized HIV epidemics.

Directory of Open Access Journals (Sweden)

David J Sharrow

Full Text Available In a given population the age pattern of mortality is an important determinant of total number of deaths, age structure, and through effects on age structure, the number of births and thereby growth. Good mortality models exist for most populations except those experiencing generalized HIV epidemics and some developing country populations. The large number of deaths concentrated at very young and adult ages in HIV-affected populations produce a unique 'humped' age pattern of mortality that is not reproduced by any existing mortality models. Both burden of disease reporting and population projection methods require age-specific mortality rates to estimate numbers of deaths and produce plausible age structures. For countries with generalized HIV epidemics these estimates should take into account the future trajectory of HIV prevalence and its effects on age-specific mortality. In this paper we present a parsimonious model of age-specific mortality for countries with generalized HIV/AIDS epidemics.The model represents a vector of age-specific mortality rates as the weighted sum of three independent age-varying components. We derive the age-varying components from a Singular Value Decomposition of the matrix of age-specific mortality rate schedules. The weights are modeled as a function of HIV prevalence and one of three possible sets of inputs: life expectancy at birth, a measure of child mortality, or child mortality with a measure of adult mortality. We calibrate the model with 320 five-year life tables for each sex from the World Population Prospects 2010 revision that come from the 40 countries of the world that have and are experiencing a generalized HIV epidemic. Cross validation shows that the model is able to outperform several existing model life table systems.We present a flexible, parsimonious model of age-specific mortality for countries with generalized HIV epidemics. Combined with the outputs of existing epidemiological and

Site-specific optimisation of the countermeasure structure on rehabilitation of radioactive contaminated territories

Energy Technology Data Exchange (ETDEWEB)

Yatsalo, B.I.; Okhrimenko, D.V.; Lisyanski, B.G.; Okhrimenko, I.V.; Mirzeabassov, O.A. [Obninsk Institute of Nuclear Power Engineering, Obninsk, Kaluga (Russian Federation)

2000-05-01

The use of 'soft' countermeasures (CMs) (agricultural CMs, some administrative ones, except for relocation/resettlement and some 'strong' measures on restriction of living conditions) allows considering the radiological and economic parameters for assessing their effectiveness. In this case cost-benefit analysis (CBA) or some its modification are used. However, the determination of various radiological and economic parameters (and their combination) is not enough for making final decisions on countermeasure implementation. All radiological, ecological and economic characteristics and other expert knowledge, corresponding standards and regulations should be taken into account, and many of them may not be used very often in analytical methods directly. The approaches to evaluating strong' CMs are based, as a rule, on expert judgements (MAUA, M-Crit). However, in practice they can lead to any result given in advance or to a choice of an weighted solution which does not comply with opinions by most experts due to considerable range of expert opinions and subjective weights for chosen attributes/criteria. Implementation of CMs on rehabilitation of contaminated territories should be based on the radiation protection principles. However, these principles are declared only when realising CMs on rehabilitation of contaminated territories after the Chernobyl accident. In practice some national or departmental standards are used and principles of justification'/'optimisation' are not examined. Taking into consideration a complex character of tasks on CM analysis and comparison of various alternatives it is quite necessary to use up-to-date computer decision support systems (DSSs). One of the systems which is directly intended for site-specific rehabilitation of territories subjected to radioactive contamination after the Chernobyl accident is the PRANA DSS. A key block of PRANA is 'analysis and optimisation of CMs structure

Site-specific optimisation of the countermeasure structure on rehabilitation of radioactive contaminated territories

International Nuclear Information System (INIS)

Yatsalo, B.I.; Okhrimenko, D.V.; Lisyanski, B.G.; Okhrimenko, I.V.; Mirzeabassov, O.A.

2000-01-01

The use of 'soft' countermeasures (CMs) (agricultural CMs, some administrative ones, except for relocation/resettlement and some 'strong' measures on restriction of living conditions) allows considering the radiological and economic parameters for assessing their effectiveness. In this case cost-benefit analysis (CBA) or some its modification are used. However, the determination of various radiological and economic parameters (and their combination) is not enough for making final decisions on countermeasure implementation. All radiological, ecological and economic characteristics and other expert knowledge, corresponding standards and regulations should be taken into account, and many of them may not be used very often in analytical methods directly. The approaches to evaluating strong' CMs are based, as a rule, on expert judgements (MAUA, M-Crit). However, in practice they can lead to any result given in advance or to a choice of an weighted solution which does not comply with opinions by most experts due to considerable range of expert opinions and subjective weights for chosen attributes/criteria. Implementation of CMs on rehabilitation of contaminated territories should be based on the radiation protection principles. However, these principles are declared only when realising CMs on rehabilitation of contaminated territories after the Chernobyl accident. In practice some national or departmental standards are used and principles of justification'/'optimisation' are not examined. Taking into consideration a complex character of tasks on CM analysis and comparison of various alternatives it is quite necessary to use up-to-date computer decision support systems (DSSs). One of the systems which is directly intended for site-specific rehabilitation of territories subjected to radioactive contamination after the Chernobyl accident is the PRANA DSS. A key block of PRANA is 'analysis and optimisation of CMs structure'. It is intended for : -determination of territories

Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

Science.gov (United States)

Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

2015-01-01

Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

Revisiting verbs of emission: an update on some relevant theoretical accounts of lexical specification and argument structure of emission verbs

Directory of Open Access Journals (Sweden)

Natasa Milivojevic

2016-06-01

Full Text Available The paper addresses the question of what semantic properties lexicalized in verbs determine their syntactic behavior in intransitive motion events and in resultative constructions in English and Serbian. Special attention is devoted to English and Serbian verbs of emission (specifically verbs of sound emission and partly also verbs of light, smell and substance emission regarding their potential to surface as main verbs in these constructions and to combine with directional phrases within specific morphosyntactic templates (unaccusatives and unergatives. The presented research promotes a theoretical view according to which the established syntactic patterns can be applied across the whole class of verbs of emission to express a full er range of atypical verb meanings in motion events. Theoretical conclusions of the research are also relevant for a wider theoretical description of motion events and resultatives in a cross - linguistic perspective. The paper puts forth additional implica tions regarding the projectionalist approach to semantic verb classes against the theoretical framework of Beth Levin (1993. Finally, the paper considers the relevant points of structurally realized similarities via relevant constructional templates in En glish and in Serbian, as well as some important points of morphosyntactic divergence between the two languages. The conclusions presented aim at a more comprehensive contrastive language typology based on language “framing” parameters.

Guide Structures in CD-ROM Dictionaries, with Specific Reference to the EWED and the ELHAT

Directory of Open Access Journals (Sweden)

Philip Louw

2011-10-01

Full Text Available

macro- and microstructural information. In order to evaluate the methods which lexicographers employ to improve dictionary accessibility, the concept of guide structures was introduced by Hausmann and Wiegand (1989. Since the appearance of that article, various academics have written articles and read papers on guide structures in print dictionaries, but few studies have focussed on the tremendous potential of guide structures in electronic dictionaries. In this article it will be shown that electronic dictionaries add dimensions to the implementation of guide structures not possible in print versions. The role of two of the guide structures in the transfer of infonnation in CD-ROM dictionaries will be discussed. The access and mediostructures of the Microsoft Encarta World English Dictionary and the Elektroniese Handwoordeboek van die Afrikaanse Taal will be analysed and critically evaluated to illustrate the advantages of electronic dictionaries over print dictionaries and the urgent need for metalexicographical discussion of this publication medium.

Keywords: ACCESS STRUCTURE; ACTIVE CROSS-REFERENCES; CD-ROM DICTIONARY; DICTIONARY ACCESSIBILITY; ENCYCLOPAEDIC DICTIONARY; GUIDE STRUCTURES; INNER ACCESS STRUCTURE; INNER SEARCH PATH; INTERNET; MEDIOSTRUCTURE; MULTIMEDIA; OUTER ACCESS STRUCTURE; OUTER SEARCH PATH; PASSIVE CROSSREFERENCING; USER-FRIENDLINESS

Opsomming: Gidsstrukture in CD-ROM-woordeboeke, met spesifieke verwysingna EWED en ELHA T. Die sukses van modeme woordeboeke hang grootliles af vandie toeganklikheid van hulle makro- en mikrostrukturele inligting. Hausmann en Wiegand (1989het die konsep van gidsstrukture ingevoer om die metodes te evalueer wat leksikograwe gebruikom woordeboektoeganklikheid Ie verbeter. Sedert hierdie artikel verskyn het, het verskeie akademic:i artikels gepubliseer en referate gelewer oor gidsstrukture in gedrukte woordeboeke, maarmin studies het gefokus op die geweldige potensiaal van

A method to determine site-specific, anisotropic fracture toughness in biological materials

International Nuclear Information System (INIS)

Bechtle, Sabine; Özcoban, Hüseyin; Yilmaz, Ezgi D.; Fett, Theo; Rizzi, Gabriele; Lilleodden, Erica T.; Huber, Norbert; Schreyer, Andreas; Swain, Michael V.; Schneider, Gerold A.

2012-01-01

Many biological materials are hierarchically structured, with highly anisotropic structures and properties on several length scales. To characterize the mechanical properties of such materials, detailed testing methods are required that allow precise and site-specific measurements on several length scales. We propose a fracture toughness measurement technique based on notched focused ion beam prepared cantilevers of lower and medium micron size scales. Using this approach, site-specific fracture toughness values in dental enamel were determined. The usefulness and challenges of the method are discussed.

Site-Specific Seismic Site Response Model for the Waste Treatment Plant, Hanford, Washington

Energy Technology Data Exchange (ETDEWEB)

Rohay, Alan C.; Reidel, Steve P.

2005-02-24

This interim report documents the collection of site-specific geologic and geophysical data characterizing the Waste Treatment Plant site and the modeling of the site-specific structure response to earthquake ground motions.

Identification of flap structure-specific endonuclease 1 as a factor involved in long-term memory formation of aversive learning.

Science.gov (United States)

Saavedra-Rodríguez, Lorena; Vázquez, Adrinel; Ortiz-Zuazaga, Humberto G; Chorna, Nataliya E; González, Fernando A; Andrés, Lissette; Rodríguez, Karen; Ramírez, Fernando; Rodríguez, Alan; Peña de Ortiz, Sandra

2009-05-06

We previously proposed that DNA recombination/repair processes play a role in memory formation. Here, we examined the possible role of the fen-1 gene, encoding a flap structure-specific endonuclease, in memory consolidation of conditioned taste aversion (CTA). Quantitative real-time PCR showed that amygdalar fen-1 mRNA induction was associated to the central processing of the illness experience related to CTA and to CTA itself, but not to the central processing resulting from the presentation of a novel flavor. CTA also increased expression of the Fen-1 protein in the amygdala, but not the insular cortex. In addition, double immunofluorescence analyses showed that amygdalar Fen-1 expression is mostly localized within neurons. Importantly, functional studies demonstrated that amygdalar antisense knockdown of fen-1 expression impaired consolidation, but not short-term memory, of CTA. Overall, these studies define the fen-1 endonuclease as a new DNA recombination/repair factor involved in the formation of long-term memories.

Some specifics considering the urban territories river discharge determination

Directory of Open Access Journals (Sweden)

Chilikova-Lubomirova Mila

2018-01-01

Full Text Available Urban territories are specific territories with a significant anthropogenic influence on the natural environment. As a result most of the existing natural conditions have been modified. Parts of them cover the natural forms of river beds and floodplains. Concerning to the humans safety, comfort and needs, while keeping ecosystems healthy function, different artificial structures also have been created. The process is connected to the well understanding and good quality data obtaining about the existing conditions and river flow behaviour, that are interconnected and relevant to the river discharge determination and its variations description – key issue for the entire river structures project, water extremes mitigation and maintaining a healthy state of the ecosystems. For the purpose various contact measurements and monitoring procedures are implemented. To clarify the process this material aims to present some specifics connected to the urban territories river discharge determination and the possibility for related monitoring networks creation. It is focused on the most used methods, their specifics and possible challenges for practical application. Main specifics connected to the related decision support systems creation and implementations are also presented. Main purpose is such state of the art dissemination, in help of decision makers and professionals in the area.

Jazz drummers recruit language-specific areas for the processing of rhythmic structure.

Science.gov (United States)

Herdener, Marcus; Humbel, Thierry; Esposito, Fabrizio; Habermeyer, Benedikt; Cattapan-Ludewig, Katja; Seifritz, Erich

2014-03-01

Rhythm is a central characteristic of music and speech, the most important domains of human communication using acoustic signals. Here, we investigated how rhythmical patterns in music are processed in the human brain, and, in addition, evaluated the impact of musical training on rhythm processing. Using fMRI, we found that deviations from a rule-based regular rhythmic structure activated the left planum temporale together with Broca's area and its right-hemispheric homolog across subjects, that is, a network also crucially involved in the processing of harmonic structure in music and the syntactic analysis of language. Comparing the BOLD responses to rhythmic variations between professional jazz drummers and musical laypersons, we found that only highly trained rhythmic experts show additional activity in left-hemispheric supramarginal gyrus, a higher-order region involved in processing of linguistic syntax. This suggests an additional functional recruitment of brain areas usually dedicated to complex linguistic syntax processing for the analysis of rhythmical patterns only in professional jazz drummers, who are especially trained to use rhythmical cues for communication.

Porous Structure of Road Concrete

OpenAIRE

Пшембаев, М. К.; Гиринский, В. В.; Ковалев, Я. Н.; Яглов, В. Н.; Будниченко, С. С.

2016-01-01

Having a great number of concrete structure classifications it is recommended to specify the following three principal types: microstructure – cement stone structure; mesostructure – structure of cement-sand mortar in concrete; macrostucture – two-component system that consists of mortar and coarse aggregate. Every mentioned-above structure has its own specific features which are related to the conditions of their formation. Thus, microstructure of cement stone can be characterized by such st...

Homophilic and Heterophilic Interactions of Type II Cadherins Identify Specificity Groups Underlying Cell-Adhesive Behavior

Directory of Open Access Journals (Sweden)

Julia Brasch

2018-05-01

Full Text Available Summary: Type II cadherins are cell-cell adhesion proteins critical for tissue patterning and neuronal targeting but whose molecular binding code remains poorly understood. Here, we delineate binding preferences for type II cadherin cell-adhesive regions, revealing extensive heterophilic interactions between specific pairs, in addition to homophilic interactions. Three distinct specificity groups emerge from our analysis with members that share highly similar heterophilic binding patterns and favor binding to one another. Structures of adhesive fragments from each specificity group confirm near-identical dimer topology conserved throughout the family, allowing interface residues whose conservation corresponds to specificity preferences to be identified. We show that targeted mutation of these residues converts binding preferences between specificity groups in biophysical and co-culture assays. Our results provide a detailed understanding of the type II cadherin interaction map and a basis for defining their role in tissue patterning and for the emerging importance of their heterophilic interactions in neural connectivity. : Type II cadherins are a family of vertebrate cell adhesion proteins expressed primarily in the CNS. Brasch et al. measure binding between adhesive fragments, revealing homophilic and extensive selective heterophilic binding with specificities that define groups of similar cadherins. Structures reveal common adhesive dimers, with residues governing cell-adhesive specificity. Keywords: cell adhesion, crystal structure, hemophilic specificity, heterophilic specificity, neural patterning, synaptic targeting, cadherin

Transitioning Existing Content: inferring organisation-specific documents

Directory of Open Access Journals (Sweden)

Arijit Sengupta

2000-11-01

Full Text Available A definition for a document type within an organization represents an organizational norm about the way the organizational actors represent products and supporting evidence of organizational processes. Generating a good organization-specific document structure is, therefore, important since it can capture a shared understanding among the organizational actors about how certain business processes should be performed. Current tools that generate document type definitions focus on the underlying technology, emphasizing tags created in a single instance document. The tools, thus, fall short of capturing the shared understanding between organizational actors about how a given document type should be represented. We propose a method for inferring organization-specific document structures using multiple instance documents as inputs. The method consists of heuristics that combine individual document definitions, which may have been compiled using standard algorithms. We propose a number of heuristics utilizing artificial intelligence and natural language processing techniques. As the research progresses, the heuristics will be tested on a suite of test cases representing multiple instance documents for different document types. The complete methodology will be implemented as a research prototype

Antibody structural modeling with prediction of immunoglobulin structure (PIGS)

KAUST Repository

Marcatili, Paolo

2014-11-06

© 2014 Nature America, Inc. All rights reserved. Antibodies (or immunoglobulins) are crucial for defending organisms from pathogens, but they are also key players in many medical, diagnostic and biotechnological applications. The ability to predict their structure and the specific residues involved in antigen recognition has several useful applications in all of these areas. Over the years, we have developed or collaborated in developing a strategy that enables researchers to predict the 3D structure of antibodies with a very satisfactory accuracy. The strategy is completely automated and extremely fast, requiring only a few minutes (~10 min on average) to build a structural model of an antibody. It is based on the concept of canonical structures of antibody loops and on our understanding of the way light and heavy chains pack together.

Crystal structure of the antigen-binding fragment of a monoclonal antibody specific for the multidrug-resistance-linked ABC transporter human P-glycoprotein

Energy Technology Data Exchange (ETDEWEB)

Esser, Lothar; Shukla, Suneet; Zhou, Fei; Ambudkar, Suresh V.; Xia, Di

2016-07-27

P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancers that plays important roles in the pharmacokinetics of a large number of drugs. The drug-resistance phenotype of P-gp can be modulated by the monoclonal antibody UIC2, which specifically recognizes human P-gp in a conformation-dependent manner. Here, the purification, sequence determination and high-resolution structure of the Fab fragment of UIC2 (UIC2/Fab) are reported. Purified UIC2/Fab binds human P-gp with a 1:1 stoichiometry. Crystals of UIC2/Fab are triclinic (space groupP1), with unit-cell parametersa= 40.67,b= 44.91,c= 58.09 Å, α = 97.62, β = 99.10, γ = 94.09°, and diffracted X-rays to 1.6 Å resolution. The structure was determined by molecular replacement and refined to 1.65 Å resolution. The asymmetric unit contains one molecule of UIC2/Fab, which exhibits a positively charged antigen-binding surface, suggesting that it might recognize an oppositely charged extracellular epitope of P-gp.

Composing a Tumor Specific Bacterial Promoter.

Directory of Open Access Journals (Sweden)

Igor V Deyneko

Full Text Available Systemically applied Salmonella enterica spp. have been shown to invade and colonize neoplastic tissues where it retards the growth of many tumors. This offers the possibility to use the bacteria as a vehicle for the tumor specific delivery of therapeutic molecules. Specificity of such delivery is solely depending on promoter sequences that control the production of a target molecule. We have established the functional structure of bacterial promoters that are transcriptionally active exclusively in tumor tissues after systemic application. We observed that the specific transcriptional activation is accomplished by a combination of a weak basal promoter and a strong FNR binding site. This represents a minimal set of control elements required for such activation. In natural promoters, additional DNA remodeling elements are found that alter the level of transcription quantitatively. Inefficiency of the basal promoter ensures the absence of transcription outside tumors. As a proof of concept, we compiled an artificial promoter sequence from individual motifs representing FNR and basal promoter and showed specific activation in a tumor microenvironment. Our results open possibilities for the generation of promoters with an adjusted level of expression of target proteins in particular for applications in bacterial tumor therapy.

A laboratory simulation of the carbonization of sunflower achenes and seeds

Energy Technology Data Exchange (ETDEWEB)

Braadbaart, F. [FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam (Netherlands); Department of Earth Sciences-Geochemistry, Faculty of Geosciences, Utrecht University, P.O. Box 80021, 3058 TA Utrecht (Netherlands); Wright, P.J. [Department of Anthropology, University of Missouri-St. Louis, St. Louis, MO 63121 (United States); Horst, J. van der; Boon, J.J. [FOM Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam (Netherlands)

2007-03-15

The current project describes physical and chemical alterations that result from the thermal exposure of sunflower achenes and seeds. Specifically, achenes and seeds were heated at temperatures ranging from 130 to 600 C under anoxic conditions for 60 min. Changes were measured in mass, relative percentages of C and N, internal and external morphology, molecular composition by direct temperature-resolved mass spectrometry (DTMS) under EI conditions, and the reflectance on polished specimens. The main constituents of sunflower seeds are lipids and protein, while the pericarps or hulls enclosing the seeds have a ligno-cellulosic structure. The morphology of achenes and seeds remains intact following exposure which makes the identification of the residues possible. The results of the sunflower experiments were compared to previous experiments conducted with peas and wheat grains. Up to approximately 340 C, the molecular conversion of polysaccharide and protein rich peas and wheat grains follow similar pathways, while the lignin present in sunflower achenes follows its own unique pathway, resulting in a different molecular composition. At higher temperatures the molecular composition of the three propagules becomes identical. In addition the reflectance of the three propagules is identical confirming the similarity in molecular composition. Lipids show a different behaviour compared to the other three biopolymers; from 370 C no oils are observed in the heated specimens and the DTMS-EI measurements show no lipid markers. Apart from evaporation of the triacylglycerides it is suggested that steroids have a high resistance against thermal degradation and are converted into aromatic moieties. (author)

Prediction of Liquid Specific Heat Capacity of Food Lipids.

Science.gov (United States)

Zhu, Xiaoyi; Phinney, David M; Paluri, Sravanti; Heldman, Dennis R

2018-04-01

Specific heat capacity (c p ) is a temperature dependent physical property of foods. Lipid-being a macromolecular component of food-provides some fraction of the food's overall heat capacity. Fats/oils are complex chemicals that are generally defined by carbon length and degree of unsaturation. The objective of this investigation was to use advanced specific heat capacity measurement to determine the effect of fatty acid chemical structure on specific heat capacity of food lipids. In this investigation, the specific heat capacity of a series of triacylglycerols were measured to quantify the influence of fatty acid composition on specific heat capacity based on two parameters; the -average carbon number (C) and the average number of double bonds (U). A prediction model for specific heat capacity of food lipids as a function of C, U and temperature (T) has been developed. A multiple linear regression to the three-parameter model (R 2 = 0.87) provided a good fit to the experimental data. The prediction model was evaluated by comparison with previously published specific heat capacity values of vegetable oils. It was found that the model provided a 0.53% error, while three other models from the literature predicted c p values with 0.85% to 1.83% average relative deviation from experimental data. The outcomes from this research confirm that the thermophysical properties of fat present in foods are directly related to the physical chemical properties. The specific heat capacity of food products is widely used in process design. Improvements of current models to predict specific heat capacity of food products will assist in the development of efficient processes and in the control of food quality and safety. Furthermore, the understanding of how changes in chemical structure of macromolecular components of foods effect thermophysical properties may begin to allude to models that are not just empirical, but represent portions of the differences in chemistry. © 2018

Structural analysis consultation using artificial intelligence

Science.gov (United States)

Melosh, R. J.; Marcal, P. V.; Berke, L.

1978-01-01

The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

Integrated flight/propulsion control - Subsystem specifications for performance

Science.gov (United States)

Neighbors, W. K.; Rock, Stephen M.

1993-01-01

A procedure is presented for calculating multiple subsystem specifications given a number of performance requirements on the integrated system. This procedure applies to problems where the control design must be performed in a partitioned manner. It is based on a structured singular value analysis, and generates specifications as magnitude bounds on subsystem uncertainties. The performance requirements should be provided in the form of bounds on transfer functions of the integrated system. This form allows the expression of model following, command tracking, and disturbance rejection requirements. The procedure is demonstrated on a STOVL aircraft design.

Improvement of Neutral Lipid and Polyunsaturated Fatty Acid Biosynthesis by Overexpressing a Type 2 Diacylglycerol Acyltransferase in Marine Diatom Phaeodactylum tricornutum

Directory of Open Access Journals (Sweden)

Ying-Fang Niu

2013-11-01

Full Text Available Microalgae have been emerging as an important source for the production of bioactive compounds. Marine diatoms can store high amounts of lipid and grow quite quickly. However, the genetic and biochemical characteristics of fatty acid biosynthesis in diatoms remain unclear. Glycerophospholipids are integral as structural and functional components of cellular membranes, as well as precursors of various lipid mediators. In addition, diacylglycerol acyltransferase (DGAT is a key enzyme that catalyzes the last step of triacylglyceride (TAG biosynthesis. However, a comprehensive sequence-structure and functional analysis of DGAT in diatoms is lacking. In this study, an isoform of diacylglycerol acyltransferase type 2 of the marine diatom Phaeodactylum tricornutum was characterized. Surprisingly, DGAT2 overexpression in P. tricornutum stimulated more oil bodies, and the neutral lipid content increased by 35%. The fatty acid composition showed a significant increase in the proportion of polyunsaturated fatty acids; in particular, EPA was increased by 76.2%. Moreover, the growth rate of transgenic microalgae remained similar, thereby maintaining a high biomass. Our results suggest that increased DGAT2 expression could alter fatty acid profile in the diatom, and the results thus represent a valuable strategy for polyunsaturated fatty acid production by genetic manipulation.

Photothermal modification of plasmonic structures

DEFF Research Database (Denmark)

2016-01-01

There is presented a method for geometrically modifying plasmonic structures on a support structure, such as for printing or recording, said method comprising changing a geometry specifically of plasmonic structures, wherein said changing the geometry is carried out by photothermally melting...... at least a portion of each of the plasmonic structures within the second plurality of plasmonic structures by irradiating, the plasmonic structures with incident electromagnetic radiation having an incident intensity in a plane of the second plurality of plasmonic structures, wherein said incident...... intensity is less than an incident intensity required to melt a film of a corresponding material and a corresponding thickness as the plasmonic structures within the second plurality of plasmonic structures....

Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

Energy Technology Data Exchange (ETDEWEB)

Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

1992-01-28

The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

Germ cell specification and ovary structure in the rotifer Brachionus plicatilis.

Science.gov (United States)

Smith, James M; Cridge, Andrew G; Dearden, Peter K

2010-08-02

The segregation of the germline from somatic tissues is an essential process in the development of all animals. Specification of the primordial germ cells (PGCs) takes place via different strategies across animal phyla; either specified early in embryogenesis by the inheritance of maternal determinants in the cytoplasm of the oocyte ('preformation') or selected later in embryonic development from undifferentiated precursors by a localized inductive signal ('epigenesis'). Here we investigate the specification and development of the germ cells in the rotifer Brachionus plicatilis, a member of the poorly-characterized superphyla Lophotrochozoa, by isolating the Brachionus homologues of the conserved germ cell markers vasa and nanos, and examining their expression using in situ hybridization. Bpvasa and Bpnos RNA expression have very similar distributions in the Brachionus ovary, showing ubiquitous expression in the vitellarium, with higher levels in the putative germ cell cluster. Bpvas RNA expression is present in freshly laid eggs, remaining ubiquitous in embryos until at least the 96 cell stage after which expression narrows to a small cluster of cells at the putative posterior of the embryo, consistent with the developing ovary. Bpnos RNA expression is also present in just-laid eggs but expression is much reduced by the four-cell stage and absent by the 16-cell stage. Shortly before hatching of the juvenile rotifer from the egg, Bpnos RNA expression is re-activated, located in a subset of posterior cells similar to those expressing Bpvas at the same stage. The observed expression of vasa and nanos in the developing B. plicatilis embryo implies an epigenetic origin of primordial germ cells in Rotifer.

Germ cell specification and ovary structure in the rotifer Brachionus plicatilis

Directory of Open Access Journals (Sweden)

Smith James M

2010-08-01

Full Text Available Abstract Background The segregation of the germline from somatic tissues is an essential process in the development of all animals. Specification of the primordial germ cells (PGCs takes place via different strategies across animal phyla; either specified early in embryogenesis by the inheritance of maternal determinants in the cytoplasm of the oocyte ('preformation' or selected later in embryonic development from undifferentiated precursors by a localized inductive signal ('epigenesis'. Here we investigate the specification and development of the germ cells in the rotifer Brachionus plicatilis, a member of the poorly-characterized superphyla Lophotrochozoa, by isolating the Brachionus homologues of the conserved germ cell markers vasa and nanos, and examining their expression using in situ hybridization. Results Bpvasa and Bpnos RNA expression have very similar distributions in the Brachionus ovary, showing ubiquitous expression in the vitellarium, with higher levels in the putative germ cell cluster. Bpvas RNA expression is present in freshly laid eggs, remaining ubiquitous in embryos until at least the 96 cell stage after which expression narrows to a small cluster of cells at the putative posterior of the embryo, consistent with the developing ovary. Bpnos RNA expression is also present in just-laid eggs but expression is much reduced by the four-cell stage and absent by the 16-cell stage. Shortly before hatching of the juvenile rotifer from the egg, Bpnos RNA expression is re-activated, located in a subset of posterior cells similar to those expressing Bpvas at the same stage. Conclusions The observed expression of vasa and nanos in the developing B. plicatilis embryo implies an epigenetic origin of primordial germ cells in Rotifer.

Hydraulic structures

CERN Document Server

Chen, Sheng-Hong

2015-01-01

This book discusses in detail the planning, design, construction and management of hydraulic structures, covering dams, spillways, tunnels, cut slopes, sluices, water intake and measuring works, ship locks and lifts, as well as fish ways. Particular attention is paid to considerations concerning the environment, hydrology, geology and materials etc. in the planning and design of hydraulic projects. It also considers the type selection, profile configuration, stress/stability calibration and engineering countermeasures, flood releasing arrangements and scouring protection, operation and maintenance etc. for a variety of specific hydraulic structures. The book is primarily intended for engineers, undergraduate and graduate students in the field of civil and hydraulic engineering who are faced with the challenges of extending our understanding of hydraulic structures ranging from traditional to groundbreaking, as well as designing, constructing and managing safe, durable hydraulic structures that are economical ...

Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

Science.gov (United States)

Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

2017-01-25

The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

A convenient method to synthesize specifically labelled cholesterol with tritium

International Nuclear Information System (INIS)

Malik, S.; Kenny, M.; Ahmad, S.; Washington Univ., Seattle, WA

1992-01-01

A simple method is described to label cholesterol with tritium. Cholesterol was first oxidized to 5-cholesten-3-one which was then purified by HPLC. Its structure was established by electron impact (EI) mass spectrometry and 1 H-NMR spectroscopy. The ketone was reduced with NaB 3 H 4 to give specifically labelled cholesterol (C-3 3 H) at low specific activity. (author)

Role of tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase.

Science.gov (United States)

Pennacchio, Angela; Esposito, Luciana; Zagari, Adriana; Rossi, Mosè; Raia, Carlo A

2009-09-01

A mutant of the thermostable NAD(+)-dependent (S)-stereospecific alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) which has a single substitution, Trp95Leu, located at the substrate binding pocket, was fully characterized to ascertain the role of Trp95 in discriminating between chiral secondary alcohols suggested by the wild-type SsADH crystallographic structure. The Trp95Leu mutant displays no apparent activity with short-chain primary and secondary alcohols and poor activity with aromatic substrates and coenzyme. Moreover, the Trp --> Leu substitution affects the structural stability of the archaeal ADH, decreasing its thermal stability without relevant changes in secondary structure. The double mutant Trp95Leu/Asn249Tyr was also purified to assist in crystallographic analysis. This mutant exhibits higher activity but decreased affinity toward aliphatic alcohols, aldehydes as well as NAD(+) and NADH compared to the wild-type enzyme. The crystal structure of the Trp95Leu/Asn249Tyr mutant apo form, determined at 2.0 A resolution, reveals a large local rearrangement of the substrate site with dramatic consequences. The Leu95 side-chain conformation points away from the catalytic metal center and the widening of the substrate site is partially counteracted by a concomitant change of Trp117 side chain conformation. Structural changes at the active site are consistent with the reduced activity on substrates and decreased coenzyme binding.

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

Science.gov (United States)

Trudell, James R.; Harris, R. Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

Structural biophysics

International Nuclear Information System (INIS)

Anon.

1979-01-01

Summaries of research projects conducted during 1978 and 1979 are presented. The structural biophysics group explores the high-resolution structure of biological macromolecules and cell organelles. Specific subject areas include: the basic characteristics of photosynthesis in plants; the chemical composition of individual fly ash particles at the site of their damaging action in tissues; direct analysis of frozen-hydrated biological samples by scanning electron microscopy; yeast genetics; the optical activity of DNA aggregates; measurement and characterization of lipoproteins; function of lipoproteins; and the effect of radiation and pollutants on mammalian cells

Crystal Structure of the 23S rRNA Fragment Specific to r-Protein L1 and Designed Model of the Ribosomal L1 Stalk from Haloarcula marismortui

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Azat Gabdulkhakov

2017-02-01

Full Text Available The crystal structure of the 92-nucleotide L1-specific fragment of 23S rRNA from Haloarcula marismortui (Hma has been determined at 3.3 Å resolution. Similar to the corresponding bacterial rRNA fragments, this structure contains joined helix 76-77 topped by an approximately globular structure formed by the residual part of the L1 stalk rRNA. The position of HmaL1 relative to the rRNA was found by its docking to the rRNA fragment using the L1-rRNA complex from Thermus thermophilus as a guide model. In spite of the anomalous negative charge of the halophilic archaeal protein, the conformation of the HmaL1-rRNA interface appeared to be very close to that observed in all known L1-rRNA complexes. The designed structure of the L1 stalk was incorporated into the H. marismortui 50S ribosomal subunit. Comparison of relative positions of L1 stalks in 50S subunits from H. marismortui and T. thermophilus made it possible to reveal the site of inflection of rRNA during the ribosome function.

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions.

Science.gov (United States)

Nagao, Chioko; Izako, Nozomi; Soga, Shinji; Khan, Samia Haseeb; Kawabata, Shigeki; Shirai, Hiroki; Mizuguchi, Kenji

2012-10-01

Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a "structure-based specificity determining position (sbSDP)" as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Copyright © 2012 Wiley Periodicals, Inc.

Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters

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GEORGE eDIALLINAS

2014-09-01

Full Text Available Transporters are ubiquitous proteins mediating the translocation of solutes across cell membranes, a biological process involved in nutrition, signaling, neurotransmission, cell communication and drug uptake or efflux. Similarly to enzymes, most transporters have a single substrate binding-site and thus their activity follows Michaelis-Menten kinetics. Substrate binding elicits a series of structural changes, which produce a transporter conformer open towards the side opposite to the one from where the substrate was originally bound. This mechanism, involving alternate outward- and inward-facing transporter conformers, has gained significant support from structural, genetic, biochemical and biophysical approaches. Most transporters are specific for a given substrate or a group of substrates with similar chemical structure, but substrate specificity and/or affinity can vary dramatically, even among members of a transporter family that show high overall amino acid sequence and structural similarity. The current view is that transporter substrate affinity or specificity is determined by a small number of interactions a given solute can make within a specific binding site. However, genetic, biochemical and in silico modeling studies with the purine transporter UapA of the filamentous ascomycete Aspergillus nidulans have challenged this dogma. This review highlights results leading to a novel concept, stating that substrate specificity, but also transport kinetics and transporter turnover, are determined by subtle intramolecular interactions between a major substrate binding site and independent outward- or cytoplasmically-facing gating domains, analogous to those present in channels. This concept is supported by recent structural evidence from several, phylogenetically and functionally distinct transporter families. The significance of this concept is discussed in relationship to the role and potential exploitation of transporters in drug action.

Specific features of the flow structure in a reactive type turbine stage

Science.gov (United States)

Chernikov, V. A.; Semakina, E. Yu.

2017-04-01

The results of experimental studies of the gas dynamics for a reactive type turbine stage are presented. The objective of the studies is the measurement of the 3D flow fields in reference cross sections, experimental determination of the stage characteristics, and analysis of the flow structure for detecting the sources of kinetic energy losses. The integral characteristics of the studied stage are obtained by averaging the results of traversing the 3D flow over the area of the reference cross sections before and behind the stage. The averaging is performed using the conservation equations for mass, total energy flux, angular momentum with respect to the axis z of the turbine, entropy flow, and the radial projection of the momentum flux equation. The flow parameter distributions along the channel height behind the stage are obtained in the same way. More thorough analysis of the flow structure is performed after interpolation of the experimentally measured point parameter values and 3D flow velocities behind the stage. The obtained continuous velocity distributions in the absolute and relative coordinate systems are presented in the form of vector fields. The coordinates of the centers and the vectors of secondary vortices are determined using the results of point measurements of velocity vectors in the cross section behind the turbine stage and their subsequent interpolation. The approach to analysis of experimental data on aerodynamics of the turbine stage applied in this study allows one to find the detailed space structure of the working medium flow, including secondary coherent vortices at the root and peripheral regions of the air-gas part of the stage. The measured 3D flow parameter fields and their interpolation, on the one hand, point to possible sources of increased power losses, and, on the other hand, may serve as the basis for detailed testing of CFD models of the flow using both integral and local characteristics. The comparison of the numerical and

Novel Mechanism of Fatty Acid Sensing in Enteroendocrine Cells: Specific Structures in Oxo-Fatty Acids Produced by Gut Bacteria are Responsible for CCK Secretion in STC-1 Cells via GPR40.

Science.gov (United States)

Hira, Tohru; Ogasawara, Shono; Yahagi, Asuka; Kamachi, Minami; Li, Jiaxin; Nishimura, Saki; Sakaino, Masayoshi; Yamashita, Takatoshi; Kishino, Shigenobu; Ogawa, Jun; Hara, Hiroshi

2018-06-25

The secretion of gut hormones, such as cholecystokinin (CCK) is stimulated by fatty acids. Although a chain length-dependent mechanism has been proposed, other structural relationships to releasing activity remain unclear. We aimed to elucidate specific structures in fatty acids that are responsible for their CCK-releasing activity, and related sensing mechanisms in enteroendocrine cells. We examined CCK secretory activities in a murine CCK-producing cell line STC-1 by exposing the cells to various modified fatty acids produced by gut lactic acid bacteria. The effects of fatty acids on gastric emptying rate as a CCK-mediated function were examined using acetaminophen- and phenol red-methods in rats. Out of more than thirty octadecanoic (C18)-derived fatty acids tested, five oxo-fatty acids potently stimulated CCK secretion without cytotoxic effects in STC-1 cells. Three fatty acids had a distinct specific structure containing one double-bond, whereas the other two had two double-bonds, nearby an oxo residue. CCK secretion induced by representative fatty acids (10-oxo-trans-11-18:1 and 13-oxo-cis-9,cis-15-18:2) was attenuated by a fatty acid-receptor GPR40 antagonist. Oral administration of 13-oxo-cis-9,cis-15-18:2 lowered the gastric emptying rate in rats in a dose- and structure-dependent manner. These results revealed a novel fatty acid-sensing mechanism in enteroendocrine cells. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Generalized structured component analysis a component-based approach to structural equation modeling

CERN Document Server

Hwang, Heungsun

2014-01-01

Winner of the 2015 Sugiyama Meiko Award (Publication Award) of the Behaviormetric Society of Japan Developed by the authors, generalized structured component analysis is an alternative to two longstanding approaches to structural equation modeling: covariance structure analysis and partial least squares path modeling. Generalized structured component analysis allows researchers to evaluate the adequacy of a model as a whole, compare a model to alternative specifications, and conduct complex analyses in a straightforward manner. Generalized Structured Component Analysis: A Component-Based Approach to Structural Equation Modeling provides a detailed account of this novel statistical methodology and its various extensions. The authors present the theoretical underpinnings of generalized structured component analysis and demonstrate how it can be applied to various empirical examples. The book enables quantitative methodologists, applied researchers, and practitioners to grasp the basic concepts behind this new a...

Reasoning About Higher-Order Relational Specifications

OpenAIRE

Wang , Yuting; Chaudhuri , Kaustuv; Gacek , Andrew; Nadathur , Gopalan

2013-01-01

International audience; The logic of hereditary Harrop formulas (HH) has proven useful for specifying a wide range of formal systems. This logic includes a form of hypothetical judgment that leads to dynamically changing sets of assumptions and that is key to encoding side conditions and contexts that occur frequently in structural operational semantics (SOS) style presentations. Specifications are often useful in reasoning about the systems they describe. The Abella theorem prover supports s...