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Sample records for binding profile study

  1. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  2. Computational studies of the binding profile of phosphoinositide PtdIns (3,4,5) P3 with the pleckstrin homology domain of an oomycete cellulose synthase

    Science.gov (United States)

    Kuang, Guanglin; Bulone, Vincent; Tu, Yaoquan

    2016-02-01

    Saprolegnia monoica is a model organism to investigate Saprolegnia parasitica, an important oomycete which causes considerable loss in aquaculture every year. S. monoica contains cellulose synthases vital for oomycete growth. However, the molecular mechanism of the cellulose biosynthesis process in the oomycete growth is still poorly understood. Some cellulose synthases of S. monoica, such as SmCesA2, are found to contain a plecsktrin homology (PH) domain, which is a protein module widely found in nature and known to bind to phosphoinositides, a class of signaling compounds involved in many biological processes. Understanding the molecular interactions between the PH domain and phosphoinositides would help to unravel the cellulose biosynthesis process of oomycetes. In this work, the binding profile of PtdIns (3,4,5) P3, a typical phosphoinositide, with SmCesA2-PH was studied by molecular docking, molecular dynamics and metadynamics simulations. PtdIns (3,4,5) P3 is found to bind at a specific site located at β1, β2 and β1-β2 loop of SmCesA2-PH. The high affinity of PtdIns (3,4,5) P3 to SmCesA2-PH is contributed by the free phosphate groups, which have electrostatic and hydrogen-bond interactions with Lys88, Lys100 and Arg102 in the binding site.

  3. Concentration profiles of actin-binding molecules in lamellipodia

    Science.gov (United States)

    Falcke, Martin

    2016-04-01

    Motile cells form lamellipodia in the direction of motion, which are flat membrane protrusions containing an actin filament network. The network flows rearward relative to the leading edge of the lamellipodium due to actin polymerization at the front. Thus, actin binding molecules are subject to transport towards the rear of the cell in the bound state and diffuse freely in the unbound state. We analyze this reaction-diffusion-advection process with respect to the concentration profiles of these species and provide an analytic approximation for them. Network flow may cause a depletion zone of actin binding molecules close to the leading edge. The existence of such zone depends on the free molecule concentration in the cell body, on the ratio of the diffusion length to the distance bound molecules travel rearward with the flow before dissociating, and the ratio of the diffusion length to the width of the region with network flow and actin binding. Our calculations suggest the existence of depletion zones for the F-actin cross-linkers filamin and α-actinin in fish keratocytes (and other cell types), which is in line with the small elastic moduli of the F-actin network close to the leading edge found in measurements of the force motile cells are able to exert.

  4. Interaction of colloidal gold nanoparticles with human blood: effects on particle size and analysis of plasma protein binding profiles

    OpenAIRE

    Dobrovolskaia, Marina A.; Patri, Anil K.; Zheng, Jiwen; Clogston, Jeffrey D.; Ayub, Nader; Aggarwal, Parag; Neun, Barry W.; Hall, Jennifer B.; McNeil, Scott E.

    2008-01-01

    Nanoparticle size and plasma binding profile contribute to a particle’s longevity in the bloodstream, which can have important consequences for therapeutic efficacy. In this study an approximate doubling in nanoparticle hydrodynamic size was observed upon in vitro incubation of 30- and 50-nm colloidal gold in human plasma. Plasma proteins that bind the surface of citrate-stabilized gold colloids have been identified. Effects of protein binding on the nanoparticle hydrodynamic size, elements o...

  5. DNA binding studies of Vinca alkaloids: experimental and computational evidence.

    Science.gov (United States)

    Pandya, Prateek; Gupta, Surendra P; Pandav, Kumud; Barthwal, Ritu; Jayaram, B; Kumar, Surat

    2012-03-01

    Fluorescence studies on the indole alkaloids vinblastine sulfate, vincristine sulfate, vincamine and catharanthine have demonstrated the DNA binding ability of these molecules. The binding mode of these molecules in the minor groove of DNA is non-specific. A new parameter of the purine-pyrimidine base sequence specificty was observed in order to define the non-specific DNA binding of ligands. Catharanthine had shown 'same' pattern of 'Pu-Py' specificity while evaluating its DNA binding profile. The proton resonances of a DNA decamer duplex were assigned. The models of the drug:DNA complexes were analyzed for DNA binding features. The effect of temperature on the DNA binding was also evaluated. PMID:22545401

  6. JASPAR: an open-access database for eukaryotic transcription factor binding profiles

    OpenAIRE

    Sandelin, Albin; Alkema, Wynand; Engström, Pär; Wasserman, Wyeth W; Lenhard, Boris

    2004-01-01

    The analysis of regulatory regions in genome sequences is strongly based on the detection of potential transcription factor binding sites. The preferred models for representation of transcription factor binding specificity have been termed position-specific scoring matrices. JASPAR is an open-access database of annotated, high-quality, matrix-based transcription factor binding site profiles for multicellular eukaryotes. The profiles were derived exclusively from sets of nucleotide sequences e...

  7. Transcriptome Profiling of Pediatric Core Binding Factor AML.

    Directory of Open Access Journals (Sweden)

    Chih-Hao Hsu

    Full Text Available The t(8;21 and Inv(16 translocations disrupt the normal function of core binding factors alpha (CBFA and beta (CBFB, respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21 (N = 17, Inv(16 (N = 14, and normal karyotype (NK, N = 33 were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21 and 474 genes in Inv(16 were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test p-value < 10(-30 are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs differentially expressed across subtypes, with 337 t(8;21-specific and 407 Inv(16-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5 x 10(-51 and p = 1.8 x 10(-54 for the two subsets. In addition to known fusions, we identified and verified 16 de novo fusions in 43 patients, including three fusions involving NUP98 in six

  8. Profiling Protein Kinases and Other ATP Binding Proteins in Arabidopsis Using Acyl-ATP Probes*

    OpenAIRE

    Villamor, J. G.; Kaschani, F.; Colby, T; Oeljeklaus, J.; Zhao, D; Kaiser, M.; Patricelli, M. P.; R. A. L. van der Hoorn

    2013-01-01

    Many protein activities are driven by ATP binding and hydrolysis. Here, we explore the ATP binding proteome of the model plant Arabidopsis thaliana using acyl-ATP (AcATP)1 probes. These probes target ATP binding sites and covalently label lysine residues in the ATP binding pocket. Gel-based profiling using biotinylated AcATP showed that labeling is dependent on pH and divalent ions and can be competed by nucleotides. The vast majority of these AcATP-labeled proteins are known ATP binding prot...

  9. Isotope-coded ATP Probe for Quantitative Affinity Profiling of ATP-binding Proteins

    OpenAIRE

    Xiao, Yongsheng; Guo, Lei; Wang, Yinsheng

    2013-01-01

    ATP-binding proteins play significant roles in numerous cellular processes. Here, we introduced a novel isotope-coded ATP-affinity probe (ICAP) as acylating agent to simultaneously enrich and incorporate isotope label to ATP-binding proteins. By taking advantage of the quantitative capability of this isotope-coded probe, we devised an affinity profiling strategy to comprehensively characterize ATP-protein interactions at the entire proteome scale. False-positive identification of ATP-binding ...

  10. Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

    NARCIS (Netherlands)

    Wolters, Justina. C.; Roelfes, Johannes; Poolman, Bert

    2011-01-01

    Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to

  11. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    OpenAIRE

    Portales-Casamar, E; Thongjuea, S.; Kwon, A. T.; Arenillas, D.; Zhao, X; Valen, E.; Yusuf, D; Lenhard, B.; Wasserman, W. W.; Sandelin, A

    2010-01-01

    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177...

  12. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) study

    KAUST Repository

    Hägg, Sara

    2009-12-04

    Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD). The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE) study was to determine whether there are functionally associated genes (rather than individual genes) important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n =66/tissue) and atherosclerotic and unaffected arterial wall (n =40/tissue) isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n =15,042/12,621 RefSeqs/genes) in each tissue, resulted in a total of 60 tissue clusters (n= 3958 genes). In the second step (performed within tissue clusters), one atherosclerotic lesion (n =49/48) and one visceral fat (n =59) cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P=0.008 and P=0.00015). The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n =55/54) relating to carotid stenosis (P =0.04), 27 genes in the two clusters relating to coronary stenosis were confirmed (n= 16/17, P<10 -27and-30). Genes in the transendothelial migration of leukocytes (TEML) pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module). In a second validation step, using three independent cohorts, the Amodule was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004). The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the

  13. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

    OpenAIRE

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J.; Chen, Chih-Yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W.; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

    2016-01-01

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in f...

  14. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

    OpenAIRE

    Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W.; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J.; Buchman, Sorana; Chen, Chih-Yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris

    2013-01-01

    JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR—the JASPAR CORE subcollection, which contains curated, non-redundant profiles—with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and ...

  15. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T;

    2009-01-01

    active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A......JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database...

  16. Distinct expression and ligand-binding profiles of two constitutively active GPR17 splice variants

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, M M

    2010-01-01

    In humans and non-human primates, the 7TM receptor GPR17 exists in two isoforms differing only by the length of the N-terminus. Of these, only the short isoform has previously been characterized. Hence, we investigated gene expression and ligand-binding profiles of both splice variants and furthe...

  17. Free-energy-based methods for binding profile determination in a congeneric series of CDK2 inhibitors.

    Science.gov (United States)

    Fidelak, Jérémy; Juraszek, Jarek; Branduardi, Davide; Bianciotto, Marc; Gervasio, Francesco Luigi

    2010-07-29

    Free-energy pathway methods show great promise in computing the mode of action and the free energy profile associated with the binding of small molecules with proteins, but are generally very computationally demanding. Here we apply a novel approach based on metadynamics and path collective variables. We show that this combination is able to find an optimal reaction coordinate and the free energy profile of binding with explicit solvent and full flexibility, while minimizing human intervention and computational costs. We apply it to predict the binding affinity of a congeneric series of 5 CDK2 inhibitors. The predicted binding free energy profiles are in accordance with experiment. PMID:20593892

  18. Adventitious match probability for autosomal profiles when primer binding site mutation is possible.

    Science.gov (United States)

    Pope, Susan; Evett, Ian; Puch-Solis, Roberto

    2016-09-01

    This paper considers the situation where two DNA systems with differing primers have been used to produce DNA profiles for loading and searching of a DNA Database. With any profiling system there exists the possibility of a "primer binding site mutation" (PBSM). When such a mutation occurs at one of the loci in a profile, it has the effect that the associated allele is not visible in the profile. In the case where a person has two different alleles at a given locus (heterozygous) the effect of a PBSM would be that the profile would appear to be that of an individual with only one allele at that locus (homozygous). The paper investigates the potential for an adventitious match as a result of a PBSM when, for example, a crime profile and person profile that have originated from two different individuals are found to be the same as a result of a PBSM in one of the profiles. It is demonstrated, both by theory and using simulations, that the effect of PBSMs is to slightly decrease the adventitious match probability from what it would had the same DNA system been used. PMID:27420391

  19. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J;

    2016-01-01

    expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous...

  20. MBPpred: Proteome-wide detection of membrane lipid-binding proteins using profile Hidden Markov Models.

    Science.gov (United States)

    Nastou, Katerina C; Tsaousis, Georgios N; Papandreou, Nikos C; Hamodrakas, Stavros J

    2016-07-01

    A large number of modular domains that exhibit specific lipid binding properties are present in many membrane proteins involved in trafficking and signal transduction. These domains are present in either eukaryotic peripheral membrane or transmembrane proteins and are responsible for the non-covalent interactions of these proteins with membrane lipids. Here we report a profile Hidden Markov Model based method capable of detecting Membrane Binding Proteins (MBPs) from information encoded in their amino acid sequence, called MBPpred. The method identifies MBPs that contain one or more of the Membrane Binding Domains (MBDs) that have been described to date, and further classifies these proteins based on their position in respect to the membrane, either as peripheral or transmembrane. MBPpred is available online at http://bioinformatics.biol.uoa.gr/MBPpred. This method was applied in selected eukaryotic proteomes, in order to examine the characteristics they exhibit in various eukaryotic kingdoms and phyla. PMID:27048983

  1. 'Perfectly' curvilinear profiles for binding as determined by ITC may in fact be multiphasic

    CERN Document Server

    Nissen, Per

    2016-01-01

    In a structural analysis of the proteasome activator PafE in Mycobacterium tuberculosis, the binding of the activator or shorter constructs to the 20S proteasome core particle (20S CP) or derivatives was measured by isothermal titration calorimetry (Bai et al. Proc Natl Acad Sci USA 113: E1983-E1992. 2016). The data were fitted by the authors by nonlinear least squares to give curvilinear profiles that, at least in part, appear to fit the data very well. However, reanalysis of the data shows that the profiles are much better (P < 0.001) represented as multiphasic, i.e. by a series of straight lines separated by discontinuous transitions, often in the form jumps, than by the conventional curvilinear profiles.

  2. Studies in neutron depth profiling

    International Nuclear Information System (INIS)

    This paper describes first the application of neutron depth profiling (NDP) for measuring the distribution of 6Li in LiAlO2 ceramics. Using a surface barrier detector for detecting 3H produced in 6Li(n, α)3H, 6Li was profiled to a depth of 14 μm in the ceramics. Secondly, a new methodology is presented for NDP with enhanced capabilities based on measuring the energy of recoiling nuclei from (n, p) and (n, α) reactions by time-of-flight mass spectrometry. The scope of recoil nucleus time-of-flight mass spectrometry (RN-TOF-MS) includes profiling of 10B, 14N, 17O, 33S, 35Cl, 40K. Probe depths may be of a few tens nanometers. RN-TOF-MS complements and refines NDP based on charged particle (p or α) spectrometry. (author) 7 refs.; 6 figs.; 1 tab

  3. DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation

    Science.gov (United States)

    Liu, Bin; Wang, Shanyi; Wang, Xiaolong

    2015-10-01

    DNA-binding proteins play an important role in most cellular processes. Therefore, it is necessary to develop an efficient predictor for identifying DNA-binding proteins only based on the sequence information of proteins. The bottleneck for constructing a useful predictor is to find suitable features capturing the characteristics of DNA binding proteins. We applied PseAAC to DNA binding protein identification, and PseAAC was further improved by incorporating the evolutionary information by using profile-based protein representation. Finally, Combined with Support Vector Machines (SVMs), a predictor called iDNAPro-PseAAC was proposed. Experimental results on an updated benchmark dataset showed that iDNAPro-PseAAC outperformed some state-of-the-art approaches, and it can achieve stable performance on an independent dataset. By using an ensemble learning approach to incorporate more negative samples (non-DNA binding proteins) in the training process, the performance of iDNAPro-PseAAC was further improved. The web server of iDNAPro-PseAAC is available at http://bioinformatics.hitsz.edu.cn/iDNAPro-PseAAC/.

  4. Reversible Albumin-Binding GH Possesses a Potential Once-Weekly Treatment Profile in Adult Growth Hormone Deficiency

    DEFF Research Database (Denmark)

    Rasmussen, Michael Højby; Janukonyté, Jurgita; Klose, Marianne;

    2016-01-01

    CONTEXT: NNC0195-0092 is a reversible, albumin-binding GH derivative, developed for once-weekly administration. OBJECTIVES: The objective of the study was to evaluate safety, local tolerability, pharmacodynamics, and pharmacokinetics of multiple, once-weekly doses of NNC0195-0092, compared with...... daily GH. DESIGN AND SETTING: This was a phase 1, randomized, open-label, active-controlled, multiple-dose, dose-escalation trial. PATIENTS: Thirty-four GH-treated adult subjects (male, n = 25) with GH deficiency participated in the study. INTERVENTIONS AND MAIN OUTCOME MEASURES: Subjects were...... assessment was performed prior to initiating treatment at the next dose level of NNC0195-0092. Daily GH treatment was discontinued 14 days before the trial start. Blood samples were drawn for assessment of safety, pharmacokinetics, pharmacodynamics (IGF-1 and IGF-binding protein-3) profiles, and...

  5. Teachers' Entrepreneurial Profile: Case Study

    Science.gov (United States)

    Stettiner, Caio Flavio; Formigoni, Alexandre; Filho, Mário Pereira Roque; de Camargo, Mauricio Ortiz; Moia, Roberto Padilha

    2015-01-01

    This article was prepared in order to investigate whether the teachers working in a Business Administration BA degree have an entrepreneurial profile, with the aim of finding whether such teachers are able to support the Pedagogical Proposal of the Institution to which they belong to in what concerns the requirement of the course and also the…

  6. Receptor binding studies of soft anticholinergic agents

    OpenAIRE

    Huang, Fenglei; Buchwald, Peter; Browne, Clinton E.; Farag, Hassan H.; Wu, Wnei-Mei; Ji, Fubao; Hochhaus, Guenther; Bodor, Nicholas

    2001-01-01

    Receptor binding studies were performed on 24 soft anticholinergic agents and 5 conventional anticholinergic agents using 4 cloned human muscarinic receptor subtypes. The measured pKi values of the soft anticholinergic agents ranged from 6.5 to 9.5, with the majority being in the range of 7.5 to 8.5. Strong correlation was observed between the pKis determined here and the pA2 values measured earlier in guinea pig ileum contraction assays. The corresponding correlation coefficients (r2) were 0...

  7. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

    Science.gov (United States)

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J; Chen, Chih-Yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

    2016-01-01

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. PMID:26531826

  8. Toxicity and Binding Profile of Lectins from the Genus Canavalia on Brine Shrimp

    OpenAIRE

    Francisco Vassiliepe Sousa Arruda; Arthur Alves Melo; Mayron Alves de Vasconcelos; Romulo Farias Carneiro; Ito Liberato Barroso-Neto; Suzete Roberta Silva; Francisco Nascimento Pereira-Junior; Celso Shiniti Nagano; Kyria Santiago Nascimento; Edson Holanda Teixeira; Silvana Saker-Sampaio; Benildo Sousa Cavada; Alexandre Holanda Sampaio

    2013-01-01

    Lectins are sugar-binding proteins widely distributed in nature with many biological functions. Although many lectins have a remarkable biotechnological potential, some of them can be cytotoxic. Thus, the aim of this study was to assess the toxicity of five lectins, purified from seeds of different species of Canavalia genus. In order to determine the toxicity, assays with Artemia nauplii were performed. In addition, a fluorescence assay was carried out to evaluate the binding of lectins to A...

  9. Lectin binding profiles of SSEA-4 enriched, pluripotent human embryonic stem cell surfaces

    Directory of Open Access Journals (Sweden)

    Shin Soojung

    2005-07-01

    Full Text Available Abstract Background Pluripotent human embryonic stem cells (hESCs have the potential to form every cell type in the body. These cells must be appropriately characterized prior to differentiation studies or when defining characteristics of the pluripotent state. Some developmentally regulated cell surface antigens identified by monoclonal antibodies in a variety of species and stem cell types have proven to be side chains of membrane glycolipids and glycoproteins. Therefore, to examine hESC surfaces for other potential pluripotent markers, we used a panel of 14 lectins, which were chosen based on their specificity for a variety of carbohydrates and carbohydrate linkages, along with stage specific embryonic antigen-4 (SSEA-4, to determine binding quantitation by flow cytometry and binding localization in adherent colonies by immunocytochemistry. Results Enriching cells for SSEA-4 expression increased the percentage of SSEA-4 positive cells to 98–99%. Using enriched high SSEA-4-expressing hESCs, we then analyzed the binding percentages of selected lectins and found a large variation in binding percentages ranging from 4% to 99% binding. Lycopersicon (tomatoesculetum lectin (TL, Ricinus communis agglutinin (RCA, and Concanavalin A (Con A bound to SSEA-4 positive regions of hESCs and with similar binding percentages as SSEA-4. In contrast, we found Dolichos biflorus agglutinin (DBA and Lotus tetragonolobus lectin (LTL did not bind to hESCs while Phaseolus vulgaris leuco-agglutinin (PHA-L, Vicia villosa agglutinin (VVA, Ulex europaeus agglutinin (UEA, Phaseolus vulgaris erythro-agglutinin (PHA-E, and Maackia amurensis agglutinin (MAA bound partially to hESCs. These binding percentages correlated well with immunocytochemistry results. Conclusion Our results provide information about types of carbohydrates and carbohydrate linkages found on pluripotent hESC surfaces. We propose that TL, RCA and Con A may be used as markers that are associated with the

  10. Genome-wide profiling of YY1 binding sites during skeletal myogenesis

    Directory of Open Access Journals (Sweden)

    Kun Sun

    2014-12-01

    Full Text Available Skeletal muscle differentiation is regulated by a network of transcription factors, epigenetic regulators and noncoding RNAs. We have recently performed ChIP-seq experiments to explore the genome-wide binding of transcription factor YY1 in skeletal muscle cells. Our results identified thousands of YY1 binding peaks, underscoring its multifaceted functions in muscle cells. In particular, we identified a very high proportion of YY1 binding peaks residing in the intergenic regions, which led to the discovery of some novel lincRNAs under YY1 regulation. Here we describe the details of the ChIP-seq experiments and data analysis procedures associated with the study published by Lu et al. in the EMBO Journal in 2013 [1].

  11. Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study

    International Nuclear Information System (INIS)

    The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented

  12. Quantum confined Stark effect in Gaussian quantum wells: A tight-binding study

    Energy Technology Data Exchange (ETDEWEB)

    Ramírez-Morales, A.; Martínez-Orozco, J. C.; Rodríguez-Vargas, I. [Unidad Académica de Física, Universidad Autónoma de Zacatecas, Calzada Solidaridad Esquina Con Paseo La Bufa S/N, 98060 Zacatecas, Zac. (Mexico)

    2014-05-15

    The main characteristics of the quantum confined Stark effect (QCSE) are studied theoretically in quantum wells of Gaussian profile. The semi-empirical tight-binding model and the Green function formalism are applied in the numerical calculations. A comparison of the QCSE in quantum wells with different kinds of confining potential is presented.

  13. Transcriptional Profiling of a Selective CREB Binding Protein Bromodomain Inhibitor Highlights Therapeutic Opportunities.

    Science.gov (United States)

    Chekler, Eugene L Piatnitski; Pellegrino, Jessica A; Lanz, Thomas A; Denny, R Aldrin; Flick, Andrew C; Coe, Jotham; Langille, Jonathan; Basak, Arindrajit; Liu, Shenping; Stock, Ingrid A; Sahasrabudhe, Parag; Bonin, Paul D; Lee, Kevin; Pletcher, Mathew T; Jones, Lyn H

    2015-12-17

    Bromodomains are involved in transcriptional regulation through the recognition of acetyl lysine modifications on diverse proteins. Selective pharmacological modulators of bromodomains are lacking, although the largely hydrophobic nature of the pocket makes these modules attractive targets for small-molecule inhibitors. This work describes the structure-based design of a highly selective inhibitor of the CREB binding protein (CBP) bromodomain and its use in cell-based transcriptional profiling experiments. The inhibitor downregulated a number of inflammatory genes in macrophages that were not affected by a selective BET bromodomain inhibitor. In addition, the CBP bromodomain inhibitor modulated the mRNA level of the regulator of G-protein signaling 4 (RGS4) gene in neurons, suggesting a potential therapeutic opportunity for CBP inhibitors in the treatment of neurological disorders. PMID:26670081

  14. Biochemical profiling of histone binding selectivity of the yeast bromodomain family.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available BACKGROUND: It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has limited our understanding of histone binding selectivity of the bromodomain family. Here, we report a systematic family-wide analysis of 14 yeast bromodomains binding to 32 lysine-acetylated peptides derived from known major acetylation sites in four core histones that are conserved in eukaryotes. METHODOLOGY: The histone binding selectivity of purified recombinant yeast bromodomains was assessed by using the native core histones in an overlay assay, as well as N-terminally biotinylated lysine-acetylated histone peptides spotted on streptavidin-coated nitrocellulose membrane in a dot blot assay. NMR binding analysis further validated the interactions between histones and selected bromodomain. Structural models of all yeast bromodomains were built using comparative modeling to provide insights into the molecular basis of their histone binding selectivity. CONCLUSIONS: Our study reveals that while not all members of the bromodomain family are privileged to interact with acetylated-lysine, identifiable sequence features from those that bind histone emerge. These include an asparagine residue at the C-terminus of the third helix in the 4-helix bundle, negatively charged residues around the ZA loop, and preponderance of aromatic

  15. Receptor binding studies of the living heart

    International Nuclear Information System (INIS)

    Receptors form a class of intrinsic membrane proteins (or glycoproteins) defined by the high affinity and specificity with which they bind ligands. Many receptors are associated directly or indirectly with membrane ion channels that open or close after a conformational change of the receptor induced by the binding of the neurotransmitter. Changes in number and/or affinity of cardiac neurotransmitter receptors have been associated with myocardial ischemia and infarction, congestive heart failure, and cardiomyopathy as well as diabetes or thyroid-induced heart muscle disease. These alterations of cardiac receptors have been demonstrated in vitro on membrane homogenates from samples collected mainly during surgery or postmortem. The disadvantage of these in vitro binding techniques is that receptors lose their natural environment and their relationships with the other components of the tissue

  16. In silico mechanistic profiling to probe small molecule binding to sulfotransferases.

    Directory of Open Access Journals (Sweden)

    Virginie Y Martiny

    Full Text Available Drug metabolizing enzymes play a key role in the metabolism, elimination and detoxification of xenobiotics, drugs and endogenous molecules. While their principal role is to detoxify organisms by modifying compounds, such as pollutants or drugs, for a rapid excretion, in some cases they render their substrates more toxic thereby inducing severe side effects and adverse drug reactions, or their inhibition can lead to drug-drug interactions. We focus on sulfotransferases (SULTs, a family of phase II metabolizing enzymes, acting on a large number of drugs and hormones and showing important structural flexibility. Here we report a novel in silico structure-based approach to probe ligand binding to SULTs. We explored the flexibility of SULTs by molecular dynamics (MD simulations in order to identify the most suitable multiple receptor conformations for ligand binding prediction. Then, we employed structure-based docking-scoring approach to predict ligand binding and finally we combined the predicted interaction energies by using a QSAR methodology. The results showed that our protocol successfully prioritizes potent binders for the studied here SULT1 isoforms, and give new insights on specific molecular mechanisms for diverse ligands' binding related to their binding sites plasticity. Our best QSAR models, introducing predicted protein-ligand interaction energy by using docking, showed accuracy of 67.28%, 78.00% and 75.46%, for the isoforms SULT1A1, SULT1A3 and SULT1E1, respectively. To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility, along with a QSAR approach, to identify small molecules that can interact with II phase dug metabolizing enzymes.

  17. AFM studies of nonspecific binding of enzyme on DNA

    Institute of Scientific and Technical Information of China (English)

    张益; 谢恒月; 等

    1996-01-01

    Atomic force microscope(AFM) is used to study restriction endonuclease digestion of plasmid DNA,pWRr plasmid DNA is digested by Hind Ⅲ,and the specific and the nonspecific binding of the restriction endonuclease are imaged,and the biological function of the enzyme binding to nonspecific sites is discussed.In addition,it is found that nonspecific binding of Hind ǚ could not induce the DNA characteristic bending angle.

  18. Evaluation of intestinal phosphate binding to improve the safety profile of oral sodium phosphate bowel cleansing.

    Directory of Open Access Journals (Sweden)

    Stef Robijn

    Full Text Available Prior to colonoscopy, bowel cleansing is performed for which frequently oral sodium phosphate (OSP is used. OSP results in significant hyperphosphatemia and cases of acute kidney injury (AKI referred to as acute phosphate nephropathy (APN; characterized by nephrocalcinosis are reported after OSP use, which led to a US-FDA warning. To improve the safety profile of OSP, it was evaluated whether the side-effects of OSP could be prevented with intestinal phosphate binders. Hereto a Wistar rat model of APN was developed. OSP administration (2 times 1.2 g phosphate by gavage with a 12h time interval induced bowel cleansing (severe diarrhea and significant hyperphosphatemia (21.79 ± 5.07 mg/dl 6h after the second OSP dose versus 8.44 ± 0.97 mg/dl at baseline. Concomitantly, serum PTH levels increased fivefold and FGF-23 levels showed a threefold increase, while serum calcium levels significantly decreased from 11.29 ± 0.53 mg/dl at baseline to 8.68 ± 0.79 mg/dl after OSP. OSP administration induced weaker NaPi-2a staining along the apical proximal tubular membrane. APN was induced: serum creatinine increased (1.5 times baseline and nephrocalcinosis developed (increased renal calcium and phosphate content and calcium phosphate deposits on Von Kossa stained kidney sections. Intestinal phosphate binding (lanthanum carbonate or aluminum hydroxide was not able to attenuate the OSP induced side-effects. In conclusion, a clinically relevant rat model of APN was developed. Animals showed increased serum phosphate levels similar to those reported in humans and developed APN. No evidence was found for an improved safety profile of OSP by using intestinal phosphate binders.

  19. Flavonoid-DNA binding studies and thermodynamic parameters

    Science.gov (United States)

    Janjua, Naveed Kausar; Shaheen, Amber; Yaqub, Azra; Perveen, Fouzia; Sabahat, Sana; Mumtaz, Misbah; Jacob, Claus; Ba, Lalla Aicha; Mohammed, Hamdoon A.

    2011-09-01

    Interactional studies of new flavonoid derivatives (Fl) with chicken blood ds.DNA were investigated spectrophotometrically in DMSO-H 2O (9:1 v/v) at various temperatures. Spectral parameters suggest considerable binding between the flavonoid derivatives studied and ds.DNA. The binding constant values lie in the enhanced-binding range. Thermodynamic parameters obtained from UV studies also point to strong spontaneous binding of Fl with ds.DNA. Viscometric studies complimented the UV results where a small linear increase in relative viscosity of the DNA solution was observed with added optimal flavonoid concentration. An overall mixed mode of interaction (intercalative plus groove binding) is proposed between DNA and flavonoids. Conclusively, investigated flavonoid derivatives are found to be strong DNA binders and seem to be promising drug candidates like their natural analogues.

  20. Cellular studies of binding, internalization and retention of a radiolabeled EGFR-binding affibody molecule

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Erika [Rudbeck Laboratory, Department of Oncology, Radiology and Clinical Immunology, Biomedical Radiation Sciences, Uppsala University, SE-751 85 Uppsala (Sweden)], E-mail: erika.nordberg@bms.uu.se; Friedman, Mikaela [Department of Molecular Biotechnology, AlbaNova University Center, Kungl Tekniska Hoegskolan (KTH), SE-106 91 Stockholm (Sweden); Goestring, Lovisa [Rudbeck Laboratory, Department of Oncology, Radiology and Clinical Immunology, Biomedical Radiation Sciences, Uppsala University, SE-751 85 Uppsala (Sweden); Affibody AB, PO Box 20137, SE-161 02 Bromma (Sweden); Adams, Gregory P. [Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111 (United States); Brismar, Hjalmar [Department of Cell Physics, AlbaNova University Center, Kungl Tekniska Hoegskolan (KTH), SE-106 91 Stockholm (Sweden); Nilsson, Fredrik Y. [Rudbeck Laboratory, Department of Oncology, Radiology and Clinical Immunology, Biomedical Radiation Sciences, Uppsala University, SE-751 85 Uppsala (Sweden); Affibody AB, PO Box 20137, SE-161 02 Bromma (Sweden); Stahl, Stefan [Department of Molecular Biotechnology, AlbaNova University Center, Kungl Tekniska Hoegskolan (KTH), SE-106 91 Stockholm (Sweden); Glimelius, Bengt [Rudbeck Laboratory, Oncology, Radiology and Clinical Immunology, Uppsala University, SE-751 85 Uppsala (Sweden); Carlsson, Joergen [Rudbeck Laboratory, Department of Oncology, Radiology and Clinical Immunology, Biomedical Radiation Sciences, Uppsala University, SE-751 85 Uppsala (Sweden)

    2007-08-15

    Introduction: The cellular binding and processing of an epidermal growth factor receptor (EGFR) targeting affibody molecule, (Z{sub EGFR:955}){sub 2}, was studied. This new and small molecule is aimed for applications in nuclear medicine. The natural ligand epidermal growth factor (EGF) and the antibody cetuximab were studied for comparison. Methods: All experiments were made with cultured A431 squamous carcinoma cells. Receptor specificity, binding time patterns, retention and preliminary receptor binding site localization studies were all made after {sup 125}I labeling. Internalization was studied using Oregon Green 488, Alexa Fluor 488 and CypHer5E markers. Results: [{sup 125}I](Z{sub EGFR:955}){sub 2} and [{sup 125}I]cetuximab gave a maximum cellular uptake of {sup 125}I within 4 to 8 h of incubation, while [{sup 125}I]EGF gave a maximum uptake already after 2 h. The retention studies showed that the cell-associated fraction of {sup 125}I after 48 h of incubation was {approx}20% when delivered as [{sup 125}I](Z{sub EGFR:955}){sub 2} and {approx}25% when delivered as [{sup 125}I]cetuximab. [{sup 125}I]EGF-mediated delivery gave a faster {sup 125}I release, where almost all cell-associated radioactivity had disappeared within 24 h. All three substances were internalized as demonstrated with confocal microscopy. Competitive binding studies showed that both EGF and cetuximab inhibited binding of (Z{sub EGFR:955}){sub 2} and indicated that the three substances competed for an overlapping binding site. Conclusion: The results gave information on cellular processing of radionuclides when delivered with (Z{sub EGFR:955}){sub 2} in comparison to delivery with EGF and cetuximab. Competition assays suggested that [{sup 125}I](Z{sub EGFR:955}){sub 2} bind to Domain III of EGFR. The affibody molecule (Z{sub EGFR:955}){sub 2} can be a candidate for EGFR imaging applications in nuclear medicine.

  1. Abnormal IGF-Binding Protein Profile in the Bone Marrow of Multiple Myeloma Patients.

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    Liesbeth Bieghs

    Full Text Available Insulin-like growth factor (IGF signalling plays a key role in homing, progression, and treatment resistance in multiple myeloma (MM. In the extracellular environment, the majority of IGF molecules are bound to one of six IGF-binding proteins (IGFBP1-6, leaving a minor fraction of total IGF free and accessible for receptor activation. In MM, high IGF-receptor type 1 expression levels correlate with a poor prognosis, but the status and role of IGF and IGFBPs in the pathobiology of MM is unknown. Here we measured total IGF1, IGF2, and intact IGFBP levels in blood and bone marrow samples from MM (n = 17, monoclonal gammopathy of undetermined significance (MGUS (n = 37, and control individuals (n = 15, using ELISA (IGFs and 125I-IGF1 Western Ligand Blotting (IGFBPs. MGUS and MM patients displayed a significant increase in intact IGFBP-2 (2.5-3.8 fold and decrease in intact IGFBP-3 (0.6-0.5 fold in the circulation compared to control individuals. Further, IGFBP-2 as well as total IGFBP levels were significantly lower in bone marrow compared to circulation in MM and MGUS only, whereas IGF1, IGF2, and IGFBP-3 were equally distributed between the two compartments. In conclusion, the profound change in IGFBP profile strongly suggests an increased IGF bioavailability in the bone marrow microenvironment in MGUS and MM, despite no change in growth factor concentration.

  2. Abnormal IGF-Binding Protein Profile in the Bone Marrow of Multiple Myeloma Patients.

    Science.gov (United States)

    Bieghs, Liesbeth; Brohus, Malene; Kristensen, Ida B; Abildgaard, Niels; Bøgsted, Martin; Johnsen, Hans E; Conover, Cheryl A; De Bruyne, Elke; Vanderkerken, Karin; Overgaard, Michael T; Nyegaard, Mette

    2016-01-01

    Insulin-like growth factor (IGF) signalling plays a key role in homing, progression, and treatment resistance in multiple myeloma (MM). In the extracellular environment, the majority of IGF molecules are bound to one of six IGF-binding proteins (IGFBP1-6), leaving a minor fraction of total IGF free and accessible for receptor activation. In MM, high IGF-receptor type 1 expression levels correlate with a poor prognosis, but the status and role of IGF and IGFBPs in the pathobiology of MM is unknown. Here we measured total IGF1, IGF2, and intact IGFBP levels in blood and bone marrow samples from MM (n = 17), monoclonal gammopathy of undetermined significance (MGUS) (n = 37), and control individuals (n = 15), using ELISA (IGFs) and 125I-IGF1 Western Ligand Blotting (IGFBPs). MGUS and MM patients displayed a significant increase in intact IGFBP-2 (2.5-3.8 fold) and decrease in intact IGFBP-3 (0.6-0.5 fold) in the circulation compared to control individuals. Further, IGFBP-2 as well as total IGFBP levels were significantly lower in bone marrow compared to circulation in MM and MGUS only, whereas IGF1, IGF2, and IGFBP-3 were equally distributed between the two compartments. In conclusion, the profound change in IGFBP profile strongly suggests an increased IGF bioavailability in the bone marrow microenvironment in MGUS and MM, despite no change in growth factor concentration. PMID:27111220

  3. Architecture of the sugar binding sites in carbohydrate binding proteins--a computer modeling study.

    Science.gov (United States)

    Rao, V S; Lam, K; Qasba, P K

    1998-11-01

    Different sugars, Gal, GalNAc and Man were docked at the monosaccharide binding sites of Erythrina corallodenron (EcorL), peanut lectin (PNA), Lathyrus ochrus (LOLI), and pea lectin (PSL). To study the lectin-carbohydrate interactions, in the complexes, the hydroxymethyl group in Man and Gal favors, gg and gt conformations respectively, and is the dominant recognition determination. The monosaccharide binding site in lectins that are specific to Gal/GalNAc is wider due to the additional amino acid residues in loop D as compared to that in lectins specific to Man/Glc, and affects the hydrogen bonds of the sugar involving residues from loop D, but not its orientation in the binding site. The invariant amino acid residues Asp from loop A, and Asn and an aromatic residue (Phe or Tyr) in loop C provides the basic architecture to recognize the common features in C4 epimers. The invariant Gly in loop B together with one or two residues in the variable region of loop D/A holds the sugar tightly at both ends. Loss of any one of these hydrogen bonds leads to weak interaction. While the subtle variations in the sequence and conformation of peptide fragment that resulted due to the size and location of gaps present in amino acid sequence in the neighborhood of the sugar binding site of loop D/A seems to discriminate the binding of sugars which differ at C4 atom (galacto and gluco configurations). The variations at loop B are important in discriminating Gal and GalNAc binding. The present study thus provides a structural basis for the observed specificities of legume lectins which uses the same four invariant residues for binding. These studies also bring out the information that is important for the design/engineering of proteins with the desired carbohydrate specificity. PMID:9849627

  4. Identification and Expression Profile Analysis of Odorant Binding Proteins in the Oriental Fruit Fly Bactrocera dorsalis

    Directory of Open Access Journals (Sweden)

    Hongyu Zhang

    2013-07-01

    Full Text Available Olfaction is crucial in many insects for critical behaviors, including those regulating survival and reproduction. Insect odorant-binding proteins (OBPs function in the first step of the olfactory system and play an essential role in the perception of odorants, such as pheromones and host chemicals. The oriental fruit fly, Bactrocera dorsalis, is a destructive fruit-eating pest, due to its wide host range of up to 250 different types of fruits and vegetables, and this fly causes severe economic damage to the fruit and vegetable industry. However, OBP genes have not been largely identified in B. dorsalis. Based on our previously constructed B. dorsalis cDNA library, ten OBP genes were identified in B. dorsalis for the first time. A phylogenetic tree was generated to show the relationships among the 10 OBPs of B. dorsalis to OBP sequences of two other Dipteran species, including Drosophila melanogaster and the mosquito Anopheles gambiae. The expression profiles of the ten OBPs in different tissues (heads, thoraxes, abdomens, legs, wings, male antennae and female antenna of the mated adults were analyzed by real-time PCR. The results showed that nine of them are highly expressed in the antenna of both sexes, except BdorOBP7. Four OBPs (BdorOBP1, BdorOBP4, BdorOBP8, and BdorOBP10 are also enriched in the abdomen, and BdorOBP7 is specifically expressed in leg, indicating that it may function in other biological processes. This work will provide insight into the roles of OBPs in chemoreception and help develop new pest-control strategies.

  5. Plasma TNF binding capacity profiles during treatment with etanercept in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Gudbrandsdottir, S; Bliddal, H; Petri, A; Terslev, L; Danneskiold-Samsøe, Bente; Bjørnhart, B; Bendtzen, K; Müller, K

    2004-01-01

    Etanercept (Enbrel) induces a rapid and sustained decline in disease activity in the majority of patients with refractory rheumatoid arthritis (RA). In these patients neutralization of TNFalpha and lymphotoxin (LT), previously termed TNFbeta is mediated by etanercept itself, as well as by naturally...... occurring soluble TNF receptors. However, the clinical response to treatment with etanercept may vary. Previously, pharmacokinetic studies have focused on the molar concentrations of etanercept, but very little is known about the kinetics of bioactive etanercept in patients treated with etanercept. The...... purpose of this study was to evaluate kinetics, including inter- and intraindividual variations of the total TNF binding capacity, in RA patients who were on a standard treatment schedule with etanercept....

  6. Profiling of Concanavalin A-Binding Glycoproteins in Human Hepatic Stellate Cells Activated with Transforming Growth Factor-β1

    Directory of Open Access Journals (Sweden)

    Yannan Qin

    2014-11-01

    Full Text Available Glycoproteins play important roles in maintaining normal cell functions depending on their glycosylations. Our previous study indicated that the abundance of glycoproteins recognized by concanavalin A (ConA was increased in human hepatic stellate cells (HSCs following activation by transforming growth factor-β1 (TGF-β1; however, little is known about the ConA-binding glycoproteins (CBGs of HSCs. In this study, we employed a targeted glycoproteomics approach using lectin-magnetic particle conjugate-based liquid chromatography-tandem mass spectrometry to compare CBG profiles between LX-2 HSCs with and without activation by TGF-β1, with the aim of discovering novel CBGs and determining their possible roles in activated HSCs. A total of 54 and 77 proteins were identified in the quiescent and activated LX-2 cells, respectively. Of the proteins identified, 14.3% were glycoproteins and 73.3% were novel potential glycoproteins. Molecules involved in protein processing in the endoplasmic reticulum (e.g., calreticulin and calcium signaling (e.g., 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase β-2 [PLCB2] were specifically identified in activated LX-2 cells. Additionally, PLCB2 expression was upregulated in the cytoplasm of the activated LX-2 cells, as well as in the hepatocytes and sinusoidal cells of liver cirrhosis tissues. In conclusion, the results of this study may aid future investigations to find new molecular mechanisms involved in HSC activation and antifibrotic therapeutic targets.

  7. Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

    International Nuclear Information System (INIS)

    Highlights: • Energetics of the interaction of proflavine with DNA has been studied. • The binding reaction was favored by both negative enthalpy and positive entropy. • Enthalpy–entropy compensation phenomenon was observed. • Non-polyelectrolytic forces played a dominant role in the binding process. • Proflavine enhanced the thermal stability of DNA remarkably. - Abstract: The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 105 · M−1 at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation

  8. Genome-wide profiling of peroxisome proliferator-activated receptor γ in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression

    DEFF Research Database (Denmark)

    Siersbæk, Majken; Loft, Anne; Jørgensen, Mads Malik Aagaard;

    2012-01-01

    epididymal, inguinal, and brown adipose tissues. While these PPARγ binding profiles are overall similar, there are clear depot-selective binding sites. Most PPARγ binding sites previously mapped in 3T3-L1 adipocytes can also be detected in primary adipocytes, but there are a large number of PPARγ binding...... how binding patterns of PPARγ differ between brown and white adipocytes and among different types of white adipocytes. Here we have employed chromatin immunoprecipitation combined with deep sequencing to map and compare PPARγ binding in in vitro differentiated primary mouse adipocytes isolated from...

  9. Roentgenographic studies on the soft tissue profile

    International Nuclear Information System (INIS)

    Modern orthodontics implies not only occlusal excellence, but also the positioning of teeth to produce optimal facial harmony for the individual patients. Several methods have been used in the study of facial height, width and depth were made from living subjects. These methods, however, complicate to control the subjects, therefore many investigators have used profile cephalometric technics. Practically, cephalometric technics were used in orthodontic treatment, maxillo-facial surgery and anthropometric studies. Author was studied to investigate the normal standards of soft tissue profile in Korean adolescences. The subjects consisted of 53 males and 54 females from 17 to 22 years of age and with normal occlusion and acceptable profile. Aluminum filter was designed to obtain both hard and soft tissue structures on a single film. Eight profile landmarks were plotted and drawn on the tracings of all cephalograms and eighteen depth, height an d angles were measured from each landmarks of the cephalograms. The following conclusions were obtained from this studies; 1. Total facial convexity was 170.75 in males and females samples and lower facial and labiomandibular convexity were each of 141.44, 171.05. 2. Maxillary and mandibular sulcus angulations were 137.61, 129.52 and upper and lower lip inclinations were each of 12 3.26 and 49.56 in male and females. 3. Soft tissue depth of several points were as follows; Subnasale 18.74 mm in males and 16.65 mm in females Pogonion 13.40 mm in males and 13.07 mm in females upper lip 14.06 mm in males and 11.91 mm in females lower lip 15.46 mm, 13.63 in males and females 4. The protrusion of nose were 16.28 mm in males and 15.56 mm in females 5. The vertical length of upper and lower lips were 25.67 mm, 52.96 mm and the lip posture was indicated 93.43 per cent (closed state) in centric occlusions.

  10. Plasma electrophoretic profiles and hemoglobin binding protein reference intervals in the eastern box turtle (Terrapene carolina carolina) and influences of age, sex, season, and location.

    Science.gov (United States)

    Flower, Jennifer E; Byrd, John; Cray, Carolyn; Allender, Matthew C

    2014-12-01

    Evaluation of plasma electrophoretic profiles and acute phase protein concentrations may play a valuable role in health assessment of reptiles; however, little is known about reference intervals in free-ranging eastern box turtles (Terrapene carolina carolina). The purpose of this study was to establish reference intervals of protein electrophoretic profiles and hemoglobin binding protein ([HBP] as determined by a haptoglobin assay) in free-ranging eastern box turtles and to assess any possible correlations between varying age class (adults vs. juvenile), sex (male, female, or unknown), season (spring, summer, or fall), or location (Tennessee vs. Illinois). Blood samples were obtained from 324 eastern box turtles from 2010 to 2012 at three sites in Illinois and one site in Tennessee, USA. Significant differences were observed with total protein (sex, season, state, Illinois location), albumin (age class, season, state, Illinois location), α-1 globulins (sex, season, Illinois location), α-2 globulins (sex, season, state, Illinois location), β globulins (age class, sex, season, state, Illinois location), γ globulins (sex, season state, Illinois location), and hemoglobin binding protein (age class, sex, state, Illinois location). The use of electrophoretic profiles and acute phase proteins is a relatively new concept in reptilian medicine, and this study allowed for establishment of references intervals in the eastern box turtle and emphasized differences that occured based on age, sex, season, and location. Future research in this area can now build on these data to determine changes in population health over time or alterations due to specific environmental or disease threats. PMID:25632671

  11. The Effects of Endogenous Non-Peptide Molecule Isatin and Hydrogen Peroxide on Proteomic Profiling of Rat Brain Amyloid-β Binding Proteins: Relevance to Alzheimer’s Disease?

    Directory of Open Access Journals (Sweden)

    Alexei E. Medvedev

    2014-12-01

    Full Text Available The amyloid-β peptide is considered as a key player in the development and progression of Alzheimer’s disease (AD. Although good evidence exists that amyloid-β accumulates inside cells, intracellular brain amyloid-binding proteins remain poorly characterized. Proteomic profiling of rat brain homogenates, performed in this study, resulted in identification of 89 individual intracellular amyloid-binding proteins, and approximately 25% of them were proteins that we had previously identified as specifically binding to isatin, an endogenous neuroprotector molecule. A significant proportion of the amyloid-binding proteins (more than 30% are differentially expressed or altered/oxidatively modified in AD patients. Incubation of brain homogenates with 70 µM hydrogen peroxide significantly influenced the profile of amyloid-β binding proteins and 0.1 mM isatin decreased the number of identified amyloid-β binding proteins both in control and hydrogen peroxide treated brain homogenates. The effects of hydrogen peroxide and isatin have been confirmed in optical biosensor experiments with purified glyceraldehyde-3-phosphate dehydrogenase, one of the known crucial amyloid-β binding proteins (also identified in this study. Data obtained suggest that isatin protects crucial intracellular protein targets against amyloid binding, and possibly favors intracellular degradation of this protein via preventing formation of amyloid-β oligomers described in the literature for some isatin derivatives.

  12. A study of microbial profile modification

    Energy Technology Data Exchange (ETDEWEB)

    Bae, J.H.; Lee, H.O.

    1995-12-31

    A microbial profile modification method using spores was investigated. A halotolerant, spore-forming, biopolymer-producing mesophile was used in Berea cores with a specifically formulated nutrient package to reduce the permeability of the rock. The degree of permeability reduction varied widely depending on the stimulation protocols used. The incubation period had a significant impact on permeability reduction, and there appeared to be an optimum incubation time for maximum permeability reduction. The reduction persisted for many PV of brine injection and appeared very stable. For our microbes used in this study, the permeability reduction was about the same when the NaCl concentration was above 2 wt% in the range from 0 wt% to 10 wt%.

  13. Prediction of heme binding residues from protein sequences with integrative sequence profiles

    OpenAIRE

    2012-01-01

    Background The heme-protein interactions are essential for various biological processes such as electron transfer, catalysis, signal transduction and the control of gene expression. The knowledge of heme binding residues can provide crucial clues to understand these activities and aid in functional annotation, however, insufficient work has been done on the research of heme binding residues from protein sequence information. Methods We propose a sequence-based approach for accurate prediction...

  14. Spectroscopic studies on Titanium ion binding to the apo lactoferrin

    International Nuclear Information System (INIS)

    Titanium is a relatively abundant element that has found growing applications in medical science and recently some of Titanium compounds are introduced as anticancer drugs. In spite of very limited data which exist on the Titanium metabolism, some proteins might be involved in the mechanism of action of Titanium up to our knowledge, there is not any report in the literature concerning binding of Titanium to apo lactoferrin. Binding of apo lactoferrin with Ti(IV)-citrate was studied by spectroflourimeterey and spectrophotometery techniques under physiological conditions. The spectroflourimeteric studies revealed a significant fluorescence quenching, that indicated binding of apo lactoferrin with Ti(IV). The same reaction was monitored through spectrophotometry technique; this represents a characteristic UV difference band at 267 nm, which is different from lac-Fe (III). Titration studies how that lactoferrin specifically binds two moles Ti(IV) as complex with citrate per mol protein. Spectroflourimeterey and spectrophotometery techniques indicated that Ti(IV) ions cause a reduction (13%-14%) in binding of Fe(III) to lactoferrin. In overall, we may come to this conclusion that this element might be involved in the iron metabolism

  15. Comparative studies on insulin binding human erythrocytes by immunoradiometric techniques

    International Nuclear Information System (INIS)

    Blood cells have been widely used to evaluate the status of the insulin receptor in man. The receptors exhibited competitive inhibition curves and nonlinear Scatchard plots similar to those reported for insulin target tissues, such as the hepatocyte and the adipocytes. This study demonstrated specific insulin binding by the erythrocytes (RBCs) of infants, children and adults. The total insulin bound by the RBCs from both children and adults gave a small difference over the physiologic range of insulin concentrations. blood RBCs of infants showed greater numbers of insulin receptors per cell and significant increase in the total amount of insulin binding than that in either children (ps for of infants, children and adults were similar to each other. It is clear that, the measurement of insulin binding by RBCs may be particularly useful in the study of infants and children with disorders of carbohydrate metabolism to elucidate the role, if any, of abnormal receptor function in their conditions

  16. A mineralogical study of the binding mechanisms in chromite briquettes

    International Nuclear Information System (INIS)

    Briquettes are made of chromite fines and a suitable binding material which are fed into a pillow-shaped mould, and pressure is applied to compact the material. The Council for Mineral Technology and Middelburg Steel and Alloys have taken out a provisional patent for the manufacturing of composite briquettes containing not only reducing agents but also fluxes, which will improve the efficiency of the reduction process. Briquettes were examined and the results were correlated with the strengths of the briquettes, which were measured in drop tests, compressive strength and abrasive resistance. The mineralogical procedures included differential thermal analysis, x-ray diffraction, infrared spectroscopy, scanning electron microscope, energy-dispersive spectroscopy and the use of the electron microprobe. The information obtained by these procedures enabled the determination of the nature of the binding mechanisms. Six different types of briquettes, with their respective binding mechanisms were studied

  17. PRELIMINARY STUDY OF EXTRACTABLE PROTEIN BINDING USING MALEIC ANHYDRIDE COPOLYMER

    Institute of Scientific and Technical Information of China (English)

    Thirawan Nipithakul; Ladawan Watthanachote; Nanticha Kalapat

    2012-01-01

    A preliminary study of using maleic anhydride copolymer for protein binding has been carried out.The polymeric films were prepared by compression of the purified resin and annealing the film to induce efficient back formation of the anhydride groups.The properties of the film surface were analyzed by attenuated total reflection Fourier transforms infrared spectroscopy and water contact angle measurements.The protein content was determined by Bradford assay.To obtain optimum conditions,immersion time for protein binding was examined.Results revealed that proteins can be successfully immobilized onto the film surface via covalent linkage.The efficiency of the covalent binding of the extractable protein to maleic anhydride-polyethylene film was estimated at 69.87 μtg/cm2,although the film had low anhydride content (3%) on the surface.

  18. Binding of nucleotides to nucleoside diphosphate kinase: a calorimetric study.

    Science.gov (United States)

    Cervoni, L; Lascu, I; Xu, Y; Gonin, P; Morr, M; Merouani, M; Janin, J; Giartosio, A

    2001-04-17

    The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric study of the binding of enzymes from two organisms to various nucleotides. Isothermal titration calorimetry has been used to characterize the binding in terms of Delta G degrees, Delta H degrees and Delta S degrees. Thermodynamic parameters of the interaction of ADP with the hexameric NDP kinase from Dictyostelium discoideum and with the tetrameric enzyme from Myxococcus xanthus, at 20 degrees C, were similar and, in both cases, binding was enthalpy-driven. The interactions of ADP, 2'deoxyADP, GDP, and IDP with the eukaryotic enzyme differed in enthalpic and entropic terms, whereas the Delta G degrees values obtained were similar due to enthalpy--entropy compensation. The binding of the enzyme to nonphysiological nucleotides, such as AMP--PNP, 3'deoxyADP, and 3'-deoxy-3'-amino-ADP, appears to differ in several respects. Crystallography of the protein bound to 3'-deoxy-3'-amino-ADP showed that the drug was in a distorted position, and was unable to interact correctly with active site side chains. The interaction of pyrimidine nucleoside diphosphates with the hexameric enzyme is characterized by a lower affinity than that with purine nucleotides. Titration showed the stoichiometry of the interaction to be abnormal, with 9--12 binding sites/hexamer. The presence of supplementary binding sites might have physiological implications. PMID:11294625

  19. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B;

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  20. Analysis of Swine Leukocyte Antigen Peptide Binding Profiles and the Identification of T cell Epitopes by Tetramer Staining

    DEFF Research Database (Denmark)

    Pedersen, Lasse Eggers

    of the specific CTL response elicited as a result of immunization against foot-and-mouth-disease virus (FMDV) and swine influenza A virus. These studies resulted in the identification of T cell epitopes from both viruses. As SLA:peptide binding data accumulates in these and similar studies, it becomes possible...

  1. XAS and Pulsed EPR Studies of the Copper Binding Site in Riboflavin Binding Protein

    Energy Technology Data Exchange (ETDEWEB)

    Smith,S.; Bencze, K.; Wasiukanis, K.; Benore-Parsons, T.; Stemmler, T.

    2008-01-01

    Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 Angstroms, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a CuO3N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

  2. Binding of amifostine to human serum albumin: a biophysical study.

    Science.gov (United States)

    Sun, Yifu; Wu, Han; Zhao, Guoqing; Shi, Ying

    2015-02-01

    The aim of this present work is to investigate the interaction between amifostine and human serum albumin (HSA) in simulated physiological conditions by spectroscopic methods to reveal potential toxic effects of the drug. The results reflected that amifostine caused fluorescence quenching of HSA through a static quenching process, which was further confirmed by the electrochemical experiments. The binding constants at 290, 297 and 304 K were obtained as 2.53 × 10(5) /M, 8.13 × 10(4) /M and 3.59 × 10(4) /M, respectively. There may be one binding site of amifostine on HSA. The thermodynamic parameters indicated that the interaction between amifostine and HSA was driven mainly by hydrogen bonding and electrostatic forces. Synchronous fluorescence spectra, circular dichroism and Fourier transform infrared spectroscopy results showed amifostine binding slightly changed the conformation of HSA with secondary structural content changes. Förster resonance energy transfer study revealed high possibility of energy transfer with amifostine-Trp-214 distance of 3.48 nm. The results of the present study may provide valuable information for studying the distribution, toxicological and pharmacological mechanisms of amifostine in vivo. PMID:24962599

  3. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  4. Calorimetric study of binding of some disaccharides with crown ethers

    International Nuclear Information System (INIS)

    Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of β-lactose, α,α-trehalose and sucrose with 15-crown-5 and 18-crown-6 in water at 298.15 K. The formation of 1:1 molecular associates has been found for the systems studied except 18-crown-6 and β-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between α,α-trehalose and 18-crown-6. The obtained values of thermodynamic parameters of binding are discussed from the point of view of solute-solvent interactions as well as conformational and structural peculiarities of the disaccharides (DS) and crown ethers (CE)

  5. Adenosine A2A receptor binding profile of two antagonists, ST1535 and KW6002: consideration on the presence of atypical adenosine A2A binding sites

    Directory of Open Access Journals (Sweden)

    Teresa Riccioni

    2010-08-01

    Full Text Available Adenosine A2A receptors seem to exist in typical (more in striatum and atypical (more in hippocampus and cortex subtypes. In the present study, we investigated the affinity of two adenosine A2A receptor antagonists, ST1535 [2 butyl -9-methyl-8-(2H-1,2,3-triazol 2-yl-9H-purin-6-xylamine] and KW6002 [(E-1,3-diethyl-8-(3,4-dimethoxystyryl-7-methyl-3,7-dihydro-1H-purine-2,6,dione] to the “typical” and “atypical” A2A binding sites. Affinity was determined by radioligand competition experiments in membranes from rat striatum and hippocampus. Displacement of the adenosine analog [3H]CGS21680 [2-p-(2-carboxyethylphenethyl-amino-5’-N-ethylcarbox-amidoadenosine] was evaluated in the absence or in the presence of either CSC [8-(3-chlorostyryl-caffeine], an adenosine A2A antagonist that pharmacologically isolates atypical binding sites, or DPCPX (8-cyclopentyl-1,3-dipropylxanthine, an adenosine A1 receptor antagonist that pharmacologically isolates typical binding site. ZM241385 [84-(2-[7-amino-2-(2-furyl [1,2,4]-triazol[2,3-a][1,3,5]triazin-5-yl amino]ethyl phenol] and SCH58261 [(5-amino-7-(β-phenylethyl-2-(8-furylpyrazolo(4,3-e-1,2,4-triazolo(1,5-c pyrimidine], two other adenosine A2A receptor antagonists, which were reported to differently bind to atypical and typical A2A receptors, were used as reference compounds. ST1535, KW6002, ZM241385 and SCH58261 displaced [3H]CGS21680 with higher affinity in striatum than in hippocampus. In hippocampus, no typical adenosine A2A binding was detected, and ST1535 was the only compound that occupied atypical A2A adenosine receptors. Present data are explained in terms of heteromeric association among adenosine A2A, A2B and A1 receptors, rather than with the presence of atypical A2A receptor subtype.

  6. (/sup 3/H)nitrobenzylthioinosine binding as a probe for the study of adenosine uptake sites in brain

    Energy Technology Data Exchange (ETDEWEB)

    Marangos, P.J.; Patel, J.; Clark-Rosenberg, R.; Martino, A.M.

    1982-07-01

    The binding of the potent adenosine uptake inhibitor (/sup 3/H)nitrobenzylthioinosine ((/sup 3/H)NBI) to brain membrane fractions was investigated. Reversible, saturable, specific, high-affinity binding was demonstrated in both rat and human brain. The KD in both was 0.15 nM with Bmax values of 140-200 fmol/mg protein. Linear Scatchard plots were routinely obtained, indicating a homogeneous population of binding sites in brain. The highest density of binding sites was found in the caudate and hypothalamus in both species. The binding site was heat labile and trypsin sensitive. Binding was also decreased by incubation of the membranes in 0.05% Triton X-100 and by treatment with dithiothreitol and iodoacetamide. Of the numerous salt and metal ions tested, only copper and zinc had significant effects on (/sup 3/H)NBI binding. The inhibitory potencies of copper and zinc were IC50 . 160 microM and 6 mM, respectively. Subcellular distribution studies revealed a high percentage of the (/sup 3/H)NBI binding sites on synaptosomes, indicating that these sites were present in the synaptic region. A study of the tissue distribution of the (/sup 3/H)NBI sites revealed very high densities of binding in erythrocyte, lung, and testis, with much lower binding densities in brain, kidney, liver, muscle, and heart. The binding affinity in the former group was approximately 1.5 nM, whereas that in the latter group was 0.15 nM, suggesting two types of binding sites. The pharmacologic profile of (/sup 3/H)NBI binding was consistent with its function as the adenosine transport site, distinct from the adenosine receptor, since thiopurines were very potent inhibitors of binding whereas adenosine receptor ligands, such as cyclohexyladenosine and 2-chloroadenosine, were three to four orders of magnitude less potent. (/sup 3/H)NBI binding in brain should provide a useful probe for the study of adenosine transport in the brain.

  7. Morphine-6-glucuronide: analgesic effects and receptor binding profile in rats

    International Nuclear Information System (INIS)

    The antinociceptive effects of morphine-6-glucuronide (M6G) were examined in two animal models of pain, the tail immersion test (reflex withdrawal to noxious heat) and the formalin test (behavioral response to minor tissue injury). In the tail immersion test, M6G produced and increase in withdrawal latency that rose rapidly between 0.01 and 0.025 ug ICV or 1 and 2 mg/kg SC. A further increase occurred at doses greater than 0.2 ug ICV or 4 mg/kg SC and was associated with marked catelepsy and cyanosis. Naloxone, 0.1 mg/kg SC, shifted the lower component of the dose-effect relation by a factor of 24. In the formalin test, 0.01 ug M6G ICV produced hyperalgesia, while between 0.05 and 0.2 ug ICV, antinociception increased rapidly without toxicity. The dose effect relations for hyperalgesia and antinociception were shifted to the right by factors of 20- and 3-fold, respectively. By comparison, ICV morphine was 60 (formalin test) to 145-200 (tail immersion test) times less potent than M6G. At sub-nanomolar concentrations, M6G enhanced the binding of [3H]-etorphine, [3H]-dihydromorphine and [3H]-naloxone to rat brain membrane receptors by 20-40%. At higher concentrations, M6G displaced each ligand from binding sites, with K/sub i/ values of about 30 nM, as compared to morphine K/sub i/ values of about 3 nM

  8. Morphine-6-glucuronide: analgesic effects and receptor binding profile in rats

    Energy Technology Data Exchange (ETDEWEB)

    Abbott, F.V.; Palmour, R.M.

    1988-01-01

    The antinociceptive effects of morphine-6-glucuronide (M6G) were examined in two animal models of pain, the tail immersion test (reflex withdrawal to noxious heat) and the formalin test (behavioral response to minor tissue injury). In the tail immersion test, M6G produced and increase in withdrawal latency that rose rapidly between 0.01 and 0.025 ug ICV or 1 and 2 mg/kg SC. A further increase occurred at doses greater than 0.2 ug ICV or 4 mg/kg SC and was associated with marked catelepsy and cyanosis. Naloxone, 0.1 mg/kg SC, shifted the lower component of the dose-effect relation by a factor of 24. In the formalin test, 0.01 ug M6G ICV produced hyperalgesia, while between 0.05 and 0.2 ug ICV, antinociception increased rapidly without toxicity. The dose effect relations for hyperalgesia and antinociception were shifted to the right by factors of 20- and 3-fold, respectively. By comparison, ICV morphine was 60 (formalin test) to 145-200 (tail immersion test) times less potent than M6G. At sub-nanomolar concentrations, M6G enhanced the binding of (/sup 3/H)-etorphine, (/sup 3/H)-dihydromorphine and (/sup 3/H)-naloxone to rat brain membrane receptors by 20-40%. At higher concentrations, M6G displaced each ligand from binding sites, with K/sub i/ values of about 30 nM, as compared to morphine K/sub i/ values of about 3 nM.

  9. Study on dopamine D2 binding capacity in vascular parkinsonism

    International Nuclear Information System (INIS)

    To investigate whether the striatal dopamine receptor function is involved in the development of vascular parkinsonism (VP), a positron emission tomography (PET) study was conducted on 9 patients with VP by using [11C] N-methylspiperone as the tracer. The rate of binding availability in the striatal dopamine D2 receptor (k3) was determined semiquantitatively, and the values were compared to the predicted normal values based on the results from 7 normal volunteers. Of 9 patients with VP, the normalized D2 receptor binding [%k3] was more than 90% in 5 patients, 89 to 87% in 3, and 75% in one. These values showed no evident correlation with the Hoehn and Yahr stage. The laterality of the striatal %k3 did not correspond to that of the parkinsonism. Thus, the striatal dopamine D2 receptor binding was not severely impaired and did not correlate with the neurological status in patients with VP. This may indicate that striatal dopamine D2 receptor function is not primarily associated with the development of the parkinsonism in VP. (author)

  10. Peptide Arrays for Binding Studies of E3 Ubiquitin Ligases.

    Science.gov (United States)

    Klecker, Maria; Dissmeyer, Nico

    2016-01-01

    The automated SPOT (synthetic peptide arrays on membrane support technique) synthesis technology has entrenched as a rapid and robust method to generate peptide libraries on cellulose membrane supports. The synthesis method is based on conventional Fmoc chemistry building up peptides with free N-terminal amino acids starting at their cellulose-coupled C-termini. Several hundreds of peptide sequences can be assembled with this technique on one membrane comprising a strong binding potential due to high local peptide concentrations. Peptide orientation on SPOT membranes qualifies this array type for assaying substrate specificities of N-recognins, the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Pioneer studies described binding capability of mammalian and yeast enzymes depending on a peptide's N-terminus. SPOT arrays have been successfully used to describe substrate specificity of N-recognins which are the recognition elements of the N-end rule pathway of targeted protein degradation (NERD). Here, we describe the implementation of SPOT binding assays with focus on the identification of N-recognin substrates, applicable also for plant NERD enzymes. PMID:27424747

  11. Volume profiles for the reversible binding of dioxygen to cobalt(II) complexes. Evidence for a substitution-controlled process

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, M.; Espenson, J.H.; Bakac, A. (Iowa State Univ., Ames, IA (United States)); Eldik, R. van (Univ. of Witten/Herdecke (Germany))

    1994-01-05

    The rate constants for the binding and release of dioxygen from two cobalt(II) macrocycles have been determined in aqueous solution as a function of pressure at 25.0[degrees]C. The products of these reactions are L[sup 1]CoOO[sup 2+] and L[sup 2]CoOO[sup 2+], where L[sup 1] = cyclam and L[sup 2] = hexamethylcyclam. The pressure dependence of the equilibrium constant for the L[sup 2] system was also evaluated, giving [delta]V[degrees] = [minus]22.- [+-] 0.4 mL mol[sup [minus]1]. The binding rate constants have [delta]V* = +0.4 [+-] 0.5 mL mol[sup [minus]1] (L[sup 1]) and [minus]4.7 [+-] 0.3 mL mol[sup [minus]1] (L[sup 2]). The reverse reaction for L[sup 2]CoOO[sup 2+] has [delta]V* = +17.9 [+-] 0.5 mL mol[sup [minus]1]. The volume profile is presented for the L[sup 2] system, from which an interchange mechanism for substitution at Co(II) is proposed. Electron transfer is not significantly advanced at the transition state. The reverse reaction, released of dioxygen from the cobalt(III)-superoxo complex, has a large positive value of [delta]V*, consistent with the electron transfer preceding the partial dissociation of O[sub 2].

  12. Transduction of Glycan-Lectin Binding using Near Infrared Fluorescent Single Walled Carbon Nanotubes for Glycan Profiling

    Science.gov (United States)

    Reuel, Nigel; Ahn, Jin-Ho; Kim, Jong-Ho; Zhang, Jingqing; Boghossian, Ardemis; Mahal, Lara; Strano, Michael

    2012-02-01

    In this work, we demonstrate a sensor array employing recombinant lectins as glycan recognition sites tethered via Histidine tags to Ni2+ complexes that act as fluorescent quenchers for semi-conducting single walled carbon nanotubes embedded in a chitosan to measure binding kinetics of model glycans. Two higher-affined glycan-lectin pairs are explored: fucose (Fuc) to PA-IIL and N-acetylglucosamine (GlcNAc) to GafD. The dissociation constants (KD) for these pairs as free glycans (106 and 19 μM respectively) and streptavidin-tethered (142 and 50 μM respectively) were found. The absolute detection limit for the current platform was found to be 2 μg of glycosylated protein or 100 ng of free glycan to 20 μg of lectin. Glycan detection is demonstrated at the single nanotube level (GlcNAc to GafD). Over a population of 1000 nanotubes, 289 of the SWNT sensors had signals strong enough to yield kinetic information (KD of 250 ± 10 μM). We are also able to identify the locations of ``strong-transducers'' on the basis of dissociation constant (4 sensors with KD 5% quench response). The ability to pinpoint strong-binding, single sensors is promising to build a nanoarray of glycan-lectin transducers as a method to profile glycans without protein labeling or glycan liberation pretreatment steps.

  13. Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7

    Directory of Open Access Journals (Sweden)

    Hennig Lars

    2010-10-01

    Full Text Available Abstract Background The clock-controlled RNA-binding protein AtGRP7 influences circadian oscillations of its own transcript at the post-transcriptional level. To identify additional targets that are regulated by AtGRP7, transcript profiles of transgenic plants constitutively overexpressing AtGRP7 (AtGRP7-ox and wild type plants were compared. Results Approximately 1.4% of the transcripts represented on the Affymetrix ATH1 microarray showed changes in steady-state abundance upon AtGRP7 overexpression. One third of the differentially expressed genes are controlled by the circadian clock, and they show a distinct bias of their phase: The up-regulated genes preferentially peak around dawn, roughly opposite to the AtGRP7 peak abundance whereas the down-regulated genes preferentially peak at the end of the day. Further, transcripts responsive to abiotic and biotic stimuli were enriched among AtGRP7 targets. Transcripts encoding the pathogenesis-related PR1 and PR2 proteins were elevated in AtGRP7-ox plants but not in plants overexpressing AtGRP7 with a point mutation in the RNA-binding domain, indicating that the regulation involves RNA binding activity of AtGRP7. Gene set enrichment analysis uncovered components involved in ribosome function and RNA metabolism among groups of genes upregulated in AtGRP7-ox plants, consistent with its role in post-transcriptional regulation. Conclusion Apart from regulating a suite of circadian transcripts in a time-of-day dependent manner AtGRP7, both directly and indirectly, affects other transcripts including transcripts responsive to abiotic and biotic stimuli. This suggests a regulatory role of AtGRP7 in the output of the endogenous clock and a complex network of transcripts responsive to external stimuli downstream of the AtGRP7 autoregulatory circuit.

  14. Abnormal IGF-Binding Protein Profile in the Bone Marrow of Multiple Myeloma Patients

    DEFF Research Database (Denmark)

    Bieghs, Liesbeth; Brohus, Malene; Kristensen, Ida B;

    2016-01-01

    and accessible for receptor activation. In MM, high IGF-receptor type 1 expression levels correlate with a poor prognosis, but the status and role of IGF and IGFBPs in the pathobiology of MM is unknown. Here we measured total IGF1, IGF2, and intact IGFBP levels in blood and bone marrow samples from MM.......6-0.5 fold) in the circulation compared to control individuals. Further, IGFBP-2 as well as total IGFBP levels were significantly lower in bone marrow compared to circulation in MM and MGUS only, whereas IGF1, IGF2, and IGFBP-3 were equally distributed between the two compartments. In conclusion, the...... profound change in IGFBP profile strongly suggests an increased IGF bioavailability in the bone marrow microenvironment in MGUS and MM, despite no change in growth factor concentration....

  15. New Roles for Corticosteroid Binding Globulin and Opposite Expression Profiles in Lung and Liver.

    Science.gov (United States)

    Gulfo, Jose; Ledda, Angelo; Gea-Sorlí, Sabrina; Bonjoch, Laia; Closa, Daniel; Grasa, Mar; Esteve, Montserrat

    2016-01-01

    Corticosteroid-binding globulin (CBG) is the specific plasma transport glycoprotein for glucocorticoids. Circulating CBG is mainly synthesized in liver but, its synthesis has been located also in other organs as placenta, kidney and adipose tissue with unknown role. Using an experimental model of acute pancreatitis in cbg-/- mice we investigated whether changes in CBG affect the progression of the disease as well as the metabolism of glucocorticoids in the lung. Lack of CBG does not modify the progression of inflammation associated to pancreatitis but resulted in the loss of gender differences in corticosterone serum levels. In the lung, CBG expression and protein level were detected, and it is noteworthy that these showed a sexual dimorphism opposite to the liver, i.e. with higher levels in males. Reduced expression of 11β-HSD2, the enzyme involved in the deactivation of corticosterone, was also observed. Our results indicate that, in addition to glucocorticoids transporter, CBG is involved in the gender differences observed in corticosteroids circulating levels and plays a role in the local regulation of corticosteroids availability in organs like lung. PMID:26741814

  16. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling.

    Science.gov (United States)

    Haines, Alicia M; Linacre, Adrian

    2016-05-01

    We report a simple screening method to assess the viability of successful DNA profiling from single hair follicles. A total of 48 hair samples (shed and plucked) were collected from male and female donors and the root tips (0.5cm) were stained using one of three DNA binding dyes (EvaGreen™, Diamond™ Nucleic Acid Dye and RedSafe™) at 20× concentration. The hairs were subsequently viewed under a Nikon Optiphot fluorescent microscope to count the approximate number of nuclei in one plane of view. The hairs were then processed using either (1) a DNA extraction kit (QIAmp(®) Mini Kit) and then amplified using the AmpFLSTR(®) NGM™ kit, which amplifies 15 short tandem repeat (STR) loci plus the gender marker amelogenin, or (2) by direct PCR amplification using the same DNA profiling kit. Diamond™ dye had the lowest background signal and plucked hairs treated with this dye produced full DNA profiles when amplified directly and was chosen to screen a further 150 mixed hair samples. These hairs were separated into one of five categories (1, >100 nuclei; 1.5, 50-99 nuclei; 2, 1-49 nuclei; 2.5, no nuclei but high fluorescent signal; 3, no nuclei and very low fluorescent signal) from which 60 of the hairs were chosen to undergo direct amplification using the NGM™ kit. It was found that there was a direct correlation to the category designation and the ability to obtain a DNA profile up-loadable to the Australian DNA Database. Approximately 91% of category 1 hairs resulted in either a full or high partial (12-29 alleles) profile by direct PCR whereas about 78% of category 3 hairs exhibited no amplification. The results show that this method can be used to predict successful STR amplification from single hair follicles. It is a rapid, sensitive, cheap, non-destructive and easy to perform methodology applicable for screening multiple hairs in order to aid forensic investigators in predicting hairs that will yield DNA results. PMID:27038658

  17. Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

    Directory of Open Access Journals (Sweden)

    Annie Yang

    Full Text Available BACKGROUND: The p53 homologs, p63 and p73, share approximately 85% amino acid identity in their DNA-binding domains, but they have distinct biological functions. PRINCIPAL FINDINGS: Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we identify p73 DNA binding sites on a genome-wide level in ME180 human cervical carcinoma cells. Strikingly, the p73 binding profile is indistinguishable from the previously described binding profile for p63 in the same cells. Moreover, the p73:p63 binding ratio is similar at all genomic loci tested, suggesting that there are few, if any, targets that are specific for one of these factors. As assayed by sequential chromatin immunoprecipitation, p63 and p73 co-occupy DNA target sites in vivo, suggesting that p63 and p73 bind primarily as heterotetrameric complexes in ME180 cells. CONCLUSIONS: The observation that p63 and p73 associate with the same genomic targets suggest that their distinct biological functions are due to cell-type specific expression and/or protein domains that involve functions other than DNA binding.

  18. STUDY OF ESTROGEN BINDING SITE ON HUMAN EJACULATED SPERMATOZOA

    Institute of Scientific and Technical Information of China (English)

    CHUJin-Shong; WANGYi-Fei

    1989-01-01

    The specific estrogen binding site for 17β-estradiol has been investigated on human spermatozoa by electron microscopec autoradiography. The results show that the binding sites were distributed over the surface of human spermatozoa: acrosomal cap, equatorial

  19. Tourette Syndrome neuropsychological profile: a study case

    Directory of Open Access Journals (Sweden)

    Eliana Gomes da Silva Almeida

    2014-04-01

    Full Text Available This article discusses findings resulting from the neuro-psychological assessment of an adolescent with Tourette Syndrome (TS, a rare neuro-developmental disorder characterized by the manifestation of physical and/or audible tics that emerge in childhood or early adolescence. Although we performed an extensive assessment of all cognitive functions, our reported findings focus on those functions that are described in prior research as relevant to the understanding of the cognitive profile of patients with this condition. The findings reported here are consistent with other reports and suggest that intellectual and long-term memory potentials are preserved, while noting deficiencies in executive functioning, reduced speed of mental and psycho-motor functions, and decreased recent memory capacity. Given the rarity of this diagnosis, our reporting of this case should contribute to the understanding of cognitive function in adolescents with TS. In addition, this article highlights and describes factors that affect the quality of neuropsychological assessment and facilitate accurate therapeutical diagnosis and referral for TS carriers.

  20. Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

    OpenAIRE

    Southall, Tony D.; Gold, Katrina S.; Egger, Boris; Davidson, Catherine M.; Caygill, Elizabeth E.; Marshall, Owen J.; Brand, Andrea H.

    2013-01-01

    Summary Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed “TaDa,” a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transc...

  1. Profile control studies for JET optimised shear regime

    Energy Technology Data Exchange (ETDEWEB)

    Litaudon, X.; Becoulet, A.; Eriksson, L.G.; Fuchs, V.; Huysmans, G.; How, J.; Moreau, D.; Rochard, F.; Tresset, G.; Zwingmann, W. [Association Euratom-CEA, CEA/Cadarache, Dept. de Recherches sur la Fusion Controlee, DRFC, 13 - Saint-Paul-lez-Durance (France); Bayetti, P.; Joffrin, E.; Maget, P.; Mayorat, M.L.; Mazon, D.; Sarazin, Y. [JET Abingdon, Oxfordshire (United Kingdom); Voitsekhovitch, I. [Universite de Provence, LPIIM, Aix-Marseille 1, 13 (France)

    2000-03-01

    This report summarises the profile control studies, i.e. preparation and analysis of JET Optimised Shear plasmas, carried out during the year 1999 within the framework of the Task-Agreement (RF/CEA/02) between JET and the Association Euratom-CEA/Cadarache. We report on our participation in the preparation of the JET Optimised Shear experiments together with their comprehensive analyses and the modelling. Emphasis is put on the various aspects of pressure profile control (core and edge pressure) together with detailed studies of current profile control by non-inductive means, in the prospects of achieving steady, high performance, Optimised Shear plasmas. (authors)

  2. Profile control studies for JET optimised shear regime

    International Nuclear Information System (INIS)

    This report summarises the profile control studies, i.e. preparation and analysis of JET Optimised Shear plasmas, carried out during the year 1999 within the framework of the Task-Agreement (RF/CEA/02) between JET and the Association Euratom-CEA/Cadarache. We report on our participation in the preparation of the JET Optimised Shear experiments together with their comprehensive analyses and the modelling. Emphasis is put on the various aspects of pressure profile control (core and edge pressure) together with detailed studies of current profile control by non-inductive means, in the prospects of achieving steady, high performance, Optimised Shear plasmas. (authors)

  3. Comparative study of methyl-CpG-binding domain proteins

    Directory of Open Access Journals (Sweden)

    Ropers H Hilger

    2003-01-01

    Full Text Available Abstract Background Methylation at CpG dinucleotides in genomic DNA is a fundamental epigenetic mechanism of gene expression control in vertebrates. Proteins with a methyl-CpG-binding domain (MBD can bind to single methylated CpGs and most of them are involved in transcription control. So far, five vertebrate MBD proteins have been described as MBD family members: MBD1, MBD2, MBD3, MBD4 and MECP2. Results We performed database searches for new proteins containing an MBD and identified six amino acid sequences which are different from the previously described ones. Here we present a comparison of their MBD sequences, additional protein motifs and the expression of the encoding genes. A calculated unrooted dendrogram indicates the existence of at least four different groups of MBDs within these proteins. Two of these polypeptides, KIAA1461 and KIAA1887, were only present as predicted amino acid sequences based on a partial human cDNA. We investigated their expression by Northern blot analysis and found transcripts of ~8 kb and ~5 kb respectively, in all eight normal tissues studied. Conclusions Eleven polypeptides with a MBD could be identified in mouse and man. The analysis of protein domains suggests a role in transcriptional regulation for most of them. The knowledge of additional existing MBD proteins and their expression pattern is important in the context of Rett syndrome.

  4. Novel binding patterns between ganoderic acids and neuraminidase: Insights from docking, molecular dynamics and MM/PBSA studies.

    Science.gov (United States)

    Yang, Zhiwei; Wu, Fei; Yuan, Xiaohui; Zhang, Lei; Zhang, Shengli

    2016-04-01

    Recently, ganoderic acids (GAs) give rise to the attractive candidates of novel neuraminidase (NA) inhibitors. However, there is still no evident conclusion about their binding patterns. To this end, docking, molecular dynamics and MM/PBSA methods were combined to study the binding profiles of GAs with the N1 protein and familiar H274Y and N294S mutations (A/Vietnam/1203/04 stain). It was found that the binding affinities of ganoderic acid DM and Z (ΔGbind, -16.83 and -10.99 kcal mol(-1)) are comparable to that of current commercial drug oseltamivir (-23.62 kcal mol(-1)). Electrostatic interaction is the main driving force, and should be one important factor to evaluate the binding quality and rational design of NA inhibitors. The 150-loop residues Asp151 and Arg152 played an important role in the binding processes. Further analysis revealed that ganoderic acid DM is a potential source of anti-influenza ingredient, with novel binding pattern and advantage over oseltamivir. It had steric hindrance on the 150 cavity of N1 protein, and exerted activities across the H274Y and N294S mutations. This work also pointed out how to effectively design dual-site NA inhibitors and reinforce their affinities. These findings should prove valuable for the in-depth understanding of interactions between NA and GAs, and warrant the experimental aspects to design novel anti-influenza drugs. PMID:26905206

  5. Lectin binding profiles of SSEA-4 enriched, pluripotent human embryonic stem cell surfaces

    OpenAIRE

    Shin Soojung; Jones Karen; Lyons Ian; Mitalipova Maisam; Venable Alison; Pierce Michael; Stice Steven

    2005-01-01

    Abstract Background Pluripotent human embryonic stem cells (hESCs) have the potential to form every cell type in the body. These cells must be appropriately characterized prior to differentiation studies or when defining characteristics of the pluripotent state. Some developmentally regulated cell surface antigens identified by monoclonal antibodies in a variety of species and stem cell types have proven to be side chains of membrane glycolipids and glycoproteins. Therefore, to examine hESC s...

  6. VHF Wind Profiling Radar Studies at Darwin, Australia

    Science.gov (United States)

    Dolman, B. K.; Reid, I. M.; May, P. T.; Vincent, R. A.

    2012-12-01

    A 54.1 MHz wind profiling radar was installed at Darwin, Australia in late 2005, to participate in the TWP-ICE campaign, and it has remained in this location. The primary purpose of the instrument was to measure the horizontal and vertical lower troposphere winds in the vertical column above the profiler. The profiler operates at 7.5 kW, and utilizes the Spaced Antenna Full Correlation Analysis (FCA) technique to measure winds, this achieving high temporal resolution. In addition to sampling the wind field, VHF profilers are capable of retrieving the rain drop size distribution (DSD), as radar returns are received from precipitation and clear-air with roughly equal magnitude. DSD retrievals then permit examination of the precipitation structure and spatial and temporal evolution in the vertical column above the profiler as rain bands pass over head. Understanding the evolution of the rain drop size distribution (DSD) in the descent from cloud to ground is important for quantitative precipitation estimation. The Darwin profiler has been used in multiple intercomparison studies. The FCA technique is well known to underestimate the wind magnitude by up to 10%, when compared to other measurement techniques, but agree well in direction. As the profiler is co-located with routine sonde launches, a large intercomparison data set exists, which can be used to investigate empirical corrections to the underestimation. Similarly, profiler vertical velocity estimates can be compared to Doppler Lidar measurements, and the relative strengths of both instruments examined. The profiler can also be used in rainfall studies. During TWP-ICE, when rainfall events passed over the profiler the DSD was retrieved. Each rain event was then separated into stratiform, convective and transitional regions. The integral rainfall parameters were then averaged through each region, and examined for evidence of a dominant microphysical process. For example, evaporation is detected through an

  7. STUDY OF PHYSIOLOGICAL PROFILE OF INDIAN BOXERS

    Directory of Open Access Journals (Sweden)

    Gulshan Lal Khanna

    2006-07-01

    Full Text Available The present study was conducted to study the morphological, physiological and biochemical characteristics of Indian National boxers as well as to assess the cardiovascular adaptation to graded exercise and actual boxing round. Two different studies were conducted. In the first study [N = 60, (junior boxers below-19 yrs, n = 30, (senior boxers-20-25 yrs, n = 30] different morphological, physiological and biochemical parameters were measured. In the second study (N = 21, Light Weight category- <54 kg, n = 7; Medium weight category <64 kg, n = 7 and Medium heavy weight category <75 kg, n = 7 cardiovascular responses were studied during graded exercise protocol and actual boxing bouts. Results showed a significantly higher (p < 0.05 stature, body mass, LBM, body fat and strength of back and grip in senior boxers compared to juniors. Moreover, the senior boxers possessed mesomorphic body conformation where as the juniors' possessed ectomorphic body conformation. Significantly lower (p < 0.05 aerobic capacity and anaerobic power were noted in junior boxers compared to seniors. Further, significantly higher (p < 0.05 maximal heart rates and recovery heart rates were observed in the seniors as compared to the juniors. Significantly higher maximum heart rates were noted during actual boxing compared to graded exercise. Blood lactate concentration was found to increase with the increase of workload during both graded exercise and actual boxing round. The senior boxers showed a significantly elevated (p < 0.05 levels of hemoblobin, blood urea, uric acid and peak lactate as compared to junior boxers. In the senior boxers significantly lower levels of total cholesterol, triglyceride and LDLC were observed as compared to junior boxers. No significant change has been noted in HDLC between the groups. The age and level of training in boxing has significant effect on Aerobic, anaerobic component. The study of physiological responses during graded exercise

  8. Studies of the silencing of Baculovirus DNA binding protein

    NARCIS (Netherlands)

    Quadt, I.; Lent, van J.W.M.; Knebel-Morsdorf, D.

    2007-01-01

    Baculovirus DNA binding protein (DBP) binds preferentially single-stranded DNA in vitro and colocalizes with viral DNA replication sites. Here, its putative role as viral replication factor has been addressed by RNA interference. Silencing of DBP in Autographa californica multiple nucleopolyhedrovir

  9. Study on Synthesis and Binding Ability of a New Anion Receptor Containing NH Binding Sites

    Institute of Scientific and Technical Information of China (English)

    QIAO,Yan-Hong; LIN,Hai; LIN,Hua-Kuan

    2007-01-01

    A new colorimetric recognition receptor 1 based on the dual capability containing NH binding sites of selectively sensing anionic guest species has been synthesized. Compared with other halide anions, its UV/Vis absorption spectrum in dimethyl sulfoxide showed the response toward the presence of fluoride anion with high selectivity,and also displayed dramatic color changes from colorless to yellow in the presence of TBAF (5 × 10-5 mol/L). The similar UV/Vis absorption spectrum change also occurred when 1 was treated with AcO- while a little change with H2PO-4 and OH-. Receptor 1 has almost not affinity abilities to Cl-, Br- and I-. The binding ability of receptor 1to fluoride with high selectivity over other halides contributes to the anion size and the ability of forming hydrogen bonding. While the different ability of binding with geometrically triangular (AcO-), tetrahedral (H2PO-4 ) and linear (OH-) anions maybe result from their geometry configuration.

  10. Cohort profile: the Young Lives study.

    Science.gov (United States)

    Barnett, Inka; Ariana, Proochista; Petrou, Stavros; Penny, Mary E; Duc, Le Thuc; Galab, S; Woldehanna, Tassew; Escobal, Javier A; Plugge, Emma; Boyden, Jo

    2013-06-01

    Young Lives is an international longitudinal study investigating the changing nature of childhood poverty in four low-income countries [Ethiopia, India (Andhra Pradesh), Peru and Vietnam] over a 15-year period. In each country, the cohort is comprised of ≈ 2000 children aged between 6 and 18 months and up to 1000 children aged between 7 and 8 years, recruited in 2002 and sampled from 20 sentinel sites. The first survey data collection from primary caregivers and older children took place in 2002, the second in 2006-07 and the third in 2009-10. Data on the community contexts were collected to complement the household surveys. To elaborate and extend the quantitative data, longitudinal qualitative research with a subgroup of the children was carried out in 2007, 2008 and 2010-11. Topic areas covered included nutrition, health and well-being, cognitive and physical development, health behaviours and education, as well as the social, demographic and economic status of the household. Survey data from the study are archived in the International Section of the UK Public Data Archive. PMID:22617687

  11. Interaction of zinc and cobalt with dipeptides and their DNA binding studies

    Indian Academy of Sciences (India)

    P Rabindra Reddy; M Radhika; K Srinivas Rao

    2004-06-01

    Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt complexes.

  12. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

    Directory of Open Access Journals (Sweden)

    Ronne Hans

    2008-11-01

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

  13. The PROTON study : profiles of transfusion recipients in the Netherlands

    NARCIS (Netherlands)

    Borkent-Raven, B.A.

    2010-01-01

    In this thesis, Barbara Borkent presents the results of the PROTON study. PROTON is a (Dutch) acronym for PROfiles of TransfusiON recipients. The aim of this study was to describe the distribution of blood products over various patient groups in the Netherlands. Quantitative information on recipient

  14. PROSPECTIVE STUDY OF LIPID PROFILE IN DIFFERENT STAGES OF DIABETES

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    Indira Bhaskar

    2016-03-01

    Full Text Available Diabetes mellitus is increasing worldwide. This study was undertaken to evaluate the lipid profile among HbA1c (Glycated haemoglobin in Type 2 diabetes and correlation of higher values of HbA1c with risk of Cardiovascular disease. The study was conducted in KPC Medical College and Hospital; 230 patients diagnosed of Type 2 diabetes aged between 21-90 years. These patients were divided into 3 groups based on their HbA1c values as controlled, under-controlled and uncontrolled diabetes. The glycated haemoglobin and lipid profile were recorded with standard procedure. Data was analysed statistically. Total number of cases were 230, males 104 and females 126. Uncontrolled diabetes had significantly high values of lipid profile. From our results, we concluded that high HbA1c have increased risk of Cardiovascular Disease.

  15. Evaluation of serum and salivary lipid profile: A correlative study

    Directory of Open Access Journals (Sweden)

    Simranjit Singh

    2014-01-01

    Full Text Available Context: The correlation of serum and salivary lipid profile has been poorly characterized. The most commonly used laboratory diagnostic procedures for lipid profile involve analysis of cellular and chemical constituents of blood/plasma. As a diagnostic aid, saliva offers many advantages over serum. Aims: To evaluate and compare the serum and salivary lipid profile levels in healthy individuals and to validate the role of saliva as a non-invasive diagnostic tool for assessing lipid profile. Settings and Design: The present study was a prospective study. Materials and Methods: A total of 100 healthy study subjects who had no complaint or any major illness in recent past were selected. The parameters assessed included serum and salivary: total cholesterol (TC, high-density lipoprotein-cholesterol (HDLC, low-density lipoprotein-cholesterol (LDLC, very low-density lipoprotein-cholesterol (VLDLC and triglycerides (TGL. Statistical Analysis Used: Evaluation of results and statistical analysis was carried out using descriptive, correlation and regression analysis. Results: There was a moderate level of correlation between serum and salivary TC, TGL, HDLC and VLDLC and there was a low and quite small correlation between serum and salivary LDLC. For all the five parameters assessed as a part of lipid profile, the correlation coefficients were highly significant statistically and also, with an increase in the serum mean values, corresponding increase in the saliva mean values for all the five parameters was noted. Conclusions: From the present study we conclude that saliva can be used as a non-invasive diagnostic tool for assessing lipid profile.

  16. Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity

    Directory of Open Access Journals (Sweden)

    Zulezwan A. Malik

    2013-12-01

    Full Text Available Two-dimensional gel electrophoresis provides robust comparative analysis of skeletal muscle, but this technique is laborious and limited by its inability to resolve all proteins. In contrast, orthogonal separation by SDS-PAGE and reverse-phase liquid chromatography (RPLC coupled to mass spectrometry (MS affords deep mining of the muscle proteome, but differential analysis between samples is challenging due to the greater level of fractionation and the complexities of quantifying proteins based on the abundances of their tryptic peptides. Here we report simple, semi-automated and time efficient (i.e., 3 h per sample proteome profiling of skeletal muscle by 1-dimensional RPLC electrospray ionisation tandem MS. Solei were analysed from rats (n = 5, in each group bred as either high- or low-capacity runners (HCR and LCR, respectively that exhibited a 6.4-fold difference (1,625 ± 112 m vs. 252 ± 43 m, p < 0.0001 in running capacity during a standardized treadmill test. Soluble muscle proteins were extracted, digested with trypsin and individual biological replicates (50 ng of tryptic peptides subjected to LC-MS profiling. Proteins were identified by triplicate LC-MS/MS analysis of a pooled sample of each biological replicate. Differential expression profiling was performed on relative abundances (RA of parent ions, which spanned three orders of magnitude. In total, 207 proteins were analysed, which encompassed almost all enzymes of the major metabolic pathways in skeletal muscle. The most abundant protein detected was type I myosin heavy chain (RA = 5,843 ± 897 and the least abundant protein detected was heat shock 70 kDa protein (RA = 2 ± 0.5. Sixteen proteins were significantly (p < 0.05 more abundant in HCR muscle and hierarchal clustering of the profiling data highlighted two protein subgroups, which encompassed proteins associated with either the respiratory chain or fatty acid oxidation. Heart-type fatty acid binding protein (FABPH was 1

  17. Study on Higher Efficiency Thermal Cycling Profile for HALT

    Institute of Scientific and Technical Information of China (English)

    TAO Jun-yong; CHU Wei-hua; CHEN Xun

    2008-01-01

    HALT (highly accelerated life test) is a new reliability test technique. This paper uses nonlinear finite element method to analyze the stress strain characteristic of solder joints of PQFP (plastic quad flat packaging) and BGA (ball grid array) under thermal cycle test, and studies influences of profile parameters of the thermal cycle, such as hot and cold soak temperature, hot and cold soak time and temperature change rate, on elastic strain range, accumulated plastic strain, fatigue life and test efficiency of two types of solder joints. Based on the above research and experimental verification, this paper presents the method to build an optimal thermal cycling profile for HALT of electronic components.

  18. The Theoretical Orientation Profile Scale-Revised: A Validation Study.

    Science.gov (United States)

    Worthington, Roger L.; Dillon, Frank R.

    2003-01-01

    This study supported evidence of reliability and validity of the Theoretical Orientation Profile Scale-Revised (TOPS-R) scores. The TOPS-R was designed to measure theoretical orientation among counselors and trainees. Factor analysis yielded a 6-factor solution accounting for 87.5% of the total variance in the scale. The 6 factors corresponded to…

  19. Case Studies: Profiles of Women Recovering from Drug Addiction.

    Science.gov (United States)

    Miller, Suzanne M.

    1995-01-01

    Profiles two women over an eight-month study who abused alcohol and other drugs while pregnant and describes their recovery from the addiction. Examines, from an ecological framework, the women's experiences with drug addiction, treatment, and recovery, and recounts their situation through each. (JPS)

  20. Molecular profiling of breast cancer: transcriptomic studies and beyond.

    Science.gov (United States)

    Culhane, A C; Howlin, J

    2007-12-01

    Utilisation of 'omics' technologies, in particular gene expression profiling, has increased dramatically in recent years. In basic research, high-throughput profiling applications are increasingly used and may now even be considered standard research tools. In the clinic, there is a need for better and more accurate diagnosis, prognosis and treatment response indicators. As such, clinicians have looked to omics technologies for potential biomarkers. These prediction profiling studies have in turn attracted the attention of basic researchers eager to uncover biological mechanisms underlying clinically useful signatures. Here we highlight some of the seminal work establishing the arrival of the omics, in particular transcriptomics, in breast cancer research and discuss a sample of the most current applications. We also discuss the challenges of data analysis and integrated data analysis with emphasis on utilising the current publicly available gene expression datasets. (Part of a Multi-author Review). PMID:17957338

  1. Myosin Binding Protein-C Slow: a multifaceted family of proteins with a complex expression profile in fast and slow twitch skeletal muscles

    Directory of Open Access Journals (Sweden)

    Maegen A Ackermann

    2013-12-01

    Full Text Available Myosin Binding Protein-C slow (sMyBP-C comprises a complex family of proteins expressed in slow and fast type skeletal muscles. Similar to its fast and cardiac counterparts, sMyBP-C functions to modulate the formation of actomyosin cross-bridges, and to organize and stabilize sarcomeric A- and M-bands. The slow form of MyBP-C was originally classified as a single protein, however several variants encoded by the single MYBPC1 gene have been recently identified. Alternative splicing of the 5’ and 3’ ends of the MYBPC1 transcript has led to the differential expression of small unique segments interspersed between common domains. In addition, the NH2-terminus of sMyBP-C undergoes complex phosphorylation. Thus, alternative splicing and phosphorylation appear to regulate the functional activities of sMyBP-C. sMyBP-C proteins are not restricted to slow twitch muscles, but they are abundantly expressed in fast twitch muscles, too. Using bioinformatic tools, we herein perform a systematic comparison of the known human and mouse sMyBP-C variants. In addition, using single fiber westerns and antibodies to a common region of all known sMyBP-C variants, we present a detailed and comprehensive characterization of the expression profile of sMyBP-C proteins in the slow twitch soleus and the fast twitch flexor digitorum brevis (FDB mouse muscles. Our studies demonstrate for the first time that distinct sMyBP-C variants are co-expressed in the same fiber, and that their expression profile differs among fibers. Given the differential expression of sMyBP-C variants in single fibers, it becomes apparent that each variant or combination thereof may play unique roles in the regulation of actomyosin cross-bridges formation and the stabilization of thick filaments.

  2. The A0 blood group genotype modifies the jejunal glycomic binding pattern profile of piglets early associated with a simple or complex microbiota.

    Science.gov (United States)

    Priori, D; Colombo, M; Koopmans, S-J; Jansman, A J M; van der Meulen, J; Trevisi, P; Bosi, P

    2016-02-01

    The intestinal epithelium glycocalyx sugar motif is an important determinant of the bacterial-host interaction and may be affected in pigs by gut microbiota and by blood group genotype. The aim was to study the effect of intestinal association with different microbiota and A0 blood group genotypes on the expressed glycomic pattern in the small intestine. Twelve caesarean-derived pigs previously associated with a simple association (SA) or complex association (CA) microbiota were selected at 26 to 37 d of age. In each subject, different jejunal loops were perfused for 8 h with enterotoxigenic K88 (ETEC), ETEC fimbriae (F4), (LAM), or a saline control. The piglets were genotyped for A0 blood group and the glycomic profile was evaluated by microscopic screening of lectin binding: peanut agglutinin (PNA), which is galactose specific; agglutinin I (UEA), which is fucose specific; lectin II (MALii), which is sialic acid specific; concavalin A, which is mannose specific; soybean agglutinin (SBA), which is -acetyl-galactosamine specific; and wheat germ agglutinin (WGA), which is -acetyl-glucosamine specific. A0 pigs had fewer UEA-positive cells, MALii-positive cells ( < 0.001), and SBA-positive cells ( < 0.10) than 00 pigs. Simple association pigs had more SBA positive cells ( < 0.01) than CA pigs. Enterotoxigenic K88-perfused intestinal loops had fewer UEA-positive cells ( < 0.01) and WGA positive cells ( < 0.001) cells and more PNA positive cells (only in SA pigs, < 0.01). No effects of introduction of F4 and LAM in the intestinal lumen were observed. The porcine A0 blood group genotype and the luminal presence of ETEC strongly affected the jejunal mucosa glycomic pattern profile whereas an early oral simple or complex microbial association had limited effects. Pig genetic background has relevance on the cross talk between intestinal epithelium glycocalyx sugar motif and ETEC and, ultimately, on the gut microbial colonization in later life. PMID:27065129

  3. Binding Cooperativity Matters: A GM1-Like Ganglioside-Cholera Toxin B Subunit Binding Study Using a Nanocube-Based Lipid Bilayer Array.

    Science.gov (United States)

    Worstell, Nolan C; Krishnan, Pratik; Weatherston, Joshua D; Wu, Hung-Jen

    2016-01-01

    Protein-glycan recognition is often mediated by multivalent binding. These multivalent bindings can be further complicated by cooperative interactions between glycans and individual glycan binding subunits. Here we have demonstrated a nanocube-based lipid bilayer array capable of quantitatively elucidating binding dissociation constants, maximum binding capacity, and binding cooperativity in a high-throughput format. Taking cholera toxin B subunit (CTB) as a model cooperativity system, we studied both GM1 and GM1-like gangliosides binding to CTB. We confirmed the previously observed CTB-GM1 positive cooperativity. Surprisingly, we demonstrated fucosyl-GM1 has approximately 7 times higher CTB binding capacity than GM1. In order to explain this phenomenon, we hypothesized that the reduced binding cooperativity of fucosyl-GM1 caused the increased binding capacity. This was unintuitive, as GM1 exhibited higher binding avidity (16 times lower dissociation constant). We confirmed the hypothesis using a theoretical stepwise binding model of CTB. Moreover, by taking a mixture of fucosyl-GM1 and GM2, we observed the mild binding avidity fucosyl-GM1 activated GM2 receptors enhancing the binding capacity of the lipid bilayer surface. This was unexpected as GM2 receptors have negligible binding avidity in pure GM2 bilayers. These unexpected discoveries demonstrate the importance of binding cooperativity in multivalent binding mechanisms. Thus, quantitative analysis of multivalent protein-glycan interactions in heterogeneous glycan systems is of critical importance. Our user-friendly, robust, and high-throughput nanocube-based lipid bilayer array offers an attractive method for dissecting these complex mechanisms. PMID:27070150

  4. Insulin binding to plastic bags: a methodologic study.

    Science.gov (United States)

    Twardowski, Z J; Nolph, K D; McGary, T J; Moore, H L; Collin, P; Ausman, R K; Slimack, W S

    1983-04-01

    A radiotracer method to assess insulin binding to commercially available plastic peritoneal dialysis solution containers was developed. A peritoneal dialysis bag (bag 2) was emptied and attached to another full bag (bag 1) of the same kind. In the syringe-to-bag method, bag 1 was symmetrically injected through the bag wall with four syringes containing dialysis solution and radioactive insulin, with or without regular insulin. The radioactivity in each syringe was measured with a gamma counter before injection, and all of the samples were counted afterwards directly in the syringes. Using a bag-to-bag transfer method, bag 1 was agitated, eight samples were taken from different parts through the wall, and then the contents were transferred to bag 2. Bag 2 was then agitated and eight samples were taken and counted. In the bag-pieces method, pieces of bag wall were cut and the radioactivity on the walls was measured to determine the amount of binding. The syringe-to-bag method gave negative results, severely underestimating the amount of insulin binding. The bag-to-bag transfer method yielded positive results in all instances. Increasing the amounts of regular insulin had no demonstrable impact on percent of binding. When the bag-to-bag method was compared with the bag-pieces method, it gave only slightly higher values; however, the bag-to-bag method was considered more reliable because the counting can be controlled more effectively. A 15-minute delay in sampling was not found to influence insulin binding. A reliable method of assessing insulin binding must be based on the following two principles: (1) The transfer of samples to intermediate containers should be avoided, and (2) radiotracer concentrations in the samples should be similar. PMID:6342377

  5. Alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome P450 encoded on the nifD excision element of Anabaena 7120

    Directory of Open Access Journals (Sweden)

    Fjetland Conrad R

    2005-03-01

    Full Text Available Abstract Background Alkanes have been hypothesized to act as universal inducers of bacterial cytochrome P450 gene expression. We tested this hypothesis on an unusual P450 gene (cyp110 found on a conserved 11 kilobase episomal DNA element of unknown function found in filamentous cyanobacteria. We also monitored the binding of potential substrates to the P450 protein and explored the distribution of P450 protein in vegetative cells and nitrogen-fixing heterocysts using immuno-electron microscopy. Results Hexadecane treatments resulted in a two-fold increase in mRNA, and a four-fold increase in P450 protein levels relative to control cultures. Hexane, octane and dodecane were toxic and induced substantial changes in membrane morphology. Long-chain saturated and unsaturated fatty acids were shown to bind the CYP110 protein using a spectroscopic spin-shift assay, but alkanes did not bind. CYP110 protein was detected in vegetative cells but not in differentiated heterocysts where nitrogen fixation occurs. Conclusion Hexadecane treatment was an effective inducer of CYP110 expression in cyanobacteria. Based on substrate binding profiles and amino acid sequence similarities it is hypothesized that CYP110 is a fatty acid ω-hydroxylase in photosynthetic cells. CYP110 was found associated with membrane fractions unlike other soluble microbial P450 proteins, and in this regard CYP110 more closely resembles eukarytotic P450s. Substrate stablization is an unlikely mechanism for alkane induction because alkanes did not bind to purified CYP110 protein.

  6. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic

    2014-09-01

    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  7. Radiometric Study of Soil Profiles in the Infrared Band

    Science.gov (United States)

    Ponomareva, T. V.; Ponomarev, E. I.

    2016-02-01

    The applicability of radiometric survey of soil profiles in the infrared range for the analysis of soil physical properties was studied. Radiometric data were obtained for different dates of the growing season for a number of soil profiles. The specificity of temperature profiles of texture-differentiated soils (Luvisols and Retisols) as related to weather conditions of the growing season was examined. The correlation analysis showed a close relationship between the air and surface soil temperatures and between the radiometric and thermodynamic soil temperatures in the upper 10 cm. In the studied profiles, the gradient of radiometric temperatures reached 0.5-0.8°C/cm in the humus horizons and sharply decreased at the depth of more than 15-20 cm. The gradient analysis of radiometric images made it possible to outline the boundaries of soil horizons. For the texture-differentiated soils, the most distinct boundaries were established between the gray-humus AY horizon and the underlying eluvial EL horizon in podzolic soils and between the AY horizon and the underlying humus-eluvial AEL horizon in gray soils.

  8. Glucagon and adenylate cyclase: binding studies and requirements for activation.

    Science.gov (United States)

    Levey, G S; Fletcher, M A; Klein, I

    1975-01-01

    Solubilization of myocardial adenylate cyclase abolished responsiveness to glucagon and catecholamines, two of the hormones which activate the membrane-bound enzyme. Adenylate cyclase freed of detergent by DEAE-cellulose chromatography continues to remain unresponsive to hormone stimulation. However, adding purified bovine brain phospholipids--phosphotidylserine and monophosphatidylinositol--restored responsiveness to glucagon and catecholamines, respectively. 125-i-glucagon binding appeared to be independent of phospholipid, since equal binding was observed in the presence or absence of detergent and in the presence or absence of phospholipids. Chromatography of the solubilized preparation on Sephadex G-100 WAS CHARACTERIZED BY 125-I-glucagon binding and fluoride-stimulatable adenylate cyclase activity appearing in the fractions consistent with the void volume, suggesting a molecular weight greater than 100,000 for the receptor-adenylate cyclase complex. Prior incubation of the binding peak with 125-I-glucagon and rechromatography of the bound glucagon on Sephadex G-100 shifted its elution to a later fraction consistent with a smaller-molecular-weight peak. The molecular weight of this material was 24,000 to 28,000, as determined by SDS polyacrylamide gel electrophoresis. The latter findings are consistent with a dissociable receptor site for glucagon on myocardial adenylate cyclase. PMID:165684

  9. Vibrational study on the cobalt binding mode of Carnosine

    Science.gov (United States)

    Torreggiani, Armida; Taddei, Paola; Tinti, Anna; Fini, Giancarlo

    2002-10-01

    The Co(II)- L-Carnosine (Carnos) system was investigated at different pH and metal/ligand molar ratios by Raman and IR spectroscopy. Raman spectra present some marker bands yielding information on the ability of the Co(II)/Carnos system to bind molecular oxygen and to identify the metal co-ordination site of the imidazole ring (N π or N τ atom) of Carnos. The existence of different oxygenated species is greatly affected by pH and the structure of the predominant complexes depends on the available nitrogen atoms. Under basic conditions, binuclear complexes binding molecular oxygen are the predominant species and two forms (monobridged and dibridged) were identified by the Raman νO-O band (750-850 cm -1). Decreasing pH to 7, the species present in the system are less able to bind oxygen. Hydrogen peroxide and a Co(III) chelate not binding O 2, were formed with a significant conversion of peroxo into superoxo complexes. A slight excess of Carnos does not enhance metal chelation. In slightly acidic conditions, the formation of H 2O 2 and superoxo species is more enhanced than at pH 7 and another Co(III) chelate is probably formed.

  10. Clinical profile of forefoot eczema: A study of 42 cases

    OpenAIRE

    Brar Kamal; Shenoi S; Balachandran C; Mehta Vandana

    2005-01-01

    BACKGROUND : Forefoot eczema (FE) is characterized by dry fissured dermatitis of the plantar surface of the feet. AIM : To study the clinical profile of FE and the possible etiological factors. METHODS : Forty-two patients with FE were included in the study. A detailed history was recorded and examination done. Fungal scrapings and patch test with Indian Standard Series (ISS) were performed in all patients. RESULTS : The most common site affected was the plantar surface of the great toe in...

  11. STUDIES ON SOME PHARMACOGNOSTIC PROFILES OF SWIETENIA MACROPHYLLA. King

    OpenAIRE

    K. Arumugasamy; Latha, K.V.; kumar, N.H. Sathish

    2004-01-01

    The aerial parts and seeds of Swietenia macrophylla King (Meliaceae) are used in exotic medicine systems. In the present study, a preliminary phytochemical and few pharmacological profiles were under taken. The physical constans, extractive and ash values were examined. The presence of secondary metabolites in the aerial parts and seeds showed that Swietenia macrophylla is a good source of active principles. TLC studies were done by treating dry treating dry powder of Swietenia macrophylla wi...

  12. Spinal patterns as predictors of personality profiles: a pilot study.

    Science.gov (United States)

    Koren, T; Rosenwinkel, E

    1992-01-01

    The present pilot study is part of an ongoing effort to further the investigation of the relationship between spinal patterns and personality. The present pilot study seeks to identify likely spinal patterns of certain personality profiles and asks whether changing posture can affect personality, and/or can emotional states alter posture? Forty patients of a private chiropractic practice participated in the study. Four radiographs (x-rays) of each subject were taken and each subject completed the Minnesota Multiphasic Personality Inventory (MMPI). Measurements obtained from the radiographs and the MMPI data were used to derive general linear models of the predictability of the MMPI in terms of the spinal/postural measures. Several models were highly significant and preliminary support for the authors' hypothesis that spinal patterns are likely to be predictive of personality profiles is suggested. Support for previous research is offered and directions for future research are discussed. PMID:1428613

  13. Roentgenographic studies of Korean adults profile with normal occlusion

    International Nuclear Information System (INIS)

    A roentgraphic cephalometric study was made on the soft and hard tissue profile of Korean adults. The subject consisted of 52 males and 54 females from 17 to 22 years of age and with normal occlusion and acceptable profile. Twenty one landmarks were plotted and two oriented lines named SnH line and SnV line were drawn on the tracings of all cephalograms. The means and the standard deviations from the subjects were calculated in each measuring category and the means were compared with those of male and female samples. The results were obtained as follow: 1. In depth and height, individual variations and sex differences of the lower facial profile were larger than the upper face. 2. The sex differences of upper facial profile were larger in height than depth. 3. The individual variations and sex differences of the top of nose were the smallest in all measuring points. 4. The thickness of the soft tissue of upper face and upper lip in male sample were larger than those of female, but the same matter were not found in mental region.

  14. Electronic structure of AlAs: A Compton profile study

    International Nuclear Information System (INIS)

    The electronic structure of AlAs through a Compton profile study is presented in this paper. Theoretical calculations are performed following the linear combination of atomic orbitals (LCAO) method and the empirical pseudopotential method (EPM). In LCAO method, to treat exchange and correlation two cases are considered. In the first case, the exchange function of Becke and the correlation function of Perdew and Wang on the basis of generalized gradient approximation (PW-GGA) is adopted. In the second case, the hybrid function B3PW is adopted. Measurement of Compton profile on the polycrystalline AlAs is performed using 59.54 keV gamma-rays. The spherically averaged theoretical Compton profiles are in good agreement with the measurement. The best agreement is, however, shown by the EPM. The anisotropies predicted by B3PW and the EPM are smaller than those from the PW-GGA calculation. On the basis of equal-valence-electron-density profiles, it is found that AlAs is more covalent compared to AlN. The charge transfer model suggests transfer of 0.6e- from Al to As on compound formation.

  15. Studies on folate binding and a radioassay for serum and whole blood folate using goat milk as binding agent

    International Nuclear Information System (INIS)

    Preparations of cow, goat, buffalo, and human milk in addition to pig plasma were tested for folate binding properties. Of these, only pig plasma and goat milk showed sufficient binding to enable use as binding agents in a radioassay for serum and whole blood folate. The binding of folate by cow mild preparations in particular was found to be very poor. (orig.)

  16. Tamoxifen and curcumin binding to serum albumin. Spectroscopic study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Maliszewska, M.; Pożycka, J.; Równicka-Zubik, J.; Góra, A.; Sułkowska, A.

    2013-07-01

    Tamoxifen (TMX) is widely used for the breast cancer treatment and is known as chemopreventive agent. Curcumin (CUR) is natural phenolic compound with broad spectrum of biological activity e.g. anti-inflammatory, antimicrobial, antiviral, antifungal and chemopreventive. Combination of tamoxifen and curcumin could be more effective with lower toxicity than each agent alone in use for the treatment or chemoprevention of breast cancer. Binding of drugs to serum albumin is an important factor, which determines toxicity and therapeutic dosage of the drugs. When two drugs are administered together the competition between them for the binding site on albumin can result in a decrease in bound fraction and an increase in the concentration of free biologically active fraction of drug.

  17. Structural study of LEDGF/p75 binding partners

    Czech Academy of Sciences Publication Activity Database

    Těšina, Petr; Čermáková, Kateřina; Procházková, Kateřina; Hořejší, Magdalena; Christ, F.; De Rijck, J.; Veverka, Václav; Řezáčová, Pavlína

    2013-01-01

    Roč. 20, č. 1 (2013), s. 12-12. ISSN 1211-5894. [Discussions in Structural Molecular Biology. Annual Meeting of the Czech Society for Structural Biology /11./. 14.03.2013-16.03.2013, Nové Hrady] R&D Projects: GA MŠk(CZ) LK11205 Institutional support: RVO:61388963 ; RVO:68378050 Keywords : LEDGF/p75 * HIV * integrase-binding domain Subject RIV: EB - Genetics ; Molecular Biology

  18. EPR studies of cooperative binding of Cu (II) to hemoglobin

    International Nuclear Information System (INIS)

    The investigation of the relative affinities of the two pairs of hemoglobin copper sites by monitoring the EPR spectra of the complexes formed by the reaction of copper with deoxyhemoglobin is reported. A model in which two sites are assumed to accept copper ions in a noncooperative way is not able to predict the experimental results. Thus it is conclude that the binding of these ions to hemoglobin is a cooperative phenomenon. (Author)

  19. Tight-binding study of bilayer graphene Josephson junctions

    OpenAIRE

    Muñoz, W. A.; Covaci, L.; Peeters, F. M.

    2012-01-01

    Using highly efficient simulations of the tight-binding Bogoliubov-de Gennes model we solved self-consistently for the pair correlation and the Josephson current in a Superconducting-Bilayer graphene-Superconducting Josephson junction. Different doping levels for the non-superconducting link are considered in the short and long junction regime. Self-consistent results for the pair correlation and superconducting current resemble those reported previously for single layer graphene except in th...

  20. Studies on a novel macrophage-specific calmodulin binding glycoprotein

    Energy Technology Data Exchange (ETDEWEB)

    Orlow, S.J.

    1986-01-01

    The murine macrophage-like cell line J774 and peritoneal exudate cells elicited with thioglycollate or starch contain a major calmodulin-binding protein which is absent in trifluoperazine-resistant variants of J774, resident peritoneal macrophages and these elicited with concanavalin A, lipopolysaccharide, proteose peptone or Bacillus Clamette Guerin. Resident murine peritoneal cells maintained in tissue culture for 3 days begin to accumulate this protein as do human peripheral blood monocytes after 7 days of culture. A specific competitive displacement radioimmunoassay was developed using a rabbit antiserum raised to the partially purified calmodulin binding protein and (/sup 125/I) calmodulin covalently crosslinked to the principal calmodulin binding protein in the preparation. The radioimmunoassay confirmed the unique cellular distribution of this protein suggesting that it may be a marker for certain stages of macrophage differentiation. Monoclonal antibodies were prepared and one of these was used to further purify the protein by immunoaffinity chromatography. A protein of molecular weight 50,000 to 60,000 was isolated. It could be selectively adsorbed to wheat germ agglutinin agarose and subsequently eluted with N-acetyl glucosamine. This property plus its sensitivity to endoglycosidase F led to the conclusion that it is a glycoprotein. The cellular distribution, subcellular localization and evidence of glycosylation suggest that this protein may be a macrophage-specific receptor with a high affinity for calcium-calmodulin.

  1. Studies on a novel macrophage-specific calmodulin binding glycoprotein

    International Nuclear Information System (INIS)

    The murine macrophage-like cell line J774 and peritoneal exudate cells elicited with thioglycollate or starch contain a major calmodulin-binding protein which is absent in trifluoperazine-resistant variants of J774, resident peritoneal macrophages and these elicited with concanavalin A, lipopolysaccharide, proteose peptone or Bacillus Clamette Guerin. Resident murine peritoneal cells maintained in tissue culture for 3 days begin to accumulate this protein as do human peripheral blood monocytes after 7 days of culture. A specific competitive displacement radioimmunoassay was developed using a rabbit antiserum raised to the partially purified calmodulin binding protein and (125I) calmodulin covalently crosslinked to the principal calmodulin binding protein in the preparation. The radioimmunoassay confirmed the unique cellular distribution of this protein suggesting that it may be a marker for certain stages of macrophage differentiation. Monoclonal antibodies were prepared and one of these was used to further purify the protein by immunoaffinity chromatography. A protein of molecular weight 50,000 to 60,000 was isolated. It could be selectively adsorbed to wheat germ agglutinin agarose and subsequently eluted with N-acetyl glucosamine. This property plus its sensitivity to endoglycosidase F led to the conclusion that it is a glycoprotein. The cellular distribution, subcellular localization and evidence of glycosylation suggest that this protein may be a macrophage-specific receptor with a high affinity for calcium-calmodulin

  2. Profiling dizziness in older primary care patients: an empirical study.

    Directory of Open Access Journals (Sweden)

    Jacquelien Dros

    Full Text Available BACKGROUND: The diagnostic approach to dizzy, older patients is not straightforward as many organ systems can be involved and evidence for diagnostic strategies is lacking. A first differentiation in diagnostic subtypes or profiles may guide the diagnostic process of dizziness and can serve as a classification system in future research. In the literature this has been done, but based on pathophysiological reasoning only. OBJECTIVE: To establish a classification of diagnostic profiles of dizziness based on empirical data. DESIGN: Cross-sectional study. PARTICIPANTS AND SETTING: 417 consecutive patients of 65 years and older presenting with dizziness to 45 primary care physicians in the Netherlands from July 2006 to January 2008. METHODS: We performed tests, including patient history, and physical and additional examination, previously selected by an international expert panel and based on an earlier systematic review. We used the results of these tests in a principal component analysis for exploration, data-reduction and finally differentiation into diagnostic dizziness profiles. RESULTS: Demographic data and the results of the tests yielded 221 variables, of which 49 contributed to the classification of dizziness into six diagnostic profiles, that may be named as follows: "frailty", "psychological", "cardiovascular", "presyncope", "non-specific dizziness" and "ENT". These explained 32% of the variance. CONCLUSIONS: Empirically identified components classify dizziness into six profiles. This classification takes into account the heterogeneity and multicausality of dizziness and may serve as starting point for research on diagnostic strategies and can be a first step in an evidence based diagnostic approach of dizzy older patients.

  3. A STUDY OF LIPID PROFILE IN CHRONIC OBSTRUCTIVE PULMONARY DISEASE

    Directory of Open Access Journals (Sweden)

    Modini Venkata

    2015-05-01

    Full Text Available BACKGROUND : Chronic obstructive pulmonary disease (COPD the third leading cause of death in the world , represents an important public health challenge that is both preventable and treatable. According to Global Initiative f or Chronic Obstructiv e Lung Disease (GOLD , Spirometric tests , Forced Expiratory Volume in first second (FEV1 less than 80% of the expected value and forced expiratory volume in first second to the forced vital capacity ratio (FEV1/FVC less than 70% is the diagnostic criteria for COPD. In COPD smoking is the major risk factor and smoking affects the lipid profile of COPD patients. MATERIALS AND METHODS: Spirometric parameters including FEV1 , FEV1/FVC ratio and lipid profile w as studied in 100 cases of COPD patients admitted Government Fever Hospital , Guntur and 40 nonsmoker healthy subjects were selected as a control group. They were correlated using Pearson’s correlation coefficient “r”. RESULTS: Majority of the cases are mal es belonging to 50 - 60years age group and all of them are smokers. Majority of the patients had moderate airflow limitation (GOLD Stages II and III. The lipid profile in COPD patients showed significant elevation of LDL cholesterol levels when compared to controls (P<0.005. CONCLUSION: Spirometric parameters FEV1 , FEV1/FVC ratio is important to diagnose as well as to assess the severity of the disease. Smoking is an important risk factor for COPD and smoking effects the lipid profile of COPD patients. Ther e was no correlation between lipid profile and severity of COPD.

  4. [Spectroscopic studies on the binding of phenazopyridine hydrochloride and bovine serum albumin].

    Science.gov (United States)

    Zhou, Hong; Chen, Chang-Yun; Xie, An-Jian

    2007-09-01

    The binding of phenazopyridine hydrochloride and bovine serum albumin under physiological conditions was studied by spectroscopic method. The quenching mechanism of the fluorescence of bovine serum albumin by phenazopyridine hydrochloride was studied with fluorescence and absorption spectroscopy. The binding constant Kb and the number of binding sites n were determined at different temperatures according to Scatchard equation, and the main binding force was discussed by thermodynamic equations. The effect of the drug on bovine serum albumin conformation was also studied by using synchronous fluorescence spectroscopy. The quenching mechanism of phenazopyridine hydrochloride to bovine serum albumin is static quenching and non-radiation energy transfer. The binding constants Kb at 15, 25 and 37 degrees C are 2.47 x 10(7), 9.15 x 10(6) and 4.36 x 10(6) mol(-1) with one binding site, respectively. The thermodynamic parameters of the reaction are DeltaH = -71.2 kJ x mol(-1), and DeltaS = 124.8 J x mol(-1) x K(-1). Binding phenazopyridine hydrochloride to bovine serum albumin is a spontaneous inter-molecular interaction in which entropy increases and Gibbs free energy decreases. The binding distance r between phenazopyridine hydrochloride and bovine serum albumin is 1.61 nm according to Forster theory of non-radiation energy transfer. The binding force is electrostatic interaction. Phenazopyridine hydrochloride can be deposited and transported by serum protein in vivo. Phenazopyridine hydrochloride does affect the serum protein conformation. PMID:18051539

  5. An experimental study for the Cross Domain Author Profiling classification

    OpenAIRE

    Garciarena Ucelay, María José; Villegas, María Paula; Cagnina, Leticia; ERRECALDE, MARCELO LUIS

    2015-01-01

    Author Profiling is the task of predicting characteristics of the author of a text, such as age, gender, personality, native language, etc. This is a task of growing importance due to the potential applications in security, crime detection and marketing, among others. An interesting point is to study the robustness of a classifier when it is trained with a dataset and tested with others containing different characteristics. Commonly this is called cross domain experimentation. Although differ...

  6. STUDY OF LIPID PROFILE IN PATIENTS WITH SUBCLINICAL HYPOTHYROIDISM

    Directory of Open Access Journals (Sweden)

    Ranjith Kumar

    2015-05-01

    Full Text Available A prospective case control study of lipid profile abnormalities in patients with subclinical hypothyroidism in J. L. N Hospital Ajmer. METHODS: 25 cases and 25 controls were included into the study. Cases had TSH> 5.0μIU/ml with normal T3 and T4 values. C ontrols were euthyroid patients. A detailed history, clinical examination, investigations like complete blood counts, fasting blood sugars, fasting thyroid profile and fasting lipid profile were done for all cases and controls. RESULTS: The mean TSH level in subclinical hypothyroidism cases (n=25 was 10.01±3 .87miIU/L, when compared to euthyroid controls (n=25, it was 2.69±1.52 miIU/L. The mean LDL cholesterol level in subclinical hypothyroidism cases (n=25 was 93.9±16.6mg/dl, when compared to controls, i t was 84.7±11.6mg/dl. CONCLUSION: The present study showed a higher prevalence of subclinical hypothyroidism among females of reproductive age group. significantly higher levels of total cholesterol, Triglyceride and VLDL cholesterol in patient with subcli nical hypothyroidism, though elevation in LDL cholesterol level was found to be statistically significant, but it remained well within the upper limit of normal, hence it is clinically significant and there was no statistically significant relation found b etween HDL cholesterol and subclinical hypothyroidism.

  7. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense.

    Directory of Open Access Journals (Sweden)

    Guoxia Liu

    Full Text Available Chemosensory proteins (CSPs are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1 was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde. This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity.

  8. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense

    Science.gov (United States)

    Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

    2016-01-01

    Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

  9. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense.

    Science.gov (United States)

    Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

    2016-01-01

    Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

  10. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    Science.gov (United States)

    Zeng, Hua-jin; Yang, Ran; You, Jing; Qu, Ling-bo; Sun, Yan-jun

    2016-01-01

    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly through electrostatic and hydrophobic interactions with one binding site. Synchronous fluorescence, three-dimensional fluorescence, and molecular docking results revealed that liquiritigenin bound directly to the enzyme cavity site and this binding influenced the microenvironment of the hyaluronidase activity site, resulting in reduced hyaluronidase activity. The present study provides useful information for clinical applications of liquiritigenin as a hyaluronidase inhibitor. PMID:27313960

  11. Spectroscopic and molecular modelling studies of binding mechanism of metformin with bovine serum albumin

    Science.gov (United States)

    Sharma, Deepti; Ojha, Himanshu; Pathak, Mallika; Singh, Bhawna; Sharma, Navneet; Singh, Anju; Kakkar, Rita; Sharma, Rakesh K.

    2016-08-01

    Metformin is a biguanide class of drug used for the treatment of diabetes mellitus. It is well known that serum protein-ligand binding interaction significantly influence the biodistribution of a drug. Current study was performed to characterize the binding mechanism of metformin with serum albumin. The binding interaction of the metformin with bovine serum albumin (BSA) was examined using UV-Vis absorption spectroscopy, fluorescence, circular dichroism, density functional theory and molecular docking studies. Absorption spectra and fluorescence emission spectra pointed out the weak binding of metformin with BSA as was apparent from the slight change in absorbance and fluorescence intensity of BSA in presence of metformin. Circular dichroism study implied the significant change in the conformation of BSA upon binding with metformin. Density functional theory calculations showed that metformin has non-planar geometry and has two energy states. The docking studies evidently signified that metformin could bind significantly to the three binding sites in BSA via hydrophobic, hydrogen bonding and electrostatic interactions. The data suggested the existence of non-covalent specific binding interaction in the complexation of metformin with BSA. The present study will certainly contribute to the development of metformin as a therapeutic molecule.

  12. The binding of cytochrome c to neuroglobin: A docking and surface plasmon resonance study

    DEFF Research Database (Denmark)

    Bønding, Signe Helbo; Henty, K.; Dingley, A.J.; Brittain, T.

    2008-01-01

    . surface plasmon resonance studies provide a value of 45 μM for the equilibrium constant for cytochrome c binding to neuroglobin, which increases significantly as the ionic strength of the solution increases. The temperature dependence of the binding constant indicates that the complex formation is...

  13. A Preliminary Study Examining the Binding Capacity of Akkermansia muciniphila and Desulfovibrio spp., to Colonic Mucin in Health and Ulcerative Colitis.

    Directory of Open Access Journals (Sweden)

    Helen Earley

    Full Text Available Akkermansia muciniphila and Desulfovibrio spp. are commensal microbes colonising the mucus gel layer of the colon. Both species have the capacity to utilise colonic mucin as a substrate. A. muciniphila degrades colonic mucin, while Desulfovibrio spp. metabolise the sulfate moiety of sulfated mucins. Altered abundances of these microorganisms have been reported in ulcerative colitis (UC. However their capacity to bind to human colonic mucin, and whether this binding capacity is affected by changes in mucin associated with UC, remain to be defined.Mucin was isolated from resected colon from control patients undergoing resection for colonic cancer (n = 7 and patients undergoing resection for UC (n = 5. Isolated mucin was purified and printed onto mucin microarrays. Binding of reference strains and three clinical isolates of A. muciniphila and Desulfovibrio spp. to purified mucin was investigated.Both A. muciniphila and Desulfovibro spp. bound to mucin. The reference strain and all clinical isolates of A. muciniphila showed increased binding capacity for UC mucin (p < .005. The Desulfovibrio reference strain showed increased affinity for UC mucin. The mucin binding profiles of clinical isolates of Desulfovibrio spp. were specific to each isolate. Two isolates showed no difference in binding. One UC isolate bound with increased affinity to UC mucin (p < .005.These preliminary data suggest that differences exist in the mucin binding capacity of isolates of A. muciniphila and Desulfovibrio spp. This study highlights the mucin microarray platform as a means of studying the ability of bacteria to interact with colonic mucin in health and disease.

  14. Laboratory and clinical profile of dengue: A study from Mumbai

    OpenAIRE

    D Turbadkar; A Ramchandran; Mathur, M; Gaikwad, S.

    2012-01-01

    Background: Dengue an endemic disease in most subtropical and tropical regions of the world is causing severe epidemics in India. An alarming rise of dengue has also been seen in Mumbai, during the recent years. Aim and Objective: The study was conducted to know the prevalence of dengue infection, based on laboratory rapid screening tests for IgM and IgG antibodies and the confirmatory IgM ELISA test and to study the seasonal variation and the clinical profile in these cases. Material and Met...

  15. STUDIES ON SOME PHARMACOGNOSTIC PROFILES OF SWIETENIA MACROPHYLLA. King.

    Science.gov (United States)

    Arumugasamy, K; Latha, K V; Kumar, N H Sathish

    2004-10-01

    The aerial parts and seeds of Swietenia macrophylla King (Meliaceae) are used in exotic medicine systems. In the present study, a preliminary phytochemical and few pharmacological profiles were under taken. The physical constans, extractive and ash values were examined. The presence of secondary metabolites in the aerial parts and seeds showed that Swietenia macrophylla is a good source of active principles. TLC studies were done by treating dry treating dry powder of Swietenia macrophylla with various acids, iodine and ferric chloride solution and UV and Visible light. PMID:22557161

  16. A study on online learner profile for supporting personalized learning

    OpenAIRE

    Jie Yang

    2013-01-01

    Digital learning as a popular learning approach has received increasing attention in modern education. The learner profile in online learning plays a critical role in supporting personalized learning. This article uses an information flow-based approach to build the learner profile for supporting personalized learning. The learner profile includes the individual profile to capture the personal features and the community profile to capture the social features in online learning environment.

  17. Identification and expression profiling of putative odorant-binding proteins in the malaria mosquitoes, Anopheles gambiae and A.arabiensis

    Institute of Scientific and Technical Information of China (English)

    LI; Zhengxi; Jing-Jiang; ZHOU; SHEN; Zuorui; Lin; FIELD

    2004-01-01

    Olfaction plays a major role in host-seeking behaviour of mosquitoes. An informatics-based genome-wide analysis of odorant-binding protein (OBP) homologues is undertaken,and 32 putative OBP genes in total in the whole genome sequences of Anopheles gambiae are identified. Tissue-specific expression patterns of all A. gambiae OBP candidates are determined by semi-quantitative Reverse Transcription (RT)-PCR using mosquito actin gene as internal expression control standard. The results showed that 20 OBP candidates had strong expression in mosquito olfactory tissues (female antennae), which indicate that OBPs may play an important role in regulating mosquito olfactory behaviours. Species-specific expression patterns of all putative anopheline OBPs are also studied in two of the most important malaria vectors in A. gambiae complex, i.e.A. gambiae and A. arabiensis, which found 12 of the putative OBP genes examined displayed species-differential expression patterns. The cumulative relative expression intensity of the OBPs in A. arabiensis antennae was higher than that in A. gambiae (the ratio is 1441.45:1314.12), which might be due to their different host preference behaviour. While A.gambiae is a highly anthropophilic mosquito, A. arabiensis is more opportunistic (varying from anthropophilic to zoophilic). So the latter should need more OBPs to support its host selection preference. Identification of mosquito OBPs and verification of their tissue- and species-specific expression patterns represent the first step towards further molecular analysis of mosquito olfactory mechanism, such as recombinant expression and ligand identification.

  18. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    DEFF Research Database (Denmark)

    Bryne, J.C.; Valen, E.; Tang, M.H.E.; Marstrand, T.; Winther, Ole; da Piedade, I.; Krogh, A.; Lenhard, B.; Sandelin, A.

    2008-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR...

  19. Tight-binding study of bilayer graphene Josephson junctions

    Science.gov (United States)

    Muñoz, W. A.; Covaci, L.; Peeters, F. M.

    2012-11-01

    Using highly efficient simulations of the tight-binding Bogoliubov-de-Gennes model, we solved self-consistently for the pair correlation and the Josephson current in a superconducting-bilayer graphene-superconducting Josephson junction. Different doping levels for the non-superconducting link are considered in the short- and long-junction regimes. Self-consistent results for the pair correlation and superconducting current resemble those reported previously for single-layer graphene except at the Dirac point, where remarkable differences in the proximity effect are found, as well as a suppression of the superconducting current in the long-junction regime. Inversion symmetry is broken by considering a potential difference between the layers and we found that the supercurrent can be switched if the junction length is larger than the Fermi length.

  20. Identification and expression profiling of odorant binding proteins and chemosensory proteins between two wingless morphs and a winged morph of the cotton aphid Aphis gossypii glover.

    Directory of Open Access Journals (Sweden)

    Shao-Hua Gu

    Full Text Available Insects interact with their environment and respond to the changes in host plant conditions using semiochemicals. Such ecological interactions are facilitated by the olfactory sensilla and the use of olfactory recognition proteins. The cotton aphid Aphis gossypii can change its phenotype in response to ecological conditions. They reproduce mainly as wingless asexual morphs but develop wings to find mates or new plant hosts under the influence of environmental factors such as temperature, plant nutrition and population density. Two groups of small soluble proteins, odorant binding proteins (OBPs and chemosensory proteins (CSPs are believed to be involved in the initial biochemical recognition steps in semiochemical perception. However, the exact molecular roles that these proteins play in insect olfaction remain to be discovered. In this study, we compared the transcriptomes of three asexual developmental stages (wingless spring and summer morphs and winged adults and characterised 9 OBP and 9 CSP genes. The gene structure analysis showed that the number and length of introns in these genes are much higher and this appears to be unique feature of aphid OBP and CSP genes in general. Another unique feature in aphids is a higher abundance of CSP transcripts than OBP transcripts, suggesting an important role of CSPs in aphid physiology and ecology. We showed that some of the transcripts are overexpressed in the antennae in comparison to the bodies and highly expressed in the winged aphids compared to wingless morphs, suggesting a role in host location. We examined the differential expression of these olfactory genes in ten aphid species and compared the expression profile with the RNA-seq analyses of 25 pea aphid transcriptome libraries hosted on AphidBase.

  1. Full quantum mechanical study of binding of HIV-1 protease drugs

    Science.gov (United States)

    Zhang, Da W.; Zhang, John Z. H.

    Fully quantum mechanical studies of detailed binding interactions between HIV-1 protease and six FDA (Food and Drug Administration)-approved drugs (saquinavir, indinavir, ritonavir, nelfinavir, amprenavir, and lopinavir) are carried out using a recently developed MFCC (molecular fractionation with conjugate caps) method. The MFCC calculation produces a quantum mechanical interaction spectrum for any protease drug binding complex. Detailed quantitative analysis on binding of lopinavir to specific residues of the protease is given from the current study. The present calculation shows that the dominant binding of lopinavir to the protease is through the formation of a strong hydrogen bond between the central hydroxyl group of the drug to the aspartate oxygen of Asp25 in one of the two chains of the protease (A chain). This is closely followed by hydrogen binding of the drug to Asp29 in the B chain and somewhat weak hydrogen bonding to Asp30, Gly27, Gly48, and Ile50 in both chains. By partitioning all six drugs into four building blocks besides the central component containing the hydroxyl group, MFCC calculation finds that block III has essentially no binding interaction with the protease and the major binding interactions of these drugs are from blocks II and IV, in addition to the dominant central hydroxyl group. This detailed quantitative information on drug binding to the protease is very useful in rational design of new and improved inhibitors of HIV-1 protease and its mutants.

  2. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

    Directory of Open Access Journals (Sweden)

    Evelyn N Kouwenhoven

    2010-08-01

    Full Text Available Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM, orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP, followed by deep sequencing (ChIP-seq in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes.

  3. Study on Integrated Thermal Cycle and Vibration Profile for HALT

    Institute of Scientific and Technical Information of China (English)

    TAO Jun-yong; CHU Wei-hua; CHEN Xun

    2009-01-01

    Focusing on electronic products, this paper establishes a finite element model for printed circuit board (PCB) assembling with enhanced ball grid array(EBGA)component under vibration environment. Based on this model, it studies relations between fatigue rate of solder joint and temperature, vibration frequency. Moreover, it analyzes propagation of micro-crack produced by thermal cycle under vibration stress. The results offer a method to optimize the thermal cycle and vibration integrated profile and to combine vibration test and thermal cycling for highly accelerated life test (HALT).

  4. Formalisation of the UML Profile for SDL - A Case Study

    OpenAIRE

    Grammes, Rüdiger

    2006-01-01

    With the UML 2.0 standard, the Unified Modeling Language took a big step towards SDL, incorporating many features of the language. SDL is a mature and complete language with formal semantics. The Z.109 standard defines a UML Profile for SDL, mapping UML constructs to corresponding counterparts in SDL, giving them a precise semantics. In this report, we present a case study for the formalisation of the Z.109 standard. The formal definition makes the mapping precise and can be used to derive to...

  5. Ligand binding studies in the mouse olfactory bulb: identification and characterisation of a L-[3H]carnosine binding site

    International Nuclear Information System (INIS)

    Binding sites for the dipeptide L-carnosine (β-alanyl-t-histidine) have been detected in membranes prepared from mouse olfactory bulbs. The binding of L-[3H]- carnosine was saturable, reversible and stereospecific and had a Ksub(d) of about 770 nM. The stereospecific binding of L-carnosine represented about 30% of the totoal binding at pH 6.8, and decreased markedly with increasing pH. Binding was stimulated by calcium, unaffected by zinc, magnesium or manganese and inhibted by sodium and potassium. Carnosine binding was sensitive to trypsin and phospholipases A and C, but not to neuraminidase. Nystatin and filipin, which interact with membrane lipids, also interfered with binding. Some peptide analogues of carnosine were potent inhibitors of binding, but a variety of drugs serving as potent inhibitors in other binding systems had no effect on carnosine binding. Carnosine binding to mouse olfactory bulb membranes was 15-fold higher than that seen in membranes prepared from cerebral hemispheres, 5-fold higher than in cerebellum membranes and 3-fold higher than in membranes from spinal medulla and the olfactory tubercle-lateral olfactory tract area. (Auth.)

  6. Preliminary study of the metal binding site of an anti-DTPA-indium antibody by equilibrium binding immunoassays and immobilized metal ion affinity chromatography.

    Science.gov (United States)

    Boden, V; Colin, C; Barbet, J; Le Doussal, J M; Vijayalakshmi, M

    1995-01-01

    Creating metal coordination sites by modifying an existing enzyme or by eliciting antibodies against metal chelate haptens is of great interest in biotechnology to create enzyme catalysts with novel specificities. Here, we investigate the metal binding potential of a monoclonal antibody raised against a DTPA-In(III) hapten (mAb 734). We study its relative binding efficiency to metals of biological relevance by equilibrium binding immunoassays and immobilized metal ion affinity chromatography, two approaches which can give complementary information regarding composition and/or structure of the metal binding site(s). Fe(III), Fe(II), Cu(II), Mg(II), Ca(II), and Zn(II) binding was compared to In(III). All of them were shown to displace indium, but their affinity for mAb 734 decreased by 100-fold compared to indium. Competitive metal binding immunoassays between Zn(II) and In(III) revealed an unusual behavior by Zn(II) which remains to be explained. Moreover, IMAC allowed us to predict the metal binding amino acids involved in the antibody paratope. The antibody metal binding site was shown to contain at least two histidine residues in a cluster, and the presence of aspartic and glutamic acid as well as cysteine residues could not be excluded. Thus, simple competition studies allows us to obtain some partial information on the metal binding structural features of this anti-metal chelate antibody and to guide our screening of its catalytic potential. PMID:7578356

  7. Comparison of [11C]cocaine binding at tracer and pharmacological doses of baboon brain: A PET study

    Energy Technology Data Exchange (ETDEWEB)

    Volkow, N.D.; Fowler, J.S.; Logan, J. [Brookhaven National Lab., Upton, NY (United States)] [and others

    1994-05-01

    In vitro studies have shown that cocaine (C) binds to both high and low affinity sites on the dopamine transporter (DAT). We have previously characterized the binding of tracer doses of [{sup 11}C]cocaine (C*)to a high affinity site on the DAT. To assess if in vivo C also binds to low affinity sites we used PET to compare binding of tracer doses (17.8{plus_minus}12.2 {mu}g C) of C* to pharmacological doses (8 mg of C coadministered with C*). Sixteen paired studies were done to assess test/retest variability, specific versus non specific binding and to characterize binding profile. Dynamic scans were started immediately after injection of C* (5-8 mCi) for 50 min on the CTI-931 (6 x 6 x 6.5 mm FWHM). Time activity curves for tissue concentration and for unchanged tracer in plasma were used to calculate the transport constant between plasma and tissue (K1) and to obtain the distribution volume (DV). The ratio of the DV in striatum (ST) to that in cerebellum (CB) (which corresponds to Bmax/Kd-1) was used as model parameter. Peak brain uptake of C* was significantly higher for tracer than for pharmacological doses (0.041 versus 0.033 % dose/cc), as were the values for K1 (1.07{plus_minus}0.21 versus 0.68{plus_minus}0.26 (t=3.0 p<0.01)). Repeated measures were reproducible for tracer ({plus_minus}2%) and pharmacological doses of C* ({plus_minus}4%). Tracer dose C* showed highest binding and slowest clearance in ST which was reduced by C (0.5-2.0 mg/kg iv, -25 to -30%) and by drugs that inhibit DAT (2mg/kg nomifensine - 21%, 0.5 mg/kg methylphenidate -12%) and was increased by serotonin transporter inhibitors (5HT-Ti) (2 mg/kg citalopram +11%, 0.5 mg/kg fluoxetine +6%) and not changed by NE transporter inhibitors (0.5 mg/kg desipramine or 2 mg/kg tomoxetine). The increase with (5HT-Ti) may reflect neurotransmitter interactions or changes in bioavailability. At pharmacological doses C* showed homogeneous distribution and was not changed by C nor by any of the above drugs.

  8. ADMET, Docking studies & binding energy calculations of some Novel ACE - inhibitors for the treatment of Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Gade Deepak Reddy

    2012-09-01

    Full Text Available Diabetic Nephropathy (DN is one of the major complications of diabetes mellitus, representing the leading of cause of chronic renal disease and a major cause of morbidity and mortality in both type 1 and type 2 diabetic patients. The Renin-Angiotensin-Aldosterone System (RAAS has been implicated in the pathophysiology of DN, and suggests a therapeutic target for blocking this system. Therefore, inhibition of RAAS plays a crucial role in the treatment of DN and therapeutic intervention mostly involves administration of angiotensin converting enzyme (ACE inhibitors and angiotensin AT1 receptor blockers. In this current study, we have used computational methods to design 37 novel ACE-inhibitors and evaluated them for the interaction with the enzyme ACE through insilico analysis. The obtained results were compared with the standard drug enalapril to find out the potential inhibitors. Here we report that ligand 4 exhibited strongest inhibitory activity among all. All the analogs are also screened for their ADME & Toxicity profiles using insilico tools and ligand 9 is having better binding affinity next to ligand 4, and also having better ADMET profile when compared to that of ligand 4. Post docking calculations were also performed for the docked complexes in order to identify the individual ligand binding energies by employing Multi-Ligand Bimolecular Association with Energetics (Embrace

  9. Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

    Indian Academy of Sciences (India)

    Beena Mishra; Atanu Barik; K Indira Priyadarsini; Hari Mohan

    2005-11-01

    Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance () was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).

  10. A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis.

    Science.gov (United States)

    Serçinoğlu, Onur; Özcan, Gülin; Kabaş, Zeynep Kutlu; Ozbek, Pemra

    2016-07-01

    A single amino acid difference (Asp116His), having a key role in a pathogenesis pathway, distinguishes HLA-B*27:05 and HLA-B*27:09 sub-types as associated and non-associated with ankylosing spondylitis, respectively. In this study, molecular docking simulations were carried out with the aim of comprehending the differences in the binding behavior of both alleles at varying pH conditions. A library of modeled peptides was formed upon single point mutations aiming to address the effect of 20 naturally occurring amino acids at the binding core peptide positions. For both alleles, computational docking was applied using Autodock 4.2. Obtained free energies of binding (FEB) were compared within the peptide library and between the alleles at varying pH conditions. The amino acid preferences of each position were studied enlightening the role of each on binding. The preferred amino acids for each position of pVIPR were found to be harmonious with experimental studies. Our results indicate that, as the pH is lowered, the capacity of HLA-B*27:05 to bind peptides in the library is largely lost. Hydrogen bonding analysis suggests that the interaction between the main anchor positions of pVIPR and their respective binding pocket residues are affected from the pH the most, causing an overall shift in the FEB profiles. PMID:27506766

  11. Analysis of the DNA-Binding Profile and Function of TALE Homeoproteins Reveals Their Specialization and Specific Interactions with Hox Genes/Proteins

    Directory of Open Access Journals (Sweden)

    Dmitry Penkov

    2013-04-01

    Full Text Available The interactions of Meis, Prep, and Pbx1 TALE homeoproteins with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA-binding sequences, Prep associating mostly with promoters and housekeeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless coregulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. During evolution, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.

  12. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    OpenAIRE

    Bryne, Jan Christian; Valen, Eivind; Tang, Man-Hung Eric; Marstrand, Troels; Winther, Ole; da Piedade, Isabelle; Krogh, Anders; Lenhard, Boris; Sandelin, Albin

    2007-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR database—the JASPAR CORE sub-database—has increased by 12% in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generat...

  13. QM/MM Molecular Dynamics Studies of Metal Binding Proteins

    Directory of Open Access Journals (Sweden)

    Pietro Vidossich

    2014-07-01

    Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

  14. Parametric study of different contributors to tumor thermal profile

    Science.gov (United States)

    Tepper, Michal; Gannot, Israel

    2014-03-01

    Treating cancer is one of the major challenges of modern medicine. There is great interest in assessing tumor development in in vivo animal and human models, as well as in in vitro experiments. Existing methods are either limited by cost and availability or by their low accuracy and reproducibility. Thermography holds the potential of being a noninvasive, low-cost, irradiative and easy-to-use method for tumor monitoring. Tumors can be detected in thermal images due to their relatively higher or lower temperature compared to the temperature of the healthy skin surrounding them. Extensive research is performed to show the validity of thermography as an efficient method for tumor detection and the possibility of extracting tumor properties from thermal images, showing promising results. However, deducing from one type of experiment to others is difficult due to the differences in tumor properties, especially between different types of tumors or different species. There is a need in a research linking different types of tumor experiments. In this research, parametric analysis of possible contributors to tumor thermal profiles was performed. The effect of tumor geometric, physical and thermal properties was studied, both independently and together, in phantom model experiments and computer simulations. Theoretical and experimental results were cross-correlated to validate the models used and increase the accuracy of simulated complex tumor models. The contribution of different parameters in various tumor scenarios was estimated and the implication of these differences on the observed thermal profiles was studied. The correlation between animal and human models is discussed.

  15. Study of Lipid profile in a population of university students

    Directory of Open Access Journals (Sweden)

    Roberto Wagner Junior Freire de Freitas

    2013-09-01

    Full Text Available OBJECTIVE: to evaluate the lipid profile in a population of university students. METHODS: cross-sectional study with 702 students, of both genders enrolled in various courses at a public university in Fortaleza-CE. The demographic data and data on lifestyle habits were collected through a self-administered questionnaire. The blood collection was performed in a clinical laboratory. RESULTS: showed a predominantly young population, with a mean age of 21.5 years with more females (62.7%. High levels of triglycerides, total cholesterol and cholesterol associated with low density lipoprotein (LDL-c were found in 23.0%, 9.7% and 5.9% of students, respectively. The cholesterol associated with high density lipoprotein (HDL-c was at reduced values in 12.0% of subjects and was significantly associated with smoking (p=0.0231 and physical inactivity (p=0.0357. CONCLUSION: changes in lipid profile are present in the young population and intervention studies should be encouraged in order to reduce the prevalence of cardiovascular disease in adulthood.

  16. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

    de Wit, Elzo; Vos, Erica S M; Holwerda, Sjoerd J B; Valdes-Quezada, Christian; Verstegen, Marjon J A M; Teunissen, Hans; Splinter, Erik; Wijchers, Patrick J; Krijger, Peter H L; de Laat, Wouter

    2015-01-01

    CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that ch

  17. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    OpenAIRE

    Endres, Christopher J.; Dima A. Hammoud; Pomper, Martin G.

    2011-01-01

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined th...

  18. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, P A [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1996-05-01

    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I{center_dot}C base pairs are functional analogs of A{center_dot}T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  19. Study on the proteins-luminol binding by use of luminol as a fluorescence probe

    Science.gov (United States)

    He, Xili; Song, Zhenghua

    2013-10-01

    In this paper, a new mathematical equation of lg(F0 - F)/F = 1/nlg[P] + 1/nlgKa, which was used to obtain interaction parameters (the binding constant Ka and the number of binding sites n) between the protein and the small molecule ligand by using the ligand as a fluorescence (FL) probe, was constructed for the first time. The interaction parameters between myoglobin, catalase, lysozyme, bovine serum albumin (BSA) and luminol were obtained by this equation with luminol used as a FL probe, showing that the binding constants Ka were 8.78 × 105, 4.47 × 105, 4.21 × 104 and 3.95 × 104 respectively, and the number of binding sites n approximately equaled to 1.0 for myoglobin, catalase, and 2.0 for lysozyme, BSA. The interactions of ferritin, ovalbumin, aldolase, chymotrypsinogen and ribonuclease with luminol were also studied by this method. The binding constants Ka were at 104-105 level, and the number of binding sites n mostly approximately equaled to 2.0. The binding ability of luminol to the studied proteins followed the pattern: myoglobin > aldolase > ferritin > ovalbumin > catalase > ribonuclease > lysozyme > BSA > chymotrypsinoge.

  20. Mother and child T cell receptor repertoires: deep profiling study

    Directory of Open Access Journals (Sweden)

    Ekaterina V Putintseva

    2013-12-01

    Full Text Available The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells (HSC and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T-cell receptor (TCR repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5х105–2х106 TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TRBV segment usage frequency and relative overlap of TCR beta CDR3 repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.

  1. STUDY OF RISK FACTORS AND CLINICAL PROFILE OF ACUTE STROKE

    Directory of Open Access Journals (Sweden)

    Tomar

    2014-05-01

    Full Text Available `INTRODUCTION: Stroke is the third leading cause of death in developed countries after cardiovascular disease and cancer. In India Community Surveys have shown a crude prevalence rate for hemiplegia 200 per 1, 00, 000 population. It accounts for nearly 1.5% of all urban admissions, 4.5 % of all medical and about 20% of neurological cases. AIMS AND OBJECTIVE: Identification of risk factors and evaluation of clinical profile of acute stroke. MATERIAL AND METHOD: INCLUSION CRITERIA: Cases of acute stoke admitted in SGMH hospital were selected for the study. EXCLUSION CRITERIA: Brain injury cases, infective, neoplastic cases producing stroke were excluded. RESULTS: Stroke was more common in male, 58 % patients were male and 42% patients were female. It was more common in 5th and 6th decade. Most common etiology was infarction. Most common risk factor was hypertension followed by smoking. In addition to limb weakness, headache and vomiting were most common presenting symptoms followed by convulsion. These symptoms were more common in hemorrhagic stroke. Right sided hemiplegia was more common than left sided. Middle cerebral artery was involved in majority of cases in atherothrombotic stroke whereas basal ganglion was most common site of bleed in hemorrhagic stroke. Coma and mortality were more in hemorrhagic stroke. CONCLUSION: The risk factors and clinical profile of acute stroke in India are similar to that of Western countries. Common risk factors are hypertension, smoking, diabetes mellitus and hyperlipidemia

  2. NMR Studies of a New Binding Mode of the Amino Acid Esters by Porphyrinatozinc(Ⅱ)

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The binding mode of the amino acid ethyl esters(guest) by 5-(2-carboxylphenyl)-10,15,20-triphenylporphyrinatozinc(Ⅱ)(host 1) was studied by means of 1H NMR spectra. The binding mode is the hydrogen-bonding between the amino group of the guest and the carboxyl group of host 1 plus the coordination between the zinc atom of porphyrinatozinc(Ⅱ) and the carbonyl group of the guest. This is a novel binding mode of the metalloporphyrin to amino acid derivatives.

  3. Laboratory and clinical profile of dengue: A study from Mumbai

    Directory of Open Access Journals (Sweden)

    D Turbadkar

    2012-01-01

    Full Text Available Background: Dengue an endemic disease in most subtropical and tropical regions of the world is causing severe epidemics in India. An alarming rise of dengue has also been seen in Mumbai, during the recent years. Aim and Objective: The study was conducted to know the prevalence of dengue infection, based on laboratory rapid screening tests for IgM and IgG antibodies and the confirmatory IgM ELISA test and to study the seasonal variation and the clinical profile in these cases. Material and Method: A retrospective study of laboratory test results and clinical profile of suspected dengue cases was carried out in a tertiary care hospital over a period between January 2004 and November 2007. Result: Of the 3 677 samples processed by rapid test for antibodies against dengue (Denguchek, 503 (13.67% gave positive results. Fifty-six samples (26.41% were positive by IgM Enzyme linked immunosorbent assay (ELISA test, of 212 rapid positive samples processed by ELISA test. Our study comprised of 315 adult and 188 pediatric cases. The common symptom of dengue was fever, icterus, myalgia, and headache. Thrombocytopenia (platelet counts <75 000/cmm was seen in 386 (76.74% cases. Seventy-seven cases (15.30% positive by rapid screening tests for dengue antibodies were also positive for IgM/IgG antibodies against Leptospira by Dridot test (Rapid test. Of these, 49 (63.64% were confirmed to be positive for dengue antibodies by the ELISA test. Conclusion: As dengue causes increased morbidity and mortality and requires prompt diagnosis and treatment for the proper management of these cases, the rapid screening test for IgM/IgG antibodies helps clinicians toward achieving this goal.

  4. Riyadh Mother and Baby Multicenter Cohort Study: The Cohort Profile

    Science.gov (United States)

    Esmaeil, Samia; Alzeidan, Rasmieh; Elawad, Mamoun; Tabassum, Rabeena; Hansoti, Shehnaz; Magzoup, Mohie Edein; Al-Kadri, Hanan; Elsherif, Elham; Al-Mandil, Hazim; Al-Shaikh, Ghadeer; Zakaria, Nasria

    2016-01-01

    Objectives To assess the effects of non-communicable diseases, such as diabetes, hypertension and obesity, on the mother and the infant. Methods A multicentre cohort study was conducted in three hospitals in the city of Riyadh in Saudi Arabia. All Saudi women and their babies who delivered in participating hospitals were eligible for recruitment. Data on socio-demographic characteristics in addition to the maternal and neonatal outcomes of pregnancy were collected. The cohort demographic profile was recorded and the prevalence of maternal conditions including gestational diabetes, pre-gestational diabetes, hypertensive disorders in pregnancy and obesity were estimated. Findings The total number of women who delivered in participating hospitals during the study period was 16,012 of which 14,568 women participated in the study. The mean age of the participants was 29 ± 5.9 years and over 40% were university graduates. Most of the participants were housewives, 70% were high or middle income and 22% were exposed to secondhand smoke. Of the total cohort, 24% were married to a first cousin. More than 68% of the participants were either overweight or obese. The preterm delivery rate was 9%, while 1.5% of the deliveries were postdate. The stillbirth rate was 13/1000 live birth. The prevalence of gestational diabetes was 24% and that of pre-gestational diabetes was 4.3%. The preeclampsia prevalence was 1.1%. The labour induction rate was 15.5% and the cesarean section rate was 25%. Conclusion Pregnant women in Saudi Arabia have a unique demographic profile. The prevalence of obesity and diabetes in pregnancy are among the highest in the world. PMID:26937965

  5. Riyadh Mother and Baby Multicenter Cohort Study: The Cohort Profile.

    Directory of Open Access Journals (Sweden)

    Hayfaa Wahabi

    Full Text Available To assess the effects of non-communicable diseases, such as diabetes, hypertension and obesity, on the mother and the infant.A multicentre cohort study was conducted in three hospitals in the city of Riyadh in Saudi Arabia. All Saudi women and their babies who delivered in participating hospitals were eligible for recruitment. Data on socio-demographic characteristics in addition to the maternal and neonatal outcomes of pregnancy were collected. The cohort demographic profile was recorded and the prevalence of maternal conditions including gestational diabetes, pre-gestational diabetes, hypertensive disorders in pregnancy and obesity were estimated.The total number of women who delivered in participating hospitals during the study period was 16,012 of which 14,568 women participated in the study. The mean age of the participants was 29 ± 5.9 years and over 40% were university graduates. Most of the participants were housewives, 70% were high or middle income and 22% were exposed to secondhand smoke. Of the total cohort, 24% were married to a first cousin. More than 68% of the participants were either overweight or obese. The preterm delivery rate was 9%, while 1.5% of the deliveries were postdate. The stillbirth rate was 13/1000 live birth. The prevalence of gestational diabetes was 24% and that of pre-gestational diabetes was 4.3%. The preeclampsia prevalence was 1.1%. The labour induction rate was 15.5% and the cesarean section rate was 25%.Pregnant women in Saudi Arabia have a unique demographic profile. The prevalence of obesity and diabetes in pregnancy are among the highest in the world.

  6. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

    Directory of Open Access Journals (Sweden)

    Ankur Bikash Pradhan

    Full Text Available Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride with single and double stranded form of polyriboadenylic acid (hereafter poly-A using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A with high affinity while it does not interact at all with the double stranded (ds form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  7. Direct zonal liquid chromatographic method for the kinetic study of actinomycin-DNA binding.

    Science.gov (United States)

    Vidal-Madjar, Claire; Florentina, Cañada-Cañada; Gherghi, Ioanna; Jaulmes, Alain; Pantazaki, Anastasia; Taverna, Myriam

    2004-07-01

    The binding of an anticancer drug (actinomycin D or ACTD) to double-stranded DNA (dsDNA) was studied by means of high-performance liquid chromatography (HPLC). ACTD is an antitumor antibiotic containing one chromophore group and two pentapeptidic lactone cycles that binds dsDNA. Incubations of ACTD with DNA were performed at physiological pH. The complexed and free ligand concentrations of the mixture were quantified at 440 nm from their separation on a size-exclusion chromatographic (SEC) column using the same buffer for the elution and the sample incubation. The DNA and the ACTD-DNA complexes were eluted at the column exclusion volume while the ligand was retained on the support. An apparent binding curve was obtained by plotting the amount emerging at the exclusion column volume against that eluted at free ACTD retention volume. A dissociating effect was evidenced and the binding parameters were significantly different from those obtained at equilibrium by visible absorbance titration. The equilibrium binding parameters determined by absorption spectroscopy were used as starting data in the numerical simulations of the chromatographic process. The results showed a strong dependency of the apparent binding parameters on the reaction kinetics. Finally the comparison of the apparent binding curve obtained from the HPLC experiments and from the numerical simulations permitted an evaluation of the dissociation rate constant (kd = 0.004 s(-1)). PMID:15296384

  8. Protein binding studies with radiolabeled compounds containing radiochemical impurities. Equilibrium dialysis versus dialysis rate determination

    DEFF Research Database (Denmark)

    Honoré, B

    1987-01-01

    The influence of radiochemical impurities in dialysis experiments with high-affinity ligands is investigated. Albumin binding of labeled decanoate (97% pure) is studied by two dialysis techniques. It is shown that equilibrium dialysis is very sensitive to the presence of impurities resulting...... in erroneously low estimates of the binding affinity and in inconsistent results at varying albumin concentrations. Dialysis rate determination (R. Brodersen et al. (1982) Anal. Biochem. 121, 395-408) is less sensitive to impurities. Udgivelsesdato: 1987-Apr...

  9. Receptor binding profiles and quantitative structure-affinity relationships of some 5-substituted-N,N-diallyltryptamines.

    Science.gov (United States)

    Cozzi, Nicholas V; Daley, Paul F

    2016-02-01

    N,N-Diallyltryptamine (DALT) and 5-methoxy-N,N-diallyltryptamine (5-MeO-DALT) are two tryptamines synthesized and tested by Alexander Shulgin. In self-experiments, 5-MeO-DALT was reported to be psychoactive in the 12-20mg range, while the unsubstituted compound DALT had few discernible effects in the 42-80 mg range. Recently, 5-MeO-DALT has been used in nonmedical settings for its psychoactive effects, but these effects have been poorly characterized and little is known of its pharmacological properties. We extended the work of Shulgin by synthesizing additional 5-substituted-DALTs. We then compared them to DALT and 5-MeO-DALT for their binding affinities at 45 cloned receptors and transporter proteins. Based on in vitro binding affinity, we identified 27 potential receptor targets for the 5-substituted-DALT compounds. Five of the DALT compounds had affinity in the 10-80 nM range for serotonin 5-HT1A and 5-HT2B receptors, while the affinity of DALT itself at 5-HT1A receptors was slightly lower at 100 nM. Among the 5-HT2 subtypes, the weakest affinity was at 5-HT2A receptors, spanning 250-730 nM. Five of the DALT compounds had affinity in the 50-400 nM range for serotonin 5-HT1D, 5-HT6, and 5-HT7 receptors; again, it was the unsubstituted DALT that had the weakest affinity at all three subtypes. The test drugs had even weaker affinity for 5-HT1B, 5-HT1E, and 5-HT5A subtypes and little or no affinity for the 5-HT3 subtype. These compounds also had generally nanomolar affinities for adrenergic α2A, α2B, and α2C receptors, sigma receptors σ1 and σ2, histamine H1 receptors, and norepinephrine and serotonin uptake transporters. They also bound to other targets in the nanomolar-to-low micromolar range. Based on these binding results, it is likely that multiple serotonin receptors, as well as several nonserotonergic sites are important for the psychoactive effects of DALT drugs. To learn whether any quantitative structure-affinity relationships existed, we evaluated

  10. The Dynamic Pollen Tube Cytoskeleton: Live Cell Studies Using Actin-Binding and Microtubule-Binding Reporter Proteins

    Institute of Scientific and Technical Information of China (English)

    Alice Y. Cheung; Qiao-hong Duan; Silvia Santos Costa; Barend H.J.de Graaf; Veronica S.Di Stilio; Jose Feijo; Hen-Ming Wu

    2008-01-01

    Pollen tubes elongate within the pistil to transport sperm cells to the embryo sac for fertilization.Growth occurs exclusively at the tube apex,rendering pollen tube elongation a most dramatic polar cell growth process.A hall-mark pollen tube feature is its cytoskeleton,which comprises elaborately organized and dynamic actin microfilaments and microtubules.Pollen tube growth is dependent on the actin cytoskeleton;its organization and regulation have been exalined extensively by various approaches.including fluorescent protein labeled actin-binding proteins in live cell studies.Using the previously described GFP-NtADF1 and GFP-LIADF1, and a new actin reporter protein NtPLIM2b-GFP,we re-affirm that the predominant actin structures in elongating tobacco and lily pollen tubes are long,streaming actin cables along the pollen tube shank,and a subapical structure comprising shorter actin cables.The subapical collection of actin microfilaments undergoes dynamic changes,giving rise to the appearance of structures that range from basket-or funnel-shaped,mesh-like to a subtle ring.NtPLIM2b-GFP is used in combination with a guanine nucleotide exchange factor for the Rho GTPases,AtROP-GEF1,to illustrate the use of these actin reporter proteins to explore the linkage between the polar cell growth process and its actin cytoskeleton.Contrary to the actin cytoskeleton,microtubules appear not to play a direct role in supporting the polar cell growth process in angiosperm pollen tubes.Using a microtubule reporter protein based on the microtubule end-binding protein from Arabidopsis AtEB1,GFP-AtEB1,we show that the extensive microtubule network in elongating pollen tubes displays varying degrees of dynamics.These reporter proteins provide versatile tools to explore the functional connection between major structural and signaling components of the polar pollen tube growth process.

  11. Study Of Clinical Profile of Allergic Contact Dermatitis In Pune

    Directory of Open Access Journals (Sweden)

    Sayal S K

    1999-01-01

    Full Text Available One hundred and twenty five cases of clinically diagnosed allergic contact dermatitis were studied. All patients were subjected to patch test with standard test allergens and also with suspected test allergens based on history and clinical profile. Allergic contact dermatitis due to Parthenium hysterophorus was commonest and found in 64% cases, followed by wearing apparel and jewellery in 16.8%, topical medicaments in 8% and cosmetics and occupational contactants in 5.6% cases each. The common individual allergens other than parthenium, were nickel in 8.8%, leather, hair dye and cement in 3.2% each, nitrofurazone and petrol, oil, lubricant (POL in 2.4% each. Patch test with suspected allergens was positive in 72% of cases.

  12. Systematic Study of Binding of μ-Conotoxins to the Sodium Channel NaV1.4

    Directory of Open Access Journals (Sweden)

    Somayeh Mahdavi

    2014-12-01

    Full Text Available Voltage-gated sodium channels (NaV are fundamental components of the nervous system. Their dysfunction is implicated in a number of neurological disorders, such as chronic pain, making them potential targets for the treatment of such disorders. The prominence of the NaV channels in the nervous system has been exploited by venomous animals for preying purposes, which have developed toxins that can block the NaV channels, thereby disabling their function. Because of their potency, such toxins could provide drug leads for the treatment of neurological disorders associated with NaV channels. However, most toxins lack selectivity for a given target NaV channel, and improving their selectivity profile among the NaV1 isoforms is essential for their development as drug leads. Computational methods will be very useful in the solution of such design problems, provided accurate models of the protein-ligand complex can be constructed. Using docking and molecular dynamics simulations, we have recently constructed a model for the NaV1.4-μ-conotoxin-GIIIA complex and validated it with the ample mutational data available for this complex. Here, we use the validated NaV1.4 model in a systematic study of binding other μ-conotoxins (PIIIA, KIIIA and BuIIIB to NaV1.4. The binding mode obtained for each complex is shown to be consistent with the available mutation data and binding constants. We compare the binding modes of PIIIA, KIIIA and BuIIIB to that of GIIIA and point out the similarities and differences among them. The detailed information about NaV1.4-μ-conotoxin interactions provided here will be useful in the design of new NaV channel blocking peptides.

  13. Cohort Profile Update: The China Jintan Child Cohort Study.

    Science.gov (United States)

    Liu, Jianghong; Cao, Siyuan; Chen, Zehang; Raine, Adrian; Hanlon, Alexandra; Ai, Yuexian; Zhou, Guoping; Yan, Chonghuai; Leung, Patrick W; McCauley, Linda; Pinto-Martin, Jennifer

    2015-10-01

    The China Jintan Child Cohort study began in 2004 with 1656 pre-school participants and a research focus on studying the impact of environmental exposures, such as lead, on children's neurobehavioural outcomes. This population cohort now includes around 1000 of the original participants, who have been assessed three times over a period of 10 years. Since the original IJE cohort profile publication in 2010, participants have experienced a critical developmental transition from pre-school to school age and then adolescence. The study has also witnessed an increase in breadth and depth of data collection from the original aim of risk assessment. This cohort has added new directions to investigate the mechanisms and protective factors for the relationship between early health factors and child physical and mental health outcomes, with an emphasis on neurobehavioural consequences. The study now encompasses 11 domains, composed of repeated measures of the original variables and new domains of biomarkers, sleep, psychophysiology, neurocognition, personality, peer relationship, mindfulness and family dynamics. Depth of evaluation has increased from parent/teacher report to self/peer report and intergenerational family report. Consequently, the cohort has additional directions to include: (i) classmates of the original cohort participants for peer relationship assessment; and (ii) parental and grandparental measures to assess personality and dynamics within families. We welcome interest in our study and ask investigators to contact the corresponding author for additional information on data acquisition. PMID:26323725

  14. Experimental and theoretical study on the binding of 2-mercaptothiazoline to bovine serum albumin

    International Nuclear Information System (INIS)

    2-Mercaptothiazoline (MTZ) is widely utilized as a brightening and stabilization agent, corrosion inhibitor and antifungal reagent. The residue of MTZ in the environment is potentially hazardous to human health. In this study, the binding mode of MTZ with bovine serum albumin (BSA) was investigated using spectroscopic and molecular docking methods under physiological conditions. MTZ could spontaneously bind with BSA through hydrogen bond and van der Waals interactions with one binding site. The site marker displacement experiments and the molecular docking revealed that MTZ bound into site II (subdomain IIIA) of BSA, which further resulted in some backbone structures and microenvironmental changes of BSA. This work is helpful for understanding the transportation, distribution and toxicity effects of MTZ in blood. - Highlights: • The mechanism was explored by multiple spectroscopic and molecular docking methods. • MTZ can spontaneously bind with BSA at subdomain IIIA (site II). • MTZ can lead to some conformational changes of BSA

  15. Study of caffeine binding to human serum albumin using optical spectroscopic methods

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The binding of caffeine to human serum albumin (HSA) under physiological conditions has been stud-ied by the methods of fluorescence,UV-vis absorbance and circular dichroism (CD) spectroscopy. The mechanism of quenching of HSA fluorescence by caffeine was shown to involve a dynamic quenching procedure. The number of binding sites n and apparent binding constant Kb were measured by the fluorescence quenching method and the thermodynamic parameters △H,△G,△S were calculated. The results indicate that the binding is mainly enthalpy-driven,with van der Waals interactions and hydrogen bonding playing major roles in the reaction. The distance r between donor (HSA) and acceptor (caffeine) was obtained according to the Frster theory of non-radiative energy transfer. Synchronous fluorescence,CD and three-dimensional fluorescence spectroscopy showed that the microenvironment and conformation of HSA were altered during the reaction.

  16. Experimental and theoretical study on the binding of 2-mercaptothiazoline to bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Yue, E-mail: tengyue@jiangnan.edu.cn; Wang, Xiang; Zou, Luyi; Huang, Ming; Du, Xianzheng

    2015-05-15

    2-Mercaptothiazoline (MTZ) is widely utilized as a brightening and stabilization agent, corrosion inhibitor and antifungal reagent. The residue of MTZ in the environment is potentially hazardous to human health. In this study, the binding mode of MTZ with bovine serum albumin (BSA) was investigated using spectroscopic and molecular docking methods under physiological conditions. MTZ could spontaneously bind with BSA through hydrogen bond and van der Waals interactions with one binding site. The site marker displacement experiments and the molecular docking revealed that MTZ bound into site II (subdomain IIIA) of BSA, which further resulted in some backbone structures and microenvironmental changes of BSA. This work is helpful for understanding the transportation, distribution and toxicity effects of MTZ in blood. - Highlights: • The mechanism was explored by multiple spectroscopic and molecular docking methods. • MTZ can spontaneously bind with BSA at subdomain IIIA (site II). • MTZ can lead to some conformational changes of BSA.

  17. Novel Bioluminescent Binding Assays for Ligand–Receptor Interaction Studies of the Fibroblast Growth Factor Family

    Science.gov (United States)

    Song, Ge; Shao, Xiao-Xia; Wu, Qing-Ping; Xu, Zeng-Guang; Liu, Ya-Li; Guo, Zhan-Yun

    2016-01-01

    We recently developed novel bioluminescent binding assays for several protein/peptide hormones to study their interactions with receptors using the so far brightest NanoLuc reporter. To validate the novel bioluminescent binding assay using a variety of protein/peptide hormones, in the present work we applied it to the fibroblast growth factor (FGF) family using the prototype member FGF2 as an example. A fully active recombinant FGF2 retaining a unique exposed cysteine (Cys) residue was chemically conjugated with an engineered NanoLuc carrying a unique exposed Cys residue at the C-terminus via formation of an intermolecular disulfide linkage. The NanoLuc-conjugated FGF2 (FGF2-Luc) retained high binding affinity to the overexpressed FGFR1 and the endogenous FGF receptor with the calculated dissociation constants of 161 ± 21 pM (n = 3) and 25 ± 4 pM (n = 3), respectively. In competition binding assays using FGF2-Luc as a tracer, receptor-binding potencies of wild-type or mutant FGF2s were accurately quantified. Thus, FGF2-Luc represents a novel non-radioactive tracer for the quantitative measurement of ligand–receptor interactions in the FGF family. These data suggest that the novel bioluminescent binding assay can be applied to a variety of protein/peptide hormones for ligand–receptor interaction studies. PMID:27414797

  18. Mapping Cannabinoid 1 Receptor Allosteric Site(s): Critical Molecular Determinant and Signaling Profile of GAT100, a Novel, Potent, and Irreversibly Binding Probe.

    Science.gov (United States)

    Laprairie, Robert B; Kulkarni, Abhijit R; Kulkarni, Pushkar M; Hurst, Dow P; Lynch, Diane; Reggio, Patricia H; Janero, David R; Pertwee, Roger G; Stevenson, Lesley A; Kelly, Melanie E M; Denovan-Wright, Eileen M; Thakur, Ganesh A

    2016-06-15

    agonism associated with Org27569 and PSNCBAM-1. Computational docking studies implicate C7.38(382) as a key feature of GAT100 ligand-binding motif. These data help inform the engineering of newer-generation, druggable CB1R allosteric modulators and demonstrate the utility of GAT100 as a covalent probe for mapping structure-function correlates characteristic of the druggable CB1R allosteric space. PMID:27046127

  19. [Electron paramagnetic resonance study of the interactions between steroid hormones and binding proteins].

    Science.gov (United States)

    Basset, M; Chambaz, E M; Defaye, G; Metz, B

    1978-01-01

    Interaction of a spin labeled corticosteroid (desoxycorticosterone nitroxyde: DOC -NO) with three purified proteins (albumin, transcortin, progesterone binding protein: PBG) was studied by electron spin resonance (ESR) spectroscopy. DOC-NO was competitive with natural corticosteroids and therefore bound at the same site to specific binding proteins. ESR spectra in the presence of each of the proteins showed an immobilized (bound) form of the spin labeled steroid and allowed the calculation of the corresponding association constant (Ka) at equilibrium. The three binding proteins could be characterized by the ESR parameters of the DOC-NO bound form. The thermodynamic parameters (deltaH, deltaS) of the steroid-protein interactions were calculated from the ESR data obtained within a wide temperature range (3--40 degrees C). The ESR spectra width (2T) was used to evaluate the polarity of the spin label environment within the steroid binding site: a hydrophobic character was observed for transcortin whereas PBG exhibited a more hydrophilic steroid binding sits. The rotational correlation time of the three protein DOC-NO complexes at equilibrium were calculated from ESR data; the results were correlated with the protein molecular size and suggested a non spherical shape for the binding macromolecule in solution. Spin labelling of biologically active steroids thus provides a novel approach for the study of the interaction of these hormones with their binding protein. Providing a suitable spin label, the ESR parameters may allow the characterization of several types of binding sites of different biological significance for the same hormone, in biological fluids as well as in target tissues. PMID:83166

  20. Lectin interactions with the Jurkat leukemic T-cell line: quantitative binding studies and interleukin-2 production

    Energy Technology Data Exchange (ETDEWEB)

    Dupuis, G.; Bastin, B.

    1988-03-01

    Phytohemagglutinin (PHA), concanavalin A (Con A), pea lectin, and wheat germ agglutinin (WGA) have been used to investigate their binding properties to Jurkat 77 6.8 leukemic human T cells and their ability to induce these cells to produce interleukin-2 (IL-2). Binding studies showed that the Jurkat cells fixed 0.82 +/- 0.11 microgram pea lectin, 2.02 +/- 0.17 micrograms Con A, 1.85 +/- 0.07 micrograms PHA and 8.88 +/- 0.61 micrograms WGA. Scatchard plots were linear, indicating that the binding process was homogeneous with respect to the binding constant. PHA and Con A bound with the highest affinity (Kass (apparent) approximately equal to 9 x 10(9) M-1), followed by pea lectin and WGA (Kass (apparent) approximately equal to 3 x 10(9) M-1). The number of lectin binding sites was in agreement with the results of saturation experiments. We also evaluated the effect of the presence of 12-O-tetradecanoylphorbol-13-acetate (TPA) on the binding process. Results show that there were no gross alterations in the value of (apparent) Kass in the case of PHA and WGA. In contrast, the presence of TPA decreased the affinity of Con A and modified the Scatchard profile for pea lectin, which was curvilinear with a concavity turned upward. In this case, data were (apparent) K1 = 17.7 x 10(9) M-1 (high-affinity sites) and (apparent) K2 = 2.6 x 10(9) M-1 (low-affinity sites). The four lectins shared the ability to stimulate Jurkat 77 6.8 cells to secrete IL-2. Optimal lectin concentrations were 20 micrograms/ml (PHA) and 50 micrograms/ml (WGA and Con A). Pea lectin failed to display a dose-response relationship, and IL-2 production increased proportionally with lectin concentration. Con A was the most efficient stimulator (250 U/ml), followed by WGA (160 U/ml) and PHA (108 U/ml).

  1. Psychological profile of women with infertility: A comparative study

    Directory of Open Access Journals (Sweden)

    Shuvabrata Poddar

    2014-01-01

    Full Text Available Background: An endeavour to probe into the psychological profile of infertile women in a comparative stance with the fertile women is not very common. This study is an attempt to explore the possible non-apparent personality factors which contribute to the unexplained pain of infertility. Methods: The main objectives of the present study were (a to examine whether infertile women are different from fertile women in terms of selected psychological variables- narcissistic components, dimensions of attachment style and uses of defensive manoeuvres; and (b whether the primary infertile women (n=18 are different from the secondary infertile women (n=12 with respect to those variables. A total of 60 individuals (30 infertile women and 30 matched fertile women were assessed through Attachment Style Questionnaire (ASQ, Narcissistic Personality Inventory (NPI and Defense Style Questionnaire (DSQ-40. General Health Questionnaire (GHQ was administered on to the fertile women to rule out the psychiatric morbidity. Results: Findings revealed that infertile women group differed from fertile women group with respect to narcissism, dimensions of attachment style and uses of defense mechanism. The primary infertile group also showed marked difference from the secondary infertile group with respect to those variables. Conclusions: This study endeavours to enrich the knowledge regarding the personality dynamics of infertile women to design psychotherapeutic programme to aid their well-being, help them to cherish the flavour of parenthood and improve their quality of life.

  2. Syntheses, DNA binding and anticancer profiles of L-glutamic acid ligand and its copper(II) and ruthenium(III) complexes.

    Science.gov (United States)

    Ali, Imran; Wani, Waseem A; Saleem, Kishwar; Wesselinova, Diana

    2013-02-01

    A new multidentate ligand (L) has been synthesized by the controlled condensation of L-glutamic acid with formaldehyde and ethylenediamine. Cu(II) and Ru(III) metal ion complexes of the synthesized ligand have also been prepared. The ligand and the metal complexes were purified by chromatography and characterized by spectroscopy and other techniques. Molar conductance measurements suggested ionic nature of the complexes. The ligand and the complexes are soluble in water with quite good stabilities; essential requirements for effective anticancer drugs. DNA binding constants (Kbs) for copper and ruthenium complexes were 1.8 x 103 and 2.6 x 103 M-1 while their Ksv values were 7.9 x 103, and 7.3 x 103; revealing strong binding of these complexes with DNA. Hemolytic assays of the reported compounds indicated their significantly less toxicity to RBCs than the standard anticancer drug letrazole. Anticancer profiles of all the compounds were determined on HepG2, HT-29, MDA-MB-231 and HeLa human cancer cell lines. All the compounds have quite good activities on HeLa cell lines but the best results were of CuL on HepG2, HT-29 and MDA-MB-231 cell lines. PMID:22741786

  3. Comparison of mHTT Antibodies in Huntington's Disease Mouse Models Reveal Specific Binding Profiles and Steady-State Ubiquitin Levels with Disease Development.

    Science.gov (United States)

    Bayram-Weston, Zubeyde; Jones, Lesley; Dunnett, Stephen B; Brooks, Simon P

    2016-01-01

    Huntington's disease (HD) cellular pathology is characterised by the aggregation of mutant huntingtin (mHTT) protein into inclusion bodies. The present paper compared the sensitivity of five widely used mHTT antibodies (S830; MW8; EM48; 1C2; ubiquitin) against mice from five commonly used HD mouse models (R6/1; YAC128; HdhQ92; B6 HdhQ150; B6 x129/Ola HdhQ150) at two ages to determine: the most sensitive antibodies for each model; whether mHTT antibody binding differed depending on aggregation stage (diffuse versus frank inclusion); the role of ubiquitin during aggregation as the ubiquitin proteosome system has been implicated in disease development. The models demonstrated unique profiles of antibody binding even when the models varied only by background strain (HdhQ150). MW8 was highly sensitive for detecting frank inclusions in all lines whereas EM48, ubiquitin and 1C2 demonstrated consistent staining in all models irrespective of age or form of mHTT. MW8 and S830 were the most sensitive antibodies with 1C2 the least. Ubiquitin levels were stable for each model regardless of age. Ubiquitin was particularly sensitive in young YAC128 mice that demonstrate an absence of inclusions until ~12 months of age suggesting high affinity to mHTT in its diffuse form. The data indicate that generalisations across models regarding the quantification of aggregations may not be valid and that mHTT antibody binding is unique to the mouse model and sensitive to changes in inclusion development. PMID:27196694

  4. Molecular docking studies in factor XIa binding site

    Science.gov (United States)

    Balaji, Govardhan A.; Balaji, Vitukudi N.; Rao, Shashidhar N.

    2016-03-01

    Factor XIa inhibitors have been identified to have potential as anticoagulants with robust efficacy and low bleeding risks. In light of their significance and the availability of their 3-D X-ray data in the PDB, we present molecular docking studies carried out with a view to obtain docking protocols that will successfully reproduce the experimentally observed protein-ligand interactions in the case of various X-ray ligands. In this context, we have specifically investigated the efficacy of various cross-docking protocols in reproducing experimental data. Our studies demonstrate that an ensemble of the three apo proteins is capable of accurately docking a majority of the X-ray ligands accurately without invoking any additional conformational flexibility than that present in their experimental structures. Further, we demonstrate that such an ensemble is successfully able to enrich a collection of known active factor XIa inhibitors embedded in a decoy database of drug-like molecules.

  5. Study of MMLV RT- Binding with DNA using Surface Plasmon Resonance Biosensor

    Institute of Scientific and Technical Information of China (English)

    Lei WU; Ming-Hui HUANG; Jian-Long ZHAO; Meng-Su YANG

    2005-01-01

    Surface plasmon resonance biosensor technique was used to study the binding of Moloney murine leukemia virus reverse transcriptase without RNase H domain (MMLV RT-) with DNA in the absence and in the presence of inhibitors. Different DNA substrates, including single-stranded DNA (ssDNA),DNA template-primer (T-P) duplex and gapped DNA, were immobilized on the biosensor chip surface using streptavidin-biotin, and MMLV RT--DNA binding kinetics were analyzed by different models. MMLV RT-could bind with ssDNA and the binding was involved in conformation change. MMLV RT- binding DNA T-P duplex and gapped DNA could be analyzed using the simple 1:1 Langmuir model. The lack of RNase H domain reduced the affinity between MMLV RT- and T-P duplex. The effects of RT inhibitors, including efavirenz, nevirapine and quercetin, on the interaction between MMLV RT- and gapped DNA were analyzed according to recovered kinetics parameters. Efavirenz slightly interfered with the binding between RT and DNA and the affinity constant in the presence of the inhibitor (KA=1.21× 106 M-1) was lower than in the absence of the inhibitor (KA=4.61× 106 M-1). Nevirapine induced relatively tight binding between RT and DNA and the affinity constant in the presence of the inhibsitor (KA=l.47×107 M-1) was approximately three folds higher than without nevirapine, mainly due to rapid association and slow dissociation. Quercetin, a flavonoid originating from plant which has previously shown strong inhibition of the activity of RT, was found to have minimal effect on the RT-DNA binding.

  6. In vivo and in vitro studies of hafnium-binding to rat serum transferrin

    Energy Technology Data Exchange (ETDEWEB)

    Then, G.M.; Appel, H.; Duffield, J.; Taylor, D.M.; Thies, W.G.

    1986-08-01

    The binding of hafnium to rat serum transferrin was studied using the time differential perturbed angular correlation (TDPAC) technique. Hafnium is interesting as a toxic metal binding to transferrin because it behaves metabolically similarly to plutonium. The isotope 181Hf offers favorable access to the TDPAC-method. Samples were prepared in vivo by intravenous injection of Hf-NTA, Hf-citrate, and Hf-oxalate solutions, respectively, into Sprague-Dawley rats and in vitro by adding Hf-NTA solution to fresh rat serum. In both cases two specific electric quadrupole interactions were observed, which correspond to two well-defined binding configurations. They may be attributed to the N-terminal and the C-terminal binding site in the transferrin molecule. The 181Hf-distribution between these two binding states depends on pH, salt and hafnium concentrations, temperature, and incubation time. With a fast TDPAC-setup of four BaF2-detectors a time resolution of about 600 ps could be achieved. The specific binding configurations of 181Hf and the comparatively slow relaxation times lead to spectra of considerable accuracy.

  7. Studies of vitamin E binding and transfer by a rat liver cytosolic protein

    Energy Technology Data Exchange (ETDEWEB)

    Posch, K.C.; Mavis, R.D.

    1986-05-01

    In vitro vitamin E binding and transfer were examined using a semipurified (sephadex G-75 fraction) vitamin E binding and transfer protein (VE-TBP) from the rat liver cytosol. Binding and transfer studies thus far indicate that the protein is very specific for d-..cap alpha..-tocopherol. Among the other lipophilic ligands examined only d-..gamma..-tocopherol at high concentrations was competitive with d-..cap alpha..-tocopherol binding. Specificity studies also indicate the protein to be stereospecific in nature since dl-..cap alpha..-tocopherol was only partially competitive. Studies using PMSF and NEM also indicate that neither a hydroxyl nor a sulfhydryl functional group on the protein is required for vitamin E binding. Transfer studies show that the VE-TBP is capable of specifically transferring equal amounts of vitamin E from liposomes to both mitochondria and microsomes when comparable protein concentrations are used. This indicates that no preferential transfer to one membrane type occurs. Pretreatment of mitochondria and microsomes with heat, pronase or trypsin also does not affect transfer of vitamin E. Thus, transfer of vitamin E is not dependent on a membrane protein. Finally, the VE-TBP is capable of unidirectional transport of vitamin E from prelabelled microsomes to vitamin E free liposomes.

  8. Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA

    Directory of Open Access Journals (Sweden)

    Jonathan K. Pokorski

    2012-01-01

    Full Text Available Folded RNA molecules have recently emerged as critical regulatory elements in biological pathways, serving not just as carriers of genetic information but also as key components in enzymatic assemblies. In particular, the transactivation response element (TAR of the HIV genome regulates transcriptional elongation by interacting specifically with the Tat protein, initiating the recruitment of the elongation complex. Preventing this interaction from occurring in vivo halts HIV replication, thus making RNA-binding molecules an intriguing pharmaceutical target. Using α-amino acids as starting materials, we have designed and synthesized a new class of polyamino-amido oligomers, called PAAs, specifically for binding to folded RNA structures. The PAA monomers were readily incorporated into a 125-member combinatorial library of PAA trimers. In order to rapidly assess RNA binding, a quantum dot-based fluorescent screen was developed to visualize RNA binding on-resin. The binding affinities of hits were quantified using a terbium footprinting assay, allowing us to identify a ligand (SFF with low micromolar affinity (kd=14 μM for TAR RNA. The work presented herein represents the development of a flexible scaffold that can be easily synthesized, screened, and subsequently modified to provide ligands specific for binding to folded RNAs.

  9. Clinical profile of forefoot eczema: A study of 42 cases

    Directory of Open Access Journals (Sweden)

    Brar Kamal

    2005-01-01

    Full Text Available BACKGROUND : Forefoot eczema (FE is characterized by dry fissured dermatitis of the plantar surface of the feet. AIM : To study the clinical profile of FE and the possible etiological factors. METHODS : Forty-two patients with FE were included in the study. A detailed history was recorded and examination done. Fungal scrapings and patch test with Indian Standard Series (ISS were performed in all patients. RESULTS : The most common site affected was the plantar surface of the great toe in 16 (38.09% patients. Hand involvement, with fissuring and soreness of the fingertips and palm, was seen in four patients (9.5%. Seven patients (16.6% had a personal history of atopy whereas family history of atopy was present in six (14.2%. Seven patients (16.6% reported aggravation of itching with plastic, rubber or leather footwear, and 13 (30.9%, with detergents and prolonged contact with water. Negative fungal scrapings in all patients ruled out a dermatophyte infection. Patch testing with ISS was performed in 19 patients and was positive in five. CONCLUSIONS : FE is a distinctive dermatosis of the second and third decade, predominantly in females, with a multifactorial etiology, possible factors being chronic irritation, atopy, footwear and seasonal influence.

  10. Remote Sensing of Salinity Profiles and Multi-sensor Profiler for Marine Estuarine Flow, Water Properties and Sediment Studies

    Science.gov (United States)

    Sanford, T. B.

    2012-12-01

    Observing the numerous characteristics of flow and water properties in marine estuaries requires many sensors and systems. As a component of CMOP (Coastal Margin Observation and Prediction), an NSF Science and Technology Center, two innovative new instruments were developed and operated in the marine estuary of the Columbia River. One determines the vertical profile of electrical conductivity (σ), which in the Columbia River can be converted to salinity. The goal of the Sigma Profiler is to provide a robust sensor for determining the salinity profile from the riverbed in a region of vessel traffic, fishing, debris and strong currents. The Sigma Profiler uses characteristics of deliberately emitted EM currents. Because the spatial attenuation of EM signals is proportional to the square root of signal frequency, the transmission of signals of many frequencies can determine the vertical structure of σ. Six frequencies between 270 Hz and 27.7 kHz are used. SP performance is determined with simultaneous CTD casts and the CMOP autonomous profiler at Saturn01. The observations are useful for comparison with numerical models simulations. The second instrument is a combination of many sensors on a tow body that is winched vertically. The sensors on the Winched Profiler include SonTek ADV, CTD, μσ, μT, dual shear probes, Wet Labs Triplet, LISST-100X, O2, acoustic altimeter, motion package, and magnetic compass. The various sensors on the Winched Profiler can be used to determine vertical eddy fluxes of salinity, mixing characteristics, dissipation rates of kinetic energy, internal waves, estuarine turbidity maxima (ETMs), terms in turbulent KE energy balance, BBL structure, turbidity, suspended sediment characteristic and transport and evaluate various turbulence closure schemes. The Winched Profiler has a real time display of 25 panels of sensor outputs and diagnostics. Results from the Sigma Profiler and Winched Profiler, which were operated extensively in May 2012

  11. Interference of anaesthetics with radioligand binding in neuroreceptor studies

    Energy Technology Data Exchange (ETDEWEB)

    Elfving, Betina; Knudsen, Gitte Moos [Neurobiology Research Unit N9201, University hospital Rigshospitalet, 9 Blegdamsvej, 2100, Copenhagen (Denmark); Bjoernholm, Berith [Department of Computational Chemistry, H. Lundbeck A/S, Copenhagen-Valby (Denmark)

    2003-06-01

    Evaluations of new emission tomography ligands are usually carried out in animals. In order to keep the animals in a restricted position during the scan session, anaesthesia is almost inevitable. In ex vivo rat studies we investigated the interference of ketamine/xylazine, zoletile mixture, isoflurane and halothane with the serotonin re-uptake site, the serotonin{sub 2A} receptor and the dopamine re-uptake site by use of [{sup 3}H]-(S)-citalopram, [{sup 18}F]altanserin and [{sup 125}I]PE2I, respectively. Ketamine/xylazine decreased the target-to-background ratio (mean {+-} SD) of [{sup 3}H]-(S)-citalopram from 1.5{+-}0.19 to 0.81{+-}0.19 (P<0.05), whereas isoflurane and halothane increased the ratio from 1.5{+-}0.19 to 1.9{+-}0.24 and 2.1{+-}0.13 (P<0.05), respectively. Only with the zoletile mixture did the ratio remain unaltered. None of the tested anaesthetics affected the target-to-background ratio of [{sup 18}F]altanserin. The [{sup 125}I]PE2I target-to-background ratio decreased with both ketamine/xylazine (from 12.4{+-}0.81 to 10.1{+-}1.4, P<0.05) and isoflurane (from 12.4{+-}0.81 to 9.5{+-}1.1, P<0.05) treated rats, whereas treatment with zoletile mixture and halothane left the ratio unaltered. It is concluded that prior to performance of neuroreceptor radioligand studies, the possible interaction between radioligands and anaesthetics should be carefully evaluated. (orig.)

  12. Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst

    Science.gov (United States)

    Kundu, Partha P.; Kumari, Gayatri; Chittoory, Arjun K.; Rajaram, Sridhar; Narayana, Chandrabhas

    2015-12-01

    Bis-camphorsulfonyl urea, a newly developed hydrogen bonding catalyst, was evaluated in an enantioselective Friedel-Crafts reaction. We observed that complexation of the sulfonyl urea with a sodium cation enhanced the selectivity of reactions in comparison to reactions performed with urea alone. To understand the role of sodium cation, we performed Infrared and Raman spectroscopic studies. The detailed band assignment of the molecule was made by calculating spectra using Density Functional theory. Our studies suggest that the binding of the cation takes place through the oxygen atoms of carbonyl and sulfonyl groups. Natural Bond Orbital (NBO) analysis shows the expected charge distribution after sodium binding. The changes in the geometrical parameter and charge distribution are in line with the experimentally observed spectral changes. Based on these studies, we conclude that binding of the sodium cation changes the conformation of the sulfonyl urea to bring the chiral camphor groups closer to the incipient chiral center.

  13. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    International Nuclear Information System (INIS)

    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (Tm) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol−1) and ∆S° (−1.22 kJ mol−1 K−1) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA

  14. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Sandhya; Jaldappagari, Seetharamappa, E-mail: jseetharam@yahoo.com

    2013-10-15

    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (T{sub m}) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol{sup −1}) and ∆S° (−1.22 kJ mol{sup −1} K{sup −1}) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA.

  15. Intact brain cells: a novel model system for studying opioid receptor binding

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, N.F.; El-Fakahany, E.E.

    1985-07-29

    The use of a novel tissue preparation to study opioid receptor binding in viable, intact cells derived from whole brains of adult rats is presented. Mechanically dissociated and sieved cells, which were not homogenized at any stage of the experimental protocol, and iso-osmotic physiological buffer were used in these experiments. This system was adapted in order to avoid mechanical and chemical disruption of cell membranes, cytoskeletal ultrastructure or receptor topography by homogenization or by the use of nonphysiological buffers, and to mimic in vivo binding conditions as much as possible. Using (/sup 3/H)naloxone as the radioligand, the studies showed saturable and stereospecific high-affinity binding of this opioid antagonist in intact cells, which in turn showed consistently high viability. (/sup 3/H)Naloxone binding was also linear over a wide range of tissue concentrations. This technique provides a very promising model for future studies of the binding of opioids and of many other classes of drugs to brain tissue receptors in a more physiologically relevant system than those commonly used to date.

  16. Intact brain cells: a novel model system for studying opioid receptor binding

    International Nuclear Information System (INIS)

    The use of a novel tissue preparation to study opioid receptor binding in viable, intact cells derived from whole brains of adult rats is presented. Mechanically dissociated and sieved cells, which were not homogenized at any stage of the experimental protocol, and iso-osmotic physiological buffer were used in these experiments. This system was adapted in order to avoid mechanical and chemical disruption of cell membranes, cytoskeletal ultrastructure or receptor topography by homogenization or by the use of nonphysiological buffers, and to mimic in vivo binding conditions as much as possible. Using [3H]naloxone as the radioligand, the studies showed saturable and stereospecific high-affinity binding of this opioid antagonist in intact cells, which in turn showed consistently high viability. [3H]Naloxone binding was also linear over a wide range of tissue concentrations. This technique provides a very promising model for future studies of the binding of opioids and of many other classes of drugs to brain tissue receptors in a more physiologically relevant system than those commonly used to date

  17. Synthesis, in vitro binding profile and biodistribution of a 125I-labeled N-benzyl pyrrolidinyl benzamide derivative: A potential radioligand for mapping dopamine D2 receptors

    International Nuclear Information System (INIS)

    cis-N-(1-Benzyl-2-methylpyrrolidine-3-yl)-5-iodo-2-methoxy-4-(methylamino) benzamide (IYM), a YM-09151-2 analog iodinated at the 5-position of the benzoyl moiety, was synthesized and evaluated as a potential radiopharmaceutical for investigating brain dopamine D2 receptors by single photon emission computer tomography (SPECT). [125I]IYM was synthesized by a halogen exchange reaction and purified by high-performance liquid chromatography (HPLC). An in vitro competitive binding study with [3H]spiperone using rat striatal synaptosomal membranes revealed that IYM had higher affinity for dopamine D2 receptors than did YM-09151-2 or spiperone. In a saturation binding study using rat striatal synaptosomal membranes, IYM had a Kd of 0.04 nM. Biodistribution studies in mice disclosed that [125I]IYM exhibited high and specific striatal uptake, with the striatal/cerebellar uptake ratio being 14 at 120 min after injection. Furthermore, the striatal uptake of [125I]IYM was saturable, and [125I]IYM was displaced only by dopaminergic compounds. Ex vivo autoradiographic studies in rats further confirmed the high uptake and retention of this agent in the striatum and total blockade of its uptake by YM-09151-2. Thus, IYM showed specific binding to dopamine D2 receptors in the rodent striatum and therefore holds great potential for use in in vivo dopamine D2 receptor studies

  18. Clostridium perfringens epsilon toxin H149A mutant as a platform for receptor binding studies.

    Science.gov (United States)

    Bokori-Brown, Monika; Kokkinidou, Maria C; Savva, Christos G; Fernandes da Costa, Sérgio; Naylor, Claire E; Cole, Ambrose R; Moss, David S; Basak, Ajit K; Titball, Richard W

    2013-05-01

    Clostridium perfringens epsilon toxin (Etx) is a pore-forming toxin responsible for a severe and rapidly fatal enterotoxemia of ruminants. The toxin is classified as a category B bioterrorism agent by the U.S. Government Centres for Disease Control and Prevention (CDC), making work with recombinant toxin difficult. To reduce the hazard posed by work with recombinant Etx, we have used a variant of Etx that contains a H149A mutation (Etx-H149A), previously reported to have reduced, but not abolished, toxicity. The three-dimensional structure of H149A prototoxin shows that the H149A mutation in domain III does not affect organisation of the putative receptor binding loops in domain I of the toxin. Surface exposed tyrosine residues in domain I of Etx-H149A (Y16, Y20, Y29, Y30, Y36 and Y196) were mutated to alanine and mutants Y30A and Y196A showed significantly reduced binding to MDCK.2 cells relative to Etx-H149A that correlated with their reduced cytotoxic activity. Thus, our study confirms the role of surface exposed tyrosine residues in domain I of Etx in binding to MDCK cells and the suitability of Etx-H149A for further receptor binding studies. In contrast, binding of all of the tyrosine mutants to ACHN cells was similar to that of Etx-H149A, suggesting that Etx can recognise different cell surface receptors. In support of this, the crystal structure of Etx-H149A identified a glycan (β-octyl-glucoside) binding site in domain III of Etx-H149A, which may be a second receptor binding site. These findings have important implications for developing strategies designed to neutralise toxin activity. PMID:23504825

  19. Development of an autonomous vertical profiler for oceanographic studies

    Digital Repository Service at National Institute of Oceanography (India)

    Dabholkar, N.; Desa, E.; Afzulpurkar, S.; Madhan, R.; Mascarenhas, A.A.M.Q.; Navelkar, G.; Maurya, P.K.; Prabhudesai, S.; Nagvekar, S.; Martins, H.; Sawkar, G.; Fernandes, P.; Manoj, K.K.

    groups. This paper is based on a concept patent on a thruster driven Autonomous Vertical profiler [AVP], and describes the developmental steps being taken on the integration of sensors, control electronics, communications and a Graphical User interface...

  20. Electricity Profile Study for Domestic and Commercial Sectors

    Directory of Open Access Journals (Sweden)

    Asmarashid Ponniran

    2012-12-01

    Full Text Available As Malaysia move towards as a developed country, it is expected that the electricity consumption in domestic and commercial sectors will increase as well as more industrials and households need. This study is to investigate the electricity profile in domestic and commercial sectors by monitoring some appropriate appliances that contribute high electricity consumption. The characteristics for every major loads are examined and the potential energy saving is compared to an efficient electrical appliances in order to obtain the effective energy consumption. Questionnaires have been used to collect respondents, appliances and equipments information. For appliances and equipments measurement data, power quality equipment has been. Samples for domestic sector involved 150 respondents from three residential classes which are high, middle and rural. While for commercial sector, 100 respondents are involved which are restaurant, hotel, workshop, and store/office. It shows, in domestic sector, refrigerator appliance consumed high electricity meanwhile in commercial sector; compressor equipment contributed high consumption in electricity. It is also indicated that by using efficient electrical appliances it can reduce the amount of electricity consumption. However, instead of using high efficient appliances, human factor also contribute significant impact on reducing electricity consumption. By integrating between human factor, high efficient appliances/equipment and government policy, the electricity consumption can be used and managed wisely. Therefore the strategies to build energy efficient society have been proposed in order to achieve efficient electricity consumption.

  1. Study of protein and metabolic profile of sugarcane workers

    International Nuclear Information System (INIS)

    Full text: The National Alcohol Program (Proalcool) is a successful Brazilian renewable fuel initiative aiming to reduce the country's oil dependence. Producing ethanol from sugar cane, the program has shown positive results although accompanied by potential damage. The environmental impact mainly derives from the particulate matter emissions due to sugarcane burning, which is potentially harmful to human health. The physical activity of sugarcane workers is repetitive and exhaustive and is carried out in presence of dust, smoke and soot. The efforts by the sugarcane workers during the labor process result in increased risks of nervous, respiratory and cardiovascular system diseases and also in premature death. The aim of the present study was to investigate the effect of occupational stress on protein and metabolic profile of sugarcane workers. Forty serum samples were analyzed by 1-DE and LC MS/MS proteomic shotgun strategy and nuclear magnetic resonance (NMR). A set of proteins was found to be altered in workers after crops when compared with controls. The analysis of NMR spectra by Chenomx also showed differences in the expression of metabolites. For example, lactate displayed higher levels in control subjects than in sugarcane workers, and vice versa for the acetate. The concentrations of the two metabolites were lower after the crop, except in the case of acetate, which remained uniform in the control subjects before and after the crop. The present findings can have important application for rational designs of preventive measures and early disease detection in sugarcane workers. (author)

  2. Study of protein and metabolic profile of sugarcane workers

    Energy Technology Data Exchange (ETDEWEB)

    Polachini, G.M.; Tajara, E.H. [Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil); Santos, U.P. [Universidade de Sao Paulo (USP), SP (Brazil); Zeri, A.C.M.; Paes Leme, A.F. [Laboratorio Nacional de Luz Sincrotron (LNLS), Campinas, SP (Brazil)

    2012-07-01

    Full text: The National Alcohol Program (Proalcool) is a successful Brazilian renewable fuel initiative aiming to reduce the country's oil dependence. Producing ethanol from sugar cane, the program has shown positive results although accompanied by potential damage. The environmental impact mainly derives from the particulate matter emissions due to sugarcane burning, which is potentially harmful to human health. The physical activity of sugarcane workers is repetitive and exhaustive and is carried out in presence of dust, smoke and soot. The efforts by the sugarcane workers during the labor process result in increased risks of nervous, respiratory and cardiovascular system diseases and also in premature death. The aim of the present study was to investigate the effect of occupational stress on protein and metabolic profile of sugarcane workers. Forty serum samples were analyzed by 1-DE and LC MS/MS proteomic shotgun strategy and nuclear magnetic resonance (NMR). A set of proteins was found to be altered in workers after crops when compared with controls. The analysis of NMR spectra by Chenomx also showed differences in the expression of metabolites. For example, lactate displayed higher levels in control subjects than in sugarcane workers, and vice versa for the acetate. The concentrations of the two metabolites were lower after the crop, except in the case of acetate, which remained uniform in the control subjects before and after the crop. The present findings can have important application for rational designs of preventive measures and early disease detection in sugarcane workers. (author)

  3. Novel bioluminescent binding assays for interaction studies of protein/peptide hormones with their receptors.

    Science.gov (United States)

    Liu, Ya-Li; Guo, Zhan-Yun

    2016-05-01

    Protein/peptide hormones are the largest group of endogenous signaling molecules and exert various biological functions by binding to specific cell membrane receptors. To study the interactions between these hormones and their receptors, quantitative ligand-receptor binding assays have been widely used for decades. However, the assays conventionally relied on the use of radioligands, which have some major drawbacks and can only be used in laboratories with a radioactive material license. We recently developed novel bioluminescent binding assays for several protein/peptide hormones using the brightest bioluminescent reporter known to date, nanoluciferase (NanoLuc). The NanoLuc reporter can be either chemically conjugated to an appropriate position, or genetically fused at one terminus, of protein/peptide hormones. Compared to conventional radioligands, these bioluminescent ligands have higher sensitivity, better safety, and longer shelf lives, and thus, represent a novel class of non-radioactive tracers for quantitative receptor binding assays. In the present review, we provide some general considerations and specific examples for setting up the bioluminescent binding assays. Such techniques can be applied to other protein/peptide hormones in future to facilitate their interaction studies with their receptors. PMID:27020777

  4. The influence of fatty acids on theophylline binding to human serum albumin. Comparative fluorescence study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka-Zubik, J.; Szkudlarek-Haśnik, A.; Zubik-Skupień, I.; Góra, A.; Dubas, M.; Korzonek-Szlacheta, I.; Wielkoszyński, T.; Żurawiński, W.; Sosada, K.

    2012-04-01

    Theophylline, popular diuretic, is used to treat asthma and bronchospasm. In blood it forms complexes with albumin, which is also the main transporter of fatty acids. The aim of the present study was to describe the influence of fatty acids (FA) on binding of theophylline (Th) to human serum albumin (HSA) in the high affinity binding sites. Binding parameters have been obtained on the basis of the fluorescence analysis. The data obtained for the complex of Th and natural human serum albumin (nHSA) obtained from blood of obese patients qualified for surgical removal of stomach was compared with our previous studies on the influence of FA on the complex of Th and commercially available defatted human serum albumin (dHSA).

  5. Targeting the Cryptococcus neoformans var. grubii Cell Wall Using Lectins: Study of the Carbohydrate-Binding Domain

    Directory of Open Access Journals (Sweden)

    Pamella de Brito Ximenes

    2015-02-01

    Full Text Available Cryptococcus neoformans var. grubii is considered to be the major cause of cryptococcosis in immunosuppressed patients. Understanding cell wall glycoproteins using lectins is of medical interest and can contribute to specific therapy. The aim of this study was to evaluate the carbohydrates on the cell wall of Cryptococcus neoformans var. grubii clinical isolates, using a fluorescein isothiocyanate-lectin binding protocol. Thirty yeast strains stocked in the culture collection were cultivated for 2 days at 30 °C with shaking. Cells were obtained by centrifugation, washed in phosphate-buffered saline, and a suspension of 107 cells/mL was obtained. To determine the binding profile of lectins, concanavalin A (Con A, wheat germ agglutinin (WGA, Ulex europaeus agglutinin I (UEA-I, and peanut agglutinin (PNA conjugated to fluorescein were used. All the tested clinical isolates of Cryptococcus neoformans var. grubii were intensely stained by WGA, moderately stained by Con A, and weakly stained by PNA and UEA-I. Thus, Cryptococcus can be detected in clinical specimens such as blood and cerebrospinal fluid using the fluorescent lectin WGA, which may be considered as an option for detection in cases of suspected cryptococcosis with low laboratory sensitivity. Future applications may be developed using this basic tool.

  6. Multi-scale molecular dynamics study of cholera pentamer binding to a GM1-phospholipid membrane.

    Science.gov (United States)

    Sridhar, Akshay; Kumar, Amit; Dasmahapatra, Ashok Kumar

    2016-07-01

    The AB5 type toxin produced by the Vibrio cholerae bacterium is the causative agent of the cholera disease. The cholera toxin (CT) has been shown to bind specifically to GM1 glycolipids on the membrane surface. This binding of CT to the membrane is the initial step in its endocytosis and has been postulated to cause significant disruption to the membrane structure. In this work, we have carried out a combination of coarse-grain and atomistic simulations to study the binding of CT to a membrane modelled as an asymmetrical GM1-DPPC bilayer. Simulation results indicate that the toxin binds to the membrane through only three of its five B subunits, in effect resulting in a tilted bound configuration. Additionally, the binding of the CT can increase the area per lipid of GM1 leaflet, which in turn can cause the membrane regions interacting with the bound subunits to experience significant bilayer thinning and lipid tail disorder across both the leaflets. PMID:27474868

  7. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors.

    Science.gov (United States)

    Ohno, Kazuki; Mitsui, Takashi; Tanida, Yoshiaki; Matsuura, Azuma; Fujitani, Hideaki; Niimi, Tatsuya; Orita, Masaya

    2011-02-01

    Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein/ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1)/inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann/surface area (MM/PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects. PMID:20480380

  8. Alteration of methotrexate binding to human serum albumin induced by oxidative stress. Spectroscopic comparative study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Sułkowska, A.; Równicka-Zubik, J.

    2016-01-01

    Changes of oxidative modified albumin conformation by comparison of non-modified (HSA) and modified (oHSA) human serum albumin absorption spectra, Red Edge Excitation Shift (REES) effect and fluorescence synchronous spectra were investigated. Studies of absorption spectra indicated that changes in the value of absorbance associated with spectral changes in the region from 200 to 250 nm involve structural alterations related to variations in peptide backbone conformation. Analysis of the REES effect allowed for the observation of changes caused by oxidation in the region of the hydrophobic pocket containing the tryptophanyl residue. Synchronous fluorescence spectroscopy confirmed changes of the position of the tryptophanyl and tyrosil residues fluorescent band. Effect of oxidative stress on binding of methotrexate (MTX) was investigated by spectrofluorescence, UV-VIS and 1HNMR spectroscopy. MTX caused the fluorescence quenching of non-modified (HSA) and modified (oHSA) human serum albumin molecule. The values of binding constants, Hill's coefficients and a number of binding sites in the protein molecule in the high affinity binding site were calculated for the binary MTX-HSA and MTX-oHSA systems. For these systems, qualitative analysis in the low affinity binding sites was performed with the use of the 1HNMR technique.

  9. Computational study of small molecule binding for both tethered and free conditions

    CERN Document Server

    Ytreberg, F Marty

    2009-01-01

    Using a calix[4]arene-benzene complex as a test system we compare the potential of mean force for when the calix[4]arene is tethered versus free. When the complex is in vacuum our results show that the difference between tethered and free is primarily due to the entropic contribution to the potential of mean force resulting in a binding free energy difference of 6.5 kJ/mol. By contrast, when the complex is in water our results suggest that the difference between tethered and free is due to the enthalpic contribution resulting in a binding free energy difference of 1.6 kJ/mol. This study elucidates the roles of entropy and enthalpy for this small molecule system and emphasizes the point that tethering the receptor has the potential to dramatically impact the binding properties. These findings should be taken into consideration when using calixarene molecules in nanosensor design.

  10. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies.

    Science.gov (United States)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper. PMID:27089183

  11. Binding of copper to lysozyme: Spectroscopic, isothermal titration calorimetry and molecular docking studies

    Science.gov (United States)

    Jing, Mingyang; Song, Wei; Liu, Rutao

    2016-07-01

    Although copper is essential to all living organisms, its potential toxicity to human health have aroused wide concerns. Previous studies have reported copper could alter physical properties of lysozyme. The direct binding of copper with lysozyme might induce the conformational and functional changes of lysozyme and then influence the body's resistance to bacterial attack. To better understand the potential toxicity and toxic mechanisms of copper, the interaction of copper with lysozyme was investigated by biophysical methods including multi-spectroscopic measurements, isothermal titration calorimetry (ITC), molecular docking study and enzyme activity assay. Multi-spectroscopic measurements proved that copper quenched the intrinsic fluorescence of lysozyme in a static process accompanied by complex formation and conformational changes. The ITC results indicated that the binding interaction was a spontaneous process with approximately three thermodynamical binding sites at 298 K and the hydrophobic force is the predominant driven force. The enzyme activity was obviously inhibited by the addition of copper with catalytic residues Glu 35 and Asp 52 locating at the binding sites. This study helps to elucidate the molecular mechanism of the interaction between copper and lysozyme and provides reference for toxicological studies of copper.

  12. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, A.

    1997-10-08

    The author`s group has previously shown that isocyanides are readily adsorbed from solutions to Au powder and bind to the Au surface in an end-on fashion through the terminal carbon. Later work demonstrated that the equilibrium constants for the reversible adsorption of electronically inequivalent isocyanides could be obtained using the Langmuir isotherm technique. This dissertation describes two projects completed which complement the initial findings of this group. Initially, several alkylisocyanides were synthesized to examine the effect of tail length on Au powder adsorption. It was observed that the length of the alkyl chain affected not only the Au surface binding affinity, but also the rate of surface saturation and saturation coverage values. Direct competition studies were also studied using a {sup 13}C-labeled isocyanide. These studies demonstrated the stabilization afforded by substrate-substrate packing forces in SAM`s formed by the longer chain isocyanides. In a second study, di and triisocyanides were synthesized to determine the effect that the length of the connecting link and the number of isocyanide groups (as points of attachment) have on Au adsorption stability. The work in this area describes the binding modes, relative binding affinities and surface coverage values for a series of flexible alkyl and xylyldiisocyanides on Au powder surfaces. This report contains only the introductory material, and general summary. Two chapters have been processed separately. 56 refs.

  13. Spectroscopic and docking studies of the binding of two stereoisomeric antioxidant catechins to serum albumins

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Durba; Dutta, Samrajnee; Maity, Shyam Sundar [Department of Chemistry, Presidency University, Kolkata 700 073 (India); Ghosh, Sanjib, E-mail: sanjibg@cal2.vsnl.net.in [Department of Chemistry, Presidency University, Kolkata 700 073 (India); Singha Roy, Atanu; Ghosh, Kalyan Sundar [Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302 (India); Dasgupta, Swagata, E-mail: swagata@chem.iitkgp.ernet.in [Department of Chemistry, Indian Institute of Technology, Kharagpur 721 302 (India)

    2012-06-15

    The interactions of two stereoisomeric antioxidant flavonoids, catechin (C) and epicatechin (EC) with bovine serum albumin (BSA) and human serum albumin (HSA), have been investigated by steady state and time resolved fluorescence, phosphorescence, circular dichroism (CD), FTIR and protein-ligand docking studies. The steady-state fluorescence studies indicate a single binding site for both the ligands. FTIR spectra suggest that in both the albumins, C and EC stabilize the {alpha}-helix at the cost of a corresponding loss in the {beta}-sheet structure. CD studies have been carried out using ({+-})C, and both the epimers (+)C and (-)C. The low temperature phosphorescence and protein-ligand [(+), (-) and ({+-}) forms of C and EC] docking studies indicate that the ligands bind in the proximity of Trp 134 of BSA and Trp 214 of HSA, thereby changing their solvent accessible surface areas (ASA). Asn 158 and Glu 130 side chains are found to be within the hydrogen bonding distance from the phenolic -OH groups of C and EC in the case of BSA complex. C and EC are located within the binding pocket of sub-domain IIa of HSA. - Highlights: Black-Right-Pointing-Pointer Binding of two biologically important stereoisomeric antioxidants. Black-Right-Pointing-Pointer To find a significant role in pharmacology. Black-Right-Pointing-Pointer To find the conformational changes of the protein leading to the perturbation of Trp residues.

  14. Electronic structure of hafnium: A Compton profile study

    Indian Academy of Sciences (India)

    S Khera; S Mathur; B L Ahuja

    2007-01-01

    In this paper, we report the first-ever isotropic Compton profile of hafnium measured at an intermediate resolution, with 661.65 keV -radiation. To compare our experimental data, the theoretical computations have also been carried out within the framework of pseudopotential using CRYSTAL03 code and the renormalized-free-atom (RFA) model. It is found that the present experimental profile is in better agreement with the RFA calculations if the outer electronic configuration is chosen as 5d3.26s0.8. The cohesive energy of Hf is also deduced from the experimental data and is compared with the available data.

  15. Compton profile study of ZrB2

    Science.gov (United States)

    Vyas, V.; Kumar, R.; Sharma, G.; Sharma, B. K.

    2013-06-01

    In this paper, we investigate the Compton profile of ZrB2. The theoretical Compton profile of ZrB2 is computed within the framework of density functional theory (DFT) based on linear combination of atomic orbitals (LCAO). To compare the spherically averaged theoretical values, the measurement on polycrystalline ZrB2 is performed using 59.54 keV gamma-rays emanating from an 241Am radioisotope. To estimate the charge transfer in ZrB2, ionic model based calculations have also been performed which suggest transfer of electron from Zr to B atoms.

  16. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Sanders

    Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

  17. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Science.gov (United States)

    Sanders, Jeffrey M; Wampole, Matthew E; Thakur, Mathew L; Wickstrom, Eric

    2013-01-01

    The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of therapeutics targeting EGF

  18. A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules.

    Directory of Open Access Journals (Sweden)

    Sagar Darvekar

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

  19. LETTER: Test of Te profile invariance by sensitivity studies

    Science.gov (United States)

    Becker, G.

    1992-06-01

    The response of the electron temperature profile shape to variations of the electron heating and density profiles is investigated in different confinement regimes. It is shown that the changes in rTe = -Te/(dTe/dr) exceed the measurement error if the shape of the electron heat diffusivity χe(r) is kept fixed. The observed constancy of rTe(r) in the outer half of the plasma is incompatible with such a fixed χe(r) shape, i.e., a Te profile constraining mechanism must be present. Local transport laws of the form χe varies as rTe-α with α gtrsim 4 and χe propto (dTe/dr)α with α >= 2 yield the experimental stiffness of the Te(r) shape but conflict with empirical χe scalings. These results support the model of a self-organizing and adjusting χe(r) causing Te profile invariance

  20. Photoelectron Spectroscopy and Theoretical Studies of Anion-pi Interactions: Binding Strength and Anion Specificity

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jian; Zhou, Bin; Sun, Zhenrong; Wang, Xue B.

    2015-01-01

    Proposed in theory and confirmed to exist, anion–π interactions have been recognized as new and important non-covalent binding forces. Despite extensive theoretical studies, numerous crystal structural identifications, and a plethora of solution phase investigations, intrinsic anion–π interaction strengths that are free from complications of condensed phases’ environments, have not been directly measured in the gas phase. Herein we present a joint photoelectron spectroscopic and theoretical study on this subject, in which tetraoxacalix[2]arene[2]triazine 1, an electron-deficient and cavity self-tunable macrocyclic was used as a charge-neutral molecular host to probe its interactions with a series of anions with distinctly different shapes and charge states (spherical halides Cl⁻, Br⁻, I⁻, linear thiocyanate SCN⁻, trigonal planar nitrate NO₃⁻, pyramidic iodate IO₃⁻, and tetrahedral sulfate SO₄²⁻). The binding energies of the resultant gaseous 1:1 complexes (1•Cl⁻,1•Br⁻, 1•I⁻, 1•SCN⁻, 1•NO₃⁻, 1•IO₃⁻ and 1•SO₄²⁻) were directly measured experimentally, exhibiting substantial non-covalent interactions with pronounced anion specific effects. The binding strengths of Cl⁻, NO₃⁻, IO₃⁻ with 1 are found to be strongest among all singly charged anions, amounting to ca. 30 kcal/mol, but only about 40% of that between 1 and SO₄²⁻. Quantum chemical calculations reveal that all anions reside in the center of the cavity of 1 with anion–π binding motif in the complexes’ optimized structures, where 1 is seen to be able to self-regulate its cavity structure to accommodate anions of different geometries and three-dimensional shapes. Electron density surface and natural bond orbital charge distribution analysis further support anion–π binding formation. The calculated binding energies of the anions and 1 nicely reproduce the experimentally estimated electron binding energy increase. This work

  1. Photoelectron spectroscopy and theoretical studies of anion-π interactions: binding strength and anion specificity.

    Science.gov (United States)

    Zhang, Jian; Zhou, Bin; Sun, Zhen-Rong; Wang, Xue-Bin

    2015-02-01

    Proposed in theory and then their existence confirmed, anion-π interactions have been recognized as new and important non-covalent binding forces. Despite extensive theoretical studies, numerous crystal structural identifications, and a plethora of solution phase investigations, anion-π interaction strengths that are free from complications of condensed-phase environments have not been directly measured in the gas phase. Herein we present a joint photoelectron spectroscopic and theoretical study on this subject, in which tetraoxacalix[2]arene[2]triazine 1, an electron-deficient and cavity self-tunable macrocyclic, was used as a charge-neutral molecular host to probe its interactions with a series of anions with distinctly different shapes and charge states (spherical halides Cl(-), Br(-), I(-), linear thiocyanate SCN(-), trigonal planar nitrate NO3(-), pyramidic iodate IO3(-), and tetrahedral sulfate SO4(2-)). The binding energies of the resultant gaseous 1 : 1 complexes (1·Cl(-), 1·Br(-), 1·I(-), 1·SCN(-), 1·NO3(-), 1·IO3(-) and 1·SO4(2-)) were directly measured experimentally, exhibiting substantial non-covalent interactions with pronounced anion-specific effects. The binding strengths of Cl(-), NO3(-), IO3(-) with 1 are found to be strongest among all singly charged anions, amounting to ca. 30 kcal mol(-1), but only about 40% of that between 1 and SO4(2-). Quantum chemical calculations reveal that all the anions reside in the center of the cavity of 1 with an anion-π binding motif in the complexes' optimized structures, where 1 is seen to be able to self-regulate its cavity structure to accommodate anions of different geometries and three-dimensional shapes. Electron density surface and charge distribution analyses further support anion-π binding formation. The calculated binding energies of the anions and 1 nicely reproduce the experimentally estimated electron binding energy increase. This work illustrates that size-selective photoelectron

  2. Synthesis, characterization, DNA binding and cleavage studies of chiral Ru(II) salen complexes

    Science.gov (United States)

    Khan, Noor-ul H.; Pandya, Nirali; Kureshy, Rukhsana I.; Abdi, Sayed H. R.; Agrawal, Santosh; Bajaj, Hari C.; Pandya, Jagruti; Gupte, Akashya

    2009-09-01

    Interaction of chiral Ru(II) salen complexes (S)-1 and (R)-1 with Calf Thymus DNA (CT-DNA) was studied by absorption spectroscopy, competitive binding study, viscosity measurements, CD measurements, thermal denaturation study and cleavage studies by agarose gel electrophoresis. The DNA binding affinity of (S)-1 (6.25 × 10 3 M -1) was found to be greater than (R)-1 (3.0 × 10 3 M -1). The antimicrobial studies of these complexes on five different gram (+)/(-) bacteria and three different fungal organisms showed selective inhibition of the growth of gram (+) bacteria and were not affective against gram (-) and fungal organisms. Further, the (S)-1 enantiomer inhibited the growth of organisms to a greater extent as compared to (R)-1 enantiomer.

  3. Insulin binding to individual rat skeletal muscles

    International Nuclear Information System (INIS)

    Studies of insulin binding to skeletal muscle, performed using sarcolemmal membrane preparations or whole muscle incubations of mixed muscle or typical red (soleus, psoas) or white [extensor digitorum longus (EDL), gastrocnemius] muscle, have suggested that red muscle binds more insulin than white muscle. We have evaluated this hypothesis using cryostat sections of unfixed tissue to measure insulin binding in a broad range of skeletal muscles; many were of similar fiber-type profiles. Insulin binding per square millimeter of skeletal muscle slice was measured by autoradiography and computer-assisted densitometry. We found a 4.5-fold range in specific insulin tracer binding, with heart and predominantly slow-twitch oxidative muscles (SO) at the high end and the predominantly fast-twitch glycolytic (FG) muscles at the low end of the range. This pattern reflects insulin sensitivity. Evaluation of displacement curves for insulin binding yielded linear Scatchard plots. The dissociation constants varied over a ninefold range (0.26-2.06 nM). Binding capacity varied from 12.2 to 82.7 fmol/mm2. Neither binding parameter was correlated with fiber type or insulin sensitivity; e.g., among three muscles of similar fiber-type profile, the EDL had high numbers of low-affinity binding sites, whereas the quadriceps had low numbers of high-affinity sites. In summary, considerable heterogeneity in insulin binding was found among hindlimb muscles of the rat, which can be attributed to heterogeneity in binding affinities and the numbers of binding sites. It can be concluded that a given fiber type is not uniquely associated with a set of insulin binding parameters that result in high or low binding

  4. Spectroscopy and molecular docking studies on the binding of propyl gallate to human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Guo-fei; Wang, Yu; Xi, Lei; Liu, Jin; Wang, Hao; Du, Lin-fang, E-mail: dulinfang@scu.edu.cn

    2015-03-15

    The interaction of propyl gallate (PG) with human serum albumin (HSA) was investigated by fluorescence, far-UV CD and FT-IR spectroscopic methods as well as molecular docking. Fluorescence emission spectra demonstrated that the HSA fluorescence was quenched by PG through static quenching and energy transfer with the binding constants in the order of 10{sup 5} L mol{sup −1}. The thermodynamic parameters (ΔH=−29.64 KJ mol{sup −1}, ΔS=2.7 J mol{sup −1} K{sup −1}) indicated that both hydrophobic force and hydrogen bond interactions played a leading role in the formation of PG–HSA complex. The results also showed the existence of a single binding site, which was located in subdomain IIA (site I) as revealed by molecular docking and competitive binding experiments. Molecular docking studies further showed the participation of several amino acids in PG–HSA complexation, which stabilized by H-bonding systems. The synchronous fluorescence spectra showed that the binding of drug caused the environment of tryptophan residues became more polar. FT-IR and CD spectroscopic further showed that drug complexation altered protein conformation by a major reduction of α-helix inducing a partial protein destabilization. - Highlights: • The interaction between propyl gallate and HSA has been investigated. • HSA fluorescence is quenched by propyl gallate through static quenching mechanism. • Both hydrophobic force and hydrogen bond play major role in the binding process. • Site I of the HSA is found to be the main binding site for propyl gallate. • The structure of HSA has been changed upon the interaction with propyl gallate.

  5. Do Personality Profiles Differ in the Pakistani Software Industry and Academia - A Case Study

    OpenAIRE

    Raza, Arif; Zaka-ul-Mustafa; Capretz, Luiz Fernando

    2015-01-01

    Effects of personality profiles and human factors in software engineering (SE) have been studied from different perspectives, such as: software life cycle, team performance, software quality attributes, and so on. This study intends to compare personality profiles of software engineers in academia and industry. In this survey we have collected personality profiles of software engineers from academia and the local industry in Pakistan. According to the Myers- Briggs Type Indicator (MBTI) instr...

  6. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV.

    Science.gov (United States)

    Endres, Christopher J; Hammoud, Dima A; Pomper, Martin G

    2011-04-21

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

  7. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    International Nuclear Information System (INIS)

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [11C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (kr2) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BPND). Compared with standard SRTM, either coupling of kr2 across regions or constraining kr2 to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BPND between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining kr2 to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the variance of parameter estimates and may better discriminate between

  8. Recombinant preparation and functional studies of EspI ATP binding domain from Mycobacterium tuberculosis.

    Science.gov (United States)

    Chen, Hanyu; Wang, Huilin; Sun, Tao; Tian, Shuangliang; Lin, Donghai; Guo, Chenyun

    2016-07-01

    The ESX-1 secretion system of Mycobacterium tuberculosis is required for the virulence of tubercle bacillus. EspI, the ESX-1 secretion-associated protein in Mycobacterium tuberculosis (MtEspI), is involved in repressing the activity of ESX-1-mediated secretion when the cellular ATP level is low. The ATP binding domain of MtEspI plays a crucial role in this regulatory process. However, further structural and functional studies of MtEspI are hindered due to the bottleneck of obtaining stable and pure recombinant protein. In this study, we systematically analyzed the structure and function of MtEspI using bioinformatics tools and tried various expression constructs to recombinantly express full-length and truncated MtEspI ATP binding domain. Finally, we prepared pure and stable MtEspI ATP binding domain, MtEspI415-493, in Escherichia coli by fusion expression and purification with dual tag, Glutathione S-transferase (GST) tag and (His)6 tag. (31)P NMR titration assay indicated that MtEspI415-493 possessed a moderate affinity (∼μM) for ATP and the residue K425 was located at the binding site. The protocol described here may provide a train of thought for recombinant preparation of other ESX-1 secretion-associated proteins. PMID:27017992

  9. Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies.

    Science.gov (United States)

    Karthikeyan, Subramani; Bharanidharan, Ganesan; Kesherwani, Manish; Mani, Karthik Ananth; Srinivasan, Narasimhan; Velmurugan, Devadasan; Aruna, Prakasarao; Ganesan, Singaravelu

    2016-06-01

    4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl acetate [Ace semi],4-[(1Z)-1-(2-carbamothioylhydrazinylidene)ethyl]phenyl propanoate [Pro semi] from the family of thiosemicarbazones derivative has been newly synthesized. It has good anticancer activity as well as antibacterial and it is also less toxic in nature, its binding characteristics are therefore of huge interest for understanding pharmacokinetic mechanism of the drug. The binding of thiosemicarbazone derivative to human serum albumin (HSA) has been investigated by studying its quenching mechanism, binding kinetics and the molecular distance (r) between donor (HSA) and acceptor (thiosemicarbazone derivative) was estimated according to Forster's theory of non-radiative energy transfer using fluorescence spectroscopy. The binding dynamics has been elaborated using synchronous fluorescence spectroscopy, and the feature of thiosemicarbazone derivative induced structural changes of HSA has been studied by circular dichorism, Fourier transform infrared spectroscopy. Molecular modelling simulations explore the hydrophobic interaction and hydrogen bonding which stabilizes the interaction. PMID:26368536

  10. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies.

    Science.gov (United States)

    Gogoi, Prerana; Chandravanshi, Monika; Mandal, Suraj Kumar; Srivastava, Ambuj; Kanaujia, Shankar Prasad

    2016-07-01

    About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature. PMID:26248730

  11. Concentration profiles in paint layers studied by differential PIXE

    Energy Technology Data Exchange (ETDEWEB)

    Smit, Z. [University of Ljubljana, Faculty of Mathematics and Physics, Jadranska 19, SI-1000 Ljubljana (Slovenia); Jozef Stefan Institute, Jamova 39, P.O.B. 3000, SI-1001 Ljubljana (Slovenia)], E-mail: ziga.smit@fmf.uni-lj.si; Ursic, M.; Pelicon, P. [Jozef Stefan Institute, Jamova 39, P.O.B. 3000, SI-1001 Ljubljana (Slovenia); Trcek-Pecak, T.; Seme, B. [University of Ljubljana, Academy of Fine Arts and Design, Erjavceva 23, SI-1001 Ljubljana (Slovenia); Smrekar, A. [National Gallery of Slovenia, Puharjeva 9, SI-1000 Ljubljana (Slovenia); Langus, I. [National Museum of Slovenia, Presernova 20, SI-1000 Ljubljana (Slovenia); Nemec, I.; Kavkler, K. [ZVKDS Restoration Centre RS, Poljanska 40, SI-1000 Ljubljana (Slovenia)

    2008-05-15

    Differential PIXE measurements varying the proton energy were used to probe the concentration profiles of metal-based pigments in paint layers. The algorithms developed earlier for metal targets were improved and enhanced to include light elements; the necessary information on chemical compounds has to be provided by complimentary methods. The de-convolution method employs slicing the target into layers characterized by mean production depths; the matrix inversion is replaced by a min {chi}{sup 2} problem. Two different methods of normalization are used: setting the sum of weight fractions of particular compounds to unity, and direct measurements of the projectile number, in our case through the argon line excited in the air. The efficiency of the two methods was compared for paint layers in frescoes, showing that smother concentration profiles are obtained using the measured proton numbers. Conversion of the layer areal densities into geometrical thicknesses is discussed.

  12. Compton profile study of gold: Theory and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ahuja, B.L.; Sharma, M. [Department of Physics, University College of Science, ML Sukhadia University, Udaipur 313001 (Raj.) (India); Bross, H. [Arnold Sommerfeld Center, University of Munich, Theresienstr, 37 IV, 80333 Muenchen (Germany)

    2007-02-15

    We present momentum densities and Compton profiles for gold calculated in the local-density approximation (LDA) by use of the modified augmented plane wave (MAPW) self-consistent scheme. Our theoretical calculations have been compared with our experimental Compton profile, measured at an intermediate resolution (0.40 a.u.) using 661.65 keV gamma-rays. We have also compared our measurements with the APW calculations of Papanicolaou et al. It is seen that our LDA-MAPW calculations with e{sup -}-e{sup -} correlation correction are in better agreement with our experimental data. (copyright 2007 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Study on profile measurement of extruding tire tread by laser

    Science.gov (United States)

    Wang, LiangCai; Zhang, Wanping; Zhu, Weihu

    1996-10-01

    This paper presents a new 2D measuring system-profile measurement of extruding tire tread by laser. It includes the thickness measurement of extruding tire tread by laser and the width measurement of extruding tire tread using Moire Fringe. The system has been applied to process line of extruding tire tread. Two measuring results have been obtained. One is a standard profile picture of extruding tire tread including seven measuring values. Another one is a series of thickness and width values. When the scanning speed < 100mm/sec and total width < 800mm. The measuring errors of width < +/- 0.5mm. While the thickness range is < 40mm. The measuring errors of thickness < +/- 0.1mm.

  14. Buffer Interference with Protein Dynamics: A Case Study on Human Liver Fatty Acid Binding Protein

    OpenAIRE

    Long, Dong; Yang, Daiwen

    2009-01-01

    Selection of suitable buffer types is often a crucial step for generating appropriate protein samples for NMR and x-ray crystallographic studies. Although the possible interaction between MES buffer (2-(N-morpholino)ethanesulfonic acid) and proteins has been discussed previously, the interaction is usually thought to have no significant effects on the structures of proteins. In this study, we demonstrate the direct, albeit weak, interaction between MES and human liver fatty acid binding prote...

  15. Study of damaged depth profiles of ion-irradiated PEEK

    Czech Academy of Sciences Publication Activity Database

    Vacík, Jiří; Hnatowicz, Vladimír; Červená, Jarmila; Apel, P. Yu.; Posta, S.; Kobayashi, Y.

    2007-01-01

    Roč. 201, 19-20 (2007), s. 8370-8372. ISSN 0257-8972 R&D Projects: GA MPO(CZ) 1H-PK2/05; GA MŠk 1P04LA213 Institutional research plan: CEZ:AV0Z10480505 Keywords : Oxygen irradiation * Poly-aryl-ether-ether ketone * Thermal neutron depth profiling (TNDP) Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.678, year: 2007

  16. Wind profile radar for study of Antarctic air circulation

    International Nuclear Information System (INIS)

    After a brief discussion of meteorological methods used in the Antarctic, the paper gives an outline of a coordinated international research project whose objective is to set up a wind profiler radar station that would give meteorologists information regarding Antarctic atmospheric dynamics useful in their investigation of the causes and effects of the hole in the ozone layer. The radar instrumentation is to provide continuous readings of wind velocity at varying altitudes above the polar continent

  17. A HOSPITAL BASED STUDY ON LIPID PROFILE IN SMOKERS AND NON SMOKERS- A COMPARATIVE STUDY

    Directory of Open Access Journals (Sweden)

    Afroz

    2012-11-01

    Full Text Available ABSTRACT: BACKGROUND: Smoking is one of the environmental factors which can alter normal lipid profile. It is one of the major risk fa ctors in the genesis of coronary atherosclerosis and development of coronary heart disease. AIMS: To evaluate and compare the lipid profile in both groups and to evaluate the existence of dose de pendent relationship and durational significance between smoking and lipid profile among smokers. SETTINGS AND DESIGN: Out of 100 apparently healthy male subjects of age group 21-4 0yrs, 50 were smokers and 50 were non smokers. All the subjects were non alcoholic, non – obese, normotensives and from same socioeconomic status. Subjects who smoke more than equal 10 cigarettes for more than 2 years were considered as smokers group. METHODS AND MATERIAL: The subjects were asked to fast overnight and early morning blood samples colle cted and analyzed for lipid profile by appropriate methods. STATISTICAL ANALYSIS USED: The student’s unpaired “t” test was used for statistical analysis. P-value of < 0.05 or P va lue <0.01 was considered statistically significant. RESULTS: In our study we found serum TC, TG, LDL and VLDL w ere higher in smokers as compared to non smokers and the serum HDL level was significantly decreased in smokers compared to non smokers showing greater risk of thes e persons to atherosclerosis and coronary heart disease. Conclusions: - We conclude our study with the obser vation that smoking causes alteration in lipid profile. Increased amount and duration of smok ing causes more dyslipidaemia .This alteration in serum lipid levels increases risk for coronary artery disease.

  18. Compton profile study and electronic properties of tantalum diboride

    International Nuclear Information System (INIS)

    We have reported the first-ever experimental Compton profile (CP) of TaB2 using 20 Ci137Cs Compton spectrometer. To compare the experimental data, we have also computed the theoretical CPs using density functional theory (DFT) and hybridization of DFT and Hartree–Fock (HF) within linear combination of the atomic orbitals (LCAO) method. In addition, we have reported energy bands and density of states of TaB2 using LCAO and full potential-linearized augmented plane wave (FP-LAPW) methods. A real space analysis of CP of TaB2 confirms its metallic character which is in tune with the cross-overs of Fermi level by energy bands and Fermi surface topology. A comparison of equal-valence-electron-density (EVED) experimental profiles of isoelectronic TaB2 and NbB2 show more covalent (or less ionic) character of TaB2 than that of NbB2 which is in agreement with available ionicity data. - Highlights: ► Reported first-ever experimental Compton profile (CP) of TaB2. ► Interpreted experimental CP using theoretical CP within density functional theory. ► Analyzed equal-valence-electron-density experimental CPs of TaB2 and NbB2. ► Established metallic character by taking Fourier transform of experimental CP. ► Reported energy bands, DOS and Fermi surface of TaB2 using LCAO and FP-LAPW

  19. Escherichia coli Single-Stranded DNA-Binding Protein: NanoESI-MS Studies of Salt-Modulated Subunit Exchange and DNA Binding Transactions

    Science.gov (United States)

    Mason, Claire E.; Jergic, Slobodan; Lo, Allen T. Y.; Wang, Yao; Dixon, Nicholas E.; Beck, Jennifer L.

    2013-02-01

    Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)70, one molecule of (dT)35, or two molecules of (dT)35] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

  20. Reproducibility of mass spectrometry based protein profiles for diagnosis of ovarian cancer across clinical studies

    DEFF Research Database (Denmark)

    Øgendahl Callesen, Anne Kjærgaard; Mogensen, Ole; Jensen, Andreas K; Kruse, Torben A; Martinussen, Torben; Jensen, Ole N; Madsen, Jonna S

    2012-01-01

    The focus of this systematic review is to give an overview of the current status of clinical protein profiling studies using MALDI and SELDI MS platforms in the search for ovarian cancer biomarkers. A total of 34 profiling studies were qualified for inclusion in the review. Comparative analysis o...... article is part of a Special Issue entitled: Clinical Proteomics SI: Clinical Proteomics....

  1. Spectroscopic and biological activity studies of the chromium-binding peptide EEEEGDD.

    Science.gov (United States)

    Arakawa, Hirohumi; Kandadi, Machender R; Panzhinskiy, Evgeniy; Belmore, Kenneth; Deng, Ge; Love, Ebony; Robertson, Preshus M; Commodore, Juliette J; Cassady, Carolyn J; Nair, Sreejayan; Vincent, John B

    2016-06-01

    While trivalent chromium has been shown at high doses to have pharmacological effects improving insulin resistance in rodent models of insulin resistance, the mechanism of action of chromium at a molecular level is not known. The chromium-binding and transport agent low-molecular-weight chromium-binding substance (LMWCr) has been proposed to be the biologically active form of chromium. LMWCr has recently been shown to be comprised of a heptapeptide of the sequence EEEEDGG. The binding of Cr(3+) to this heptapeptide has been examined. Mass spectrometric and a variety of spectroscopic studies have shown that multiple chromic ions bind to the peptide in an octahedral fashion through carboxylate groups and potentially small anionic ligands such as oxide and hydroxide. A complex of Cr and the peptide when administered intravenously to mice is able to decrease area under the curve in intravenous glucose tolerance tests. It can also restore insulin-stimulated glucose uptake in myotubes rendered insulin resistant by treating them with a high-glucose media. PMID:26898644

  2. Hepatic binding and uptake kinetics of epidermal growth factor: studies with isolated rat hepatocytes

    International Nuclear Information System (INIS)

    Hepatocytes are known to bind and internalize a variety of small molecular weight proteins by a process known as receptor-mediated endocytosis (RME). The purpose of this investigation was to characterize the binding and uptake kinetics of a small protein known to be taken up by the liver by RME, epidermal growth factor (EGF), using suspensions of freshly isolated rat hepatocytes. Rat hepatocytes accumulated 125I-EGF (90pM) in a temperature-dependent fashion. Isolated hepatocytes incubated at 370C with 125I-EGF began to release a TCA-soluble radiolabeled material into the incubation medium with a lag period of 20 min. EGF uptake by isolated hepatocytes was linear for only 60 seconds and displayed saturation kinetics. Hepatocytes incubated at 40C bound, but did not internalize, EGF. Under these conditions, EGF binding was saturable at concentrations above 8 nM. A Scatchard analysis revealed that the average number of receptors per hepatocyte was 7.7 x 104 with a dissociation constant of 2.6 nM. These data demonstrate that freshly isolated hepatocytes are capable of binding, internalizing and metabolizing EGF and thus are a good model to study RME of small molecular weight proteins. 15 references, 5 figures

  3. Sedative-Hypnotic and Receptor Binding Studies of Fermented Marine Organisms.

    Science.gov (United States)

    Joung, Hye-Young; Kang, Young Mi; Lee, Bae-Jin; Chung, Sun Yong; Kim, Kyung-Soo; Shim, Insop

    2015-09-01

    This study was performed to investigate the sedative-hypnotic activity of γ-aminobutyric acid (GABA)-enriched fermented marine organisms (FMO), including sea tangle (FST) and oyster (FO) by Lactobacillus brevis BJ20 (L. brevis BJ20). FST and FO were tested for their binding activity of the GABAA-benzodiazepine and 5-HT2C receptors, which are well-known molecular targets for sleep aids. We also measured the sleep latency and sleep duration during pentobarbital-induced sleep in mice after oral administration of FST and FO. In GABAA and 5-HT2C receptor binding assays, FST displayed an effective concentration-dependent binding affinity to GABAA receptor, similar to the binding affinity to 5-HT2C receptor. FO exhibited higher affinity to 5-HT2C receptor, compared with the GABAA receptor. The oral administration of FST and FO produced a dose-dependent decrease in sleep latency and increase in sleep duration in pentobarbital-induced hypnosis. The data demonstrate that FST and FO possess sedative-hypnotic activity possibly by modulating GABAA and 5-HT2C receptors. We propose that FST and FO might be effective agents for treatment of insomnia. PMID:26336589

  4. Cloning, purification, crystallization and preliminary crystallographic study of calcium-binding protein 5 from Entamoeba histolytica

    International Nuclear Information System (INIS)

    Calcium-binding protein 5 from E. histolytica was cloned, expressed in E. coli and purified. The purified protein crystallized in space group C222 and the crystals diffracted to 2 Å resolution. Entamoeba histolytica is the causative agent of human amoebiasis. Phagocytosis is the major route of food intake by this parasite and is responsible for its virulence. Calcium and calcium-binding proteins play major roles in its phagocytosis. Calcium-binding protein 5 from E. histolytica (EhCaBP5) is a cytoplasmic protein; its expression is very sensitive to serum starvation and it seems to be involved in binding to myosin I. In this study, EhCaBP5 was cloned, expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. The purified protein crystallized in space group C222 and the crystals diffracted to 2 Å resolution. The Matthews coefficient indicated the presence of one molecule in the asymmetric unit, with a VM of 2.35 Å3 Da−1 and a solvent content of 47.7%

  5. Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis

    Energy Technology Data Exchange (ETDEWEB)

    Morgunova, Ekaterina [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden); Illarionov, Boris; Saller, Sabine [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Popov, Aleksander [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble CEDEX 09 (France); Sambaiah, Thota [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Bacher, Adelbert [Chemistry Department, Technical University of Munich, 85747 Garching (Germany); Cushman, Mark [Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University (United States); Fischer, Markus [Institut für Lebensmittelchemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg (Germany); Ladenstein, Rudolf, E-mail: rudolf.ladenstein@ki.se [Karolinska Institutet NOVUM, Center of Structural Biochemistry, Hälsovägen 7-9, 141 57 Huddinge (Sweden)

    2010-09-01

    Crystallographic studies of lumazine synthase, the penultimate enzyme of the riboflavin-biosynthetic pathway in B. anthracis, provide a structural framework for the design of antibiotic inhibitors, together with calorimetric and kinetic investigations of inhibitor binding. The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R{sub cryst} = 23.7% (R{sub free} = 28.4%) at a resolution of 3.5 Å. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.

  6. The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations.

    Science.gov (United States)

    Furukawa-Hagiya, Tomoka; Furuta, Tadaomi; Chiba, Shuntaro; Sohma, Yoshiro; Sakurai, Minoru

    2013-01-10

    Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a "closed-apo" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions. PMID:23214920

  7. Seasonal variations in the heterologous binding of viscacha spermatozoa. A scanning electron microscope study.

    Science.gov (United States)

    Merlo, Claudia Aguilera; Muñoz, Estela; Dominguez, Susana; Fóscolo, Mabel; Scardapane, Luis; de Rosas, Juan Carlos

    2005-12-01

    Seasonal changes in the reproductive activity of the adult male viscacha (Lagostomus maximus maximus) were investigated during the annual reproductive cycle. Assays of heterologous in vitro binding between compatible gametes were used to evaluate the ability of viscacha spermatozoa to achieve primary binding during its annual reproductive cycle. Sperm were collected by mincing cauda epididymis in HECM-3 medium and the sperm concentration and motility were evaluated. Cumulus-free and zona-free oocytes obtained from superovulated hamsters were inseminated in vitro with capacitated sperm suspensions, incubated at 37 degrees C, 5% CO2 for 3 h, and then processed for studies by scanning electronic microscopy. Statistical analysis was used to compare the quantitative differences. The number of spermatozoa significantly decreases during the regression period, while sperm motility was progressive speed in both periods. During the active period elevated sperm binding to cumulus-free and zona-free oocytes was observed, while the binding during the regression period decreased drastically. In both periods, oocyte microvilli covered sperm heads and tails. These results suggest that the ability of viscacha spermatozoa to participate in gamete recognition is profoundly affected. This would likely be related to different functional stages of the spermatozoa and their epididymal microenvironment during the annual reproductive cycle of viscacha. PMID:16524245

  8. Structural Studies of GABAA Receptor Binding Sites: Which Experimental Structure Tells us What?

    Science.gov (United States)

    Puthenkalam, Roshan; Hieckel, Marcel; Simeone, Xenia; Suwattanasophon, Chonticha; Feldbauer, Roman V; Ecker, Gerhard F; Ernst, Margot

    2016-01-01

    Atomic resolution structures of cys-loop receptors, including one of a γ-aminobutyric acid type A receptor (GABAA receptor) subtype, allow amazing insights into the structural features and conformational changes that these pentameric ligand-gated ion channels (pLGICs) display. Here we present a comprehensive analysis of more than 30 cys-loop receptor structures of homologous proteins that revealed several allosteric binding sites not previously described in GABAA receptors. These novel binding sites were examined in GABAA receptor homology models and assessed as putative candidate sites for allosteric ligands. Four so far undescribed putative ligand binding sites were proposed for follow up studies based on their presence in the GABAA receptor homology models. A comprehensive analysis of conserved structural features in GABAA and glycine receptors (GlyRs), the glutamate gated ion channel, the bacterial homologs Erwinia chrysanthemi (ELIC) and Gloeobacter violaceus GLIC, and the serotonin type 3 (5-HT3) receptor was performed. The conserved features were integrated into a master alignment that led to improved homology models. The large fragment of the intracellular domain that is present in the structure of the 5-HT3 receptor was utilized to generate GABAA receptor models with a corresponding intracellular domain fragment. Results of mutational and photoaffinity ligand studies in GABAA receptors were analyzed in the light of the model structures. This led to an assignment of candidate ligands to two proposed novel pockets, candidate binding sites for furosemide and neurosteroids in the trans-membrane domain were identified. The homology models can serve as hypotheses generators, and some previously controversial structural interpretations of biochemical data can be resolved in the light of the presented multi-template approach to comparative modeling. Crystal and cryo-EM microscopic structures of the closest homologs that were solved in different conformational

  9. Terverticillate penicillia studied by direct electrospray mass spectrometric profiling of crude extracts II. Database and identification

    DEFF Research Database (Denmark)

    Smedsgaard, Jørn

    1997-01-01

    A mass spectral database was built using standard instrument software from 678 electrospray mass spectra (mass profiles) from crude fungal extracts of terverticillate taxa within the genus Penicillium. The match factors calculated from searching all the mass profiles stored in the database were...... isolates stored according to classical taxonomic criteria. Mass profiles collected in previous studies could be identified by a search in the database. (C) 1997 Elsevier Science Ltd....

  10. Vegan diet and blood lipid profiles: a cross-sectional study of pre and postmenopausal women

    OpenAIRE

    Huang, Yee-Wen; Jian, Zhi-Hong; Chang, Hui-Chin; Nfor, Oswald Ndi; Ko, Pei-Chieh; Lung, Chia-Chi; Lin, Long-Yau; Ho, Chien-Chang; Chiang, Yi-Chen; Liaw, Yung-Po

    2014-01-01

    Background Vegan diet has been associated with lower risk of cardiovascular diseases and mortality, partly due to its effects on serum lipid profiles. Lipid profiles [high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol (LDL-C) and triglycerides (TG)] have not been fully elucidated either in pre and postmenopausal vegans or in ovo-lacto vegetarians. This study aimed to compare lipid profiles among vegans, ovo-lacto vegetarians and omnivores. Methods Demographic da...

  11. Variational implicit-solvent modeling of host-guest binding: A case study on cucurbit[7]uril

    OpenAIRE

    S. Zhou; Rogers, KE; De Oliveira, CAF; Baron, R; Cheng, LT; Dzubiella, J.; Li, B.; McCammon, JA

    2013-01-01

    The synthetic host cucurbit[7]uril (CB[7]) binds aromatic guests or metal complexes with ultrahigh affinity compared with that typically displayed in protein-ligand binding. Due to its small size, CB[7] serves as an ideal receptor-ligand system for developing computational methods for molecular recognition. Here, we apply the recently developed variational implicit-solvent model (VISM), numerically evaluated by the level-set method, to study hydration effects in the high-affinity binding of t...

  12. A comparative study of recombinant and native frutalin binding to human prostate tissues

    Directory of Open Access Journals (Sweden)

    Domingues Lucília

    2009-09-01

    Full Text Available Abstract Background Numerous studies indicate that cancer cells present an aberrant glycosylation pattern that can be detected by lectin histochemistry. Lectins have shown the ability to recognise these modifications in several carcinomas, namely in the prostate carcinoma, one of the most lethal diseases in man. Thus, the aim of this work was to investigate if the α-D-galactose-binding plant lectin frutalin is able to detect such changes in the referred carcinoma. Frutalin was obtained from different sources namely, its natural source (plant origin and a recombinant source (Pichia expression system. Finally, the results obtained with the two lectins were compared and their potential use as prostate tumour biomarkers was discussed. Results The binding of recombinant and native frutalin to specific glycoconjugates expressed in human prostate tissues was assessed by using an immuhistochemical technique. A total of 20 cases of prostate carcinoma and 25 cases of benign prostate hyperplasia were studied. Lectins bound directly to the tissues and anti-frutalin polyclonal antibody was used as the bridge to react with the complex biotinilated anti-rabbit IgG plus streptavidin-conjugated peroxidase. DAB was used as visual indicator to specifically localise the binding of the lectins to the tissues. Both lectins bound to the cells cytoplasm of the prostate carcinoma glands. The binding intensity of native frutalin was stronger in the neoplasic cells than in hyperplasic cells; however no significant statistical correlation could be found (P = 0.051. On the other hand, recombinant frutalin bound exclusively to the neoplasic cells and a significant positive statistical correlation was obtained (P Conclusion Native and recombinant frutalin yielded different binding responses in the prostate tissues due to their differences in carbohydrate-binding affinities. Also, this study shows that both lectins may be used as histochemical biomarkers for the prostate

  13. Characterisation of peptide microarrays for studying antibody-antigen binding using surface plasmon resonance imagery.

    Directory of Open Access Journals (Sweden)

    Claude Nogues

    Full Text Available BACKGROUND: Non-specific binding to biosensor surfaces is a major obstacle to quantitative analysis of selective retention of analytes at immobilized target molecules. Although a range of chemical antifouling monolayers has been developed to address this problem, many macromolecular interactions still remain refractory to analysis due to the prevalent high degree of non-specific binding. We describe how we use the dynamic process of the formation of self assembling monolayers and optimise physical and chemical properties thus reducing considerably non-specific binding and allowing analysis of specific binding of analytes to immobilized target molecules. METHODOLOGY/PRINCIPAL FINDINGS: We illustrate this approach by the production of specific protein arrays for the analysis of interactions between the 65kDa isoform of human glutamate decarboxylase (GAD65 and a human monoclonal antibody. Our data illustrate that we have effectively eliminated non-specific interactions with the surface containing the immobilised GAD65 molecules. The findings have several implications. First, this approach obviates the dubious process of background subtraction and gives access to more accurate kinetic and equilibrium values that are no longer contaminated by multiphase non-specific binding. Second, an enhanced signal to noise ratio increases not only the sensitivity but also confidence in the use of SPR to generate kinetic constants that may then be inserted into van't Hoff type analyses to provide comparative DeltaG, DeltaS and DeltaH values, making this an efficient, rapid and competitive alternative to ITC measurements used in drug and macromolecular-interaction mechanistic studies. Third, the accuracy of the measurements allows the application of more intricate interaction models than simple Langmuir monophasic binding. CONCLUSIONS: The detection and measurement of antibody binding by the type 1 diabetes autoantigen GAD65 represents an example of an antibody

  14. Binding studies of the antitumoral radiopharmaceutical 125I-Crotoxin to Ehrlich ascites tumor cells

    Energy Technology Data Exchange (ETDEWEB)

    Silveira, Marina B.; Santos, Raquel G. dos [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN-MG), Belo Horizonte, MG (Brazil); Dias, Consuelo L. Fortes [Fundacao Ezequiel Dias (FUNED), Belo Horizonte, MG (Brazil)], e-mail: consuelo@pq.cnpq.br; Cassali, Geovanni D. [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Lab. de Patologia Comparada], e-mail: cassalig@icb.ufmg.br

    2009-07-01

    The development of tools for functional diagnostic imaging is mainly based on radiopharmaceuticals that specifically target membrane receptors. Crotoxin (Crtx), a polypeptide isolated from Crotalus durissus terrificus venom, has been shown to have an antitumoral activity and is a promising bioactive tracer for tumor detection. More specific radiopharmaceuticals are being studied to complement the techniques applied in the conventional medicine against breast cancer, the most frequent cause of death from malignant disease in women. Crtx's effect has been shown to be related with the overexpression of epidermal growth factor receptor (EGFR), present in high levels in 30 to 60% of breast tumor cells. Our objective was to evaluate Crtx as a tracer for cancer diagnosis, investigating its properties as an EGFR-targeting agent. Ehrlich ascites tumor cells (EAT cells) were used due to its origin and similar characteristics to breast tumor cells, specially the presence of EGFR. Crtx was labeled with 125I and binding experiments were performed. To evaluate the specific binding in vitro of Crtx, competition binding assay was carried out in the presence of increasing concentrations of non-labelled crotoxin and epidermal growth factor (EGF). Specific binding of 125I-Crtx to EAT cells was determined and the binding was considered saturable, with approximately 70% of specificity, high affinity (Kd = 19.7 nM) and IC50 = 1.6 x 10-11 M. Our results indicate that Crtx's interaction with EAT cells is partially related with EGFR and increases the biotechnological potential of Crtx as a template for radiopharmaceutical design for cancer diagnosis. (author)

  15. Binding studies of the antitumoral radiopharmaceutical 125I-Crotoxin to Ehrlich ascites tumor cells

    International Nuclear Information System (INIS)

    The development of tools for functional diagnostic imaging is mainly based on radiopharmaceuticals that specifically target membrane receptors. Crotoxin (Crtx), a polypeptide isolated from Crotalus durissus terrificus venom, has been shown to have an antitumoral activity and is a promising bioactive tracer for tumor detection. More specific radiopharmaceuticals are being studied to complement the techniques applied in the conventional medicine against breast cancer, the most frequent cause of death from malignant disease in women. Crtx's effect has been shown to be related with the overexpression of epidermal growth factor receptor (EGFR), present in high levels in 30 to 60% of breast tumor cells. Our objective was to evaluate Crtx as a tracer for cancer diagnosis, investigating its properties as an EGFR-targeting agent. Ehrlich ascites tumor cells (EAT cells) were used due to its origin and similar characteristics to breast tumor cells, specially the presence of EGFR. Crtx was labeled with 125I and binding experiments were performed. To evaluate the specific binding in vitro of Crtx, competition binding assay was carried out in the presence of increasing concentrations of non-labelled crotoxin and epidermal growth factor (EGF). Specific binding of 125I-Crtx to EAT cells was determined and the binding was considered saturable, with approximately 70% of specificity, high affinity (Kd = 19.7 nM) and IC50 = 1.6 x 10-11 M. Our results indicate that Crtx's interaction with EAT cells is partially related with EGFR and increases the biotechnological potential of Crtx as a template for radiopharmaceutical design for cancer diagnosis. (author)

  16. A numerical study of ionospheric profiles for mid-latitudes

    Directory of Open Access Journals (Sweden)

    S.-R. Zhang

    Full Text Available This paper presents a numerical model and results for the mid-latitude ionospheric profile below the peak of the F2-layer. The basis of the model is the solving of equations for four ionic species O+, NO+, O+2 and N+2, as well as the meta-stable O+(2D and O+(2P. Diffusion and wind-induced drifts and 21 photo-chemical reactions are also taken into account. Neutral atmospheric density and temperature are derived from the MSIS86 model and solar extreme ultraviolate irradiance from the EUV91 model. In an effort to obtain a more realistic ionospheric profile, the key point at foF2 and hmF2 is fitted from the simulation to observations. The model also utilizes the vertical drifts derived from ionosonde data with the help of the Servo model. It is shown that the ionospheric height of peak can be reproduced more accurately under the derived vertical drifts from the Servo theory than with the HWM90 model. Results from the simulation are given for Wuchang (30.5°N, 114.4°E and Wakkanai (45.6°N, 141.7°E, showing the profile changes with season and solar activity, and the E-F valley structure (the depth and the width. This simulation also reveals the importance of meta-stable ions and dynamical transport processes on the formation of the F1-ledge and F1-F2 valley.

  17. Binding study of tetracyclines to human serum albumin using difference spectrophotometry.

    Science.gov (United States)

    Zia, H; Price, J C

    1976-02-01

    The binding of several tetracyclines to human serum albumin was studied using difference spectrophotometry and a spectrophotometric probe, 2-(4'-hydroxybenzeneazo)benzoic acid. Difference spectra observed for the interaction between the probe and human serum albumin were similar to probe-bovine serum albumin spectra but were less intense for a given concentration of probe and did not reach saturation as quickly. Difference spectra for the tetracyclines were dependent on the characteristics of the ring substituents. More hydrophobic substituents on the D and C rings tended to give more intense difference spectra, but charge-transfer complexing may also have been involved since methacycline with a methylene group in the 6-position showed the most intense spectra of the compounds studied. Solvent perturbation, pH, and urea studies tended to confirm that something other than hydrophobic binding of the tetracyclines was involved. Drug-probe displacement studies showed that methacycline gave the greatest probe displacement followed by doxycycline, chlortetracycline, oxytetracycline, and tetracycline. This order of displacement of the anionic probe indicates that both hydrophobic and charge-transfer binding are involved. Experiments with calcium ion and ethylenediaminetetraacetic acid showed that the difference spectra obtained with the tetracyclines and human serum albumin were not the result of metallic bridge-chelate formation. PMID:3641

  18. Integrated approach for the study of new road profiles

    OpenAIRE

    ESPIE, S; AUBERLET,JM; ZHANG, MY

    2002-01-01

    La modification de profils routiers ou la conception de nouvelles routes sont des problèmes complexes pour lesquels le concepteur doit prendre en compte les aspects capacité et sécurité du trafic. Les usagers ne sont pas toujours directement impliqués dans la conception. L'utilisation finale de l'infrastructure est seulement prévue. Cela se traduit le plus souvent par une différence entre les prévisions et la situation réelle pouvant entrainer des dysfonctionnements en termes de capacité et d...

  19. Rapid preparation of plasma membranes from avian lymphoid cells and fibroblasts for virus binding studies.

    Science.gov (United States)

    Nieper, H; Müller, H

    1998-06-01

    A simple and rapid protocol for the preparation of plasma membranes from chicken embryo fibroblasts and chicken lymphoid cells was developed. Characterization of the preparations by morphological, biochemical and serological methods indicated the specific enrichment of the plasma membranes as well as cell surface proteins. Binding of infectious bursal disease virus (IBDV) particles was demonstrated after immobilization of the plasma membranes, and cell type-specific differences were observed. Although the results of these studies reflect the interaction between IBDV and isolated cells only partially, the advantages of these plasma membrane preparations, the specific enrichment of cell surface proteins, their constant quality and the possibility to store aliquots over several months, make them a useful tool for virus binding studies with avian cells. PMID:9694323

  20. Comparative expression profiling of insulin-like growth factor binding protein-5 in milk of Bos indicus and Bubalus bubalis during lactation.

    Science.gov (United States)

    Mohapatra, S K; Singh, S; Kumar, S; Dang, A K; Datta, T K; Das, S K; Mohanty, T K; Kaushik, J K; Mohanty, A K

    2015-04-01

    Insulin-like growth factor binding protein-5 (IGFBP-5) is a key molecule in mammary gland development, which facilitates the removal of mammary epithelial cells (MECs) by apoptosis that takes place during remodeling of the mammary gland during involution. IGFBP-5 binds with IGFs for their bioavailability. IGFBP-5 has been reported to perform pleiotropic roles such as cellular apoptosis, proliferation and differentiation. To understand the role of IGFBP-5 during lactation and clinical mastitis, expression profiling of IGFBP-5 at the protein level was performed in both indigenous cows (Bos indicus) and buffaloes (Bubalus bubalis) belonging to two different breeds - Sahiwal cows and Murrah buffaloes. Reverse-transcriptase PCR (RT-PCR) of IGFBP-5 mRNA confirmed its expression in milk somatic cells and MECs of Sahiwal cows. ELISA was performed for quantitative measurement of IGFBP-5 concentrations in milk during different days (0, 50, 100, 150, 200, 250 and 300) of lactation, during the involution period and in animals exhibiting short lactation and clinical mastitis. The highest concentration of IGFBP-5 in milk was observed during the involution period followed by colostrum, late and early lactation, respectively, in both cattle and buffaloes. No significant difference in the concentration of IGFBP-5 was observed during the first 150 days of lactation between cows and buffaloes. However, higher concentration of IGFBP-5 was observed in cows during late lactation (200 to 300 days) in comparison with buffaloes. To validate the ELISA data, quantitative real-time PCR was performed in MECs of Sahiwal cows. The relative mRNA abundance of IGFBP-5 was found to be significantly (Pcows. Highest mRNA expression of IGFBP-5 was observed around 300 days of lactation followed by 200 and 250 days (Pmilk as compared with Sahiwal cows during lactation in ELISA. Animals having history of short lactation length (short lactating animals) showed higher levels of IGFBP-5 expression (at

  1. Comparative study on ChIP-seq data: normalization and binding pattern characterization

    OpenAIRE

    Taslim, Cenny; Wu, Jiejun; Yan, Pearlly; Singer, Greg; Parvin, Jeffrey; Huang, Tim; Lin, Shili; Huang, Kun

    2009-01-01

    Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their ...

  2. Gyrokinetic Study of L-H Transition with Profile Evolution

    Science.gov (United States)

    Xie, Hua-Sheng; GTC Team

    2015-11-01

    Recent simulations based on gyrokinetic toroidal code (GTC) and theory based on model eigen equation (H. S. Xie and Y. Xiao, arXiv:1503.04440) have found that the eigenstates of mirco-instabilities (trapped electron mode TEM or ion temperature gradient mode ITG) under strong and weak gradients are not the same. Under weak gradient, the most unstable mode is on the ground state, with conventional ballooning mode structure. When the gradient exceed a critical value, the most unstable mode jump to non-ground state. The mode structures of non-ground state are rich and unconventional, and thus can reduced the transport level, which can provide a explanation to the H-mode in the mirco-scale aspect. Nonlinear simulations (H. S. Xie, Y. Xiao and Z. Lin, 9th West Lake International Symposium on Plasma Simulation, May. 18-21, 2015, Hangzhou, China) verified this and have also found a turning point of the gradient. The turbulent transport coefficient would decrease with the gradient increasing when the gradient exceed a critical value. This provide a new route for the L to H transition without invoking shear flow or zonal flow. In the above works, the profiles are fixed. In this work, we will give some preliminary results on self-consistent simulations of L-H transition including the evolution of the radial plasma profiles. Collaboration with GTC team.

  3. Compton profile study and electronic properties of tantalum diboride.

    Science.gov (United States)

    Raykar, Veera; Bhamu, K C; Ahuja, B L

    2013-07-01

    We have reported the first-ever experimental Compton profile (CP) of TaB2 using 20 Ci(137)Cs Compton spectrometer. To compare the experimental data, we have also computed the theoretical CPs using density functional theory (DFT) and hybridization of DFT and Hartree-Fock (HF) within linear combination of the atomic orbitals (LCAO) method. In addition, we have reported energy bands and density of states of TaB2 using LCAO and full potential-linearized augmented plane wave (FP-LAPW) methods. A real space analysis of CP of TaB2 confirms its metallic character which is in tune with the cross-overs of Fermi level by energy bands and Fermi surface topology. A comparison of equal-valence-electron-density (EVED) experimental profiles of isoelectronic TaB2 and NbB2 show more covalent (or less ionic) character of TaB2 than that of NbB2 which is in agreement with available ionicity data. PMID:23518037

  4. The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation.

    Science.gov (United States)

    Rodor, Julie; Pan, Qun; Blencowe, Benjamin J; Eyras, Eduardo; Cáceres, Javier F

    2016-09-01

    Acinus (apoptotic chromatin condensation inducer in the nucleus) is an RNA-binding protein (RBP) originally identified for its role in apoptosis. It was later found to be an auxiliary component of the exon junction complex (EJC), which is deposited at exon junctions as a consequence of pre-mRNA splicing. To uncover the cellular functions of Acinus and investigate its role in splicing, we mapped its endogenous RNA targets using the cross-linking immunoprecipitation protocol (iCLIP). We observed that Acinus binds to pre-mRNAs, associating specifically to a subset of suboptimal introns, but also to spliced mRNAs. We also confirmed the presence of Acinus as a peripheral factor of the EJC. RNA-seq was used to investigate changes in gene expression and alternative splicing following siRNA-mediated depletion of Acinus in HeLa cells. This analysis revealed that Acinus is preferentially required for the inclusion of specific alternative cassette exons and also controls the faithful splicing of a subset of introns. Moreover, a large number of splicing changes can be related to Acinus binding, suggesting a direct role of Acinus in exon and intron definition. In particular, Acinus regulates the splicing of DFFA/ICAD transcript, a major regulator of DNA fragmentation. Globally, the genome-wide identification of RNA targets of Acinus revealed its role in splicing regulation as well as its involvement in other cellular pathways, including cell cycle progression. Altogether, this study uncovers new cellular functions of an RBP transiently associated with the EJC. PMID:27365209

  5. Structural-functional insights and studies on saccharide binding of Sophora japonica seed lectin.

    Science.gov (United States)

    Yadav, Priya; Shahane, Ganesh; Ramasamy, Sureshkumar; Sengupta, Durba; Gaikwad, Sushama

    2016-10-01

    Functional and conformational transitions of the Sophora japonica seed lectin (SJL) were studied in detail using bioinformatics and biophysical tools. Homology model of the lectin displayed all the characteristics of the legume lectin monomer and the experimental observations correlated well with the structural information. In silico studies were performed by protein-ligand docking, calculating the respective binding energies and the residues involved in the interactions were derived from LigPlot(+) analysis. Fluorescence titrations showed three times higher affinity of T-antigen disaccharide than N-acetyl galactosamine (GalNAc) towards SJL indicating extended sugar binding site of the lectin. Thermodynamic parameters of T-antigen binding to SJL indicated the process to be endothermic and entropically driven while those of GalNAc showed biphasic process. SDS-PAGE showed post-translationally modified homotetrameric species of the lectin under native conditions. In presence of guanidine hydrochloride (0.5-5.0M), the tetramer first dissociated into dimers followed by unfolding of the protein as indicated by size exclusion chromatography, fluorescence and CD spectroscopy. Different structural rearrangements were observed during thermal denaturation of SJL at physiological pH 7.2, native pH 8.5 and molten globule inducing pH 1.0. Topological information revealed by solute quenching studies at respective pH indicated differential hydrophobic environment and charge density around tryptophan residues. PMID:27185070

  6. Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies.

    Science.gov (United States)

    Ruan, Qiaoqiao; Skinner, Joseph P; Tetin, Sergey Y

    2009-10-15

    The purpose of this article is to highlight the versatility of nonfluorescent Förster resonance energy transfer (FRET) acceptors in determination of protein equilibrium dissociation constants and kinetic rates. Using a nonfluorescent acceptor eliminates the necessity to spectrally isolate the donor fluorescence when performing binding titrations covering a broad range of reagent concentrations. Moreover, random distribution of the donor and acceptor chromophores on the surface of proteins increases the probability of FRET occurring on their interaction. Three high-affinity antibodies are presented in this study as characteristic protein systems. Monoclonal antibody (mAb) 106.3 binds brain natriuretic peptide (BNP)5-13(C10A) and full-length BNP1-32 with the dissociation constants 0.26+/-0.01 and 0.05+/-0.02 nM, respectively, which was confirmed by kinetic measurements. For anti-hCG (human chorionic gonadotropin) mAb 8F11, studied at two incorporation ratios (IRs=1.9 and 3.8) of the nonfluorescent FRET acceptor, K(D) values of 0.04+/-0.02 and 0.059(-0.004)(+0.006) nM, respectively, were obtained. Likewise, the binding of goat anti-hamster immunoglobulin G (IgG) antibody was not affected by conjugation and yielded K(D) values of 1.26+/-0.04, 1.25+/-0.05, and 1.14+/-0.04 nM at IRs of 1.7, 4.7, and 8.1, respectively. We conclude that this FRET-based method offers high sensitivity, practical simplicity, and versatility in protein binding studies. PMID:19563765

  7. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.

    Directory of Open Access Journals (Sweden)

    Ze Tian

    Full Text Available BACKGROUND: Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study. METHODS AND FINDINGS: We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal. CONCLUSION: We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.

  8. Synthesis of 4,4-ditritio-(+)-nicotine: comparative binding and distribution studies with natural enantiomer

    International Nuclear Information System (INIS)

    The preparation of 4,4-ditritio-(+)-nicotine (Vb) (specific activity 10.3 Ci/mmole)from (+)-nicotine (Ib) via (-) 4,4-dibromocotinine (IIIb) is described. Although Ib is 10-30 times less potent than (-)-nicotine (Ia) in the CNS, its binding affinity for the crude mitochondrial or nuclear fraction of whole rat brain is only three times less than that of Ia. However, distribution studies showed that the maximum brain levels of (-)-[3H] nicotine are nearly twice those of (+)-[3H]-nicotine following administration of a 2-micrograms/kg dose. Binding affinity and disposition of the stereoisomers account for a portion of the pharmacological stereospecificity of nicotine

  9. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ruthenium-fluoroquinolone complexes

    Indian Academy of Sciences (India)

    Mohan N Patel; Hardik N Joshi; Chintan R Patel

    2014-05-01

    Six new Ru(II) and Ru(III) complexes have been synthesized and characterized by elemental analysis, LC-MS, electronic spectra, IR spectra and magnetic moment measurements. DNA-binding properties of Ru complexes have been studied by means of absorption spectrophotometry and viscosity measurements as well as their HS DNA cleavage properties by means of agarose gel electrophoresis. The experimental results show that all the complexes can bind to DNA via partial intercalative mode. The b values of complexes were found in the range 2.14 × 104 to 2.70 × 105 M-1. All the complexes show excellent efficiency of cleaving DNA than respective fluoroquinolones. Brine shrimp lethality bioassay has been performed to check the cytotoxic activity. The IC50 values of the complexes are in the range of 6.27 to 16.05 g mL-1.

  10. STUDY OF CLINICAL PROFILE OF NON - TOXIC GOITER WITH SPECIAL REFERENCE TO CORRELATION OF PATHOLOGY, LIPID PROFILE AND ANTIBODY LEVEL

    Directory of Open Access Journals (Sweden)

    Santanu

    2014-11-01

    Full Text Available OBJECTIVE : To evaluate the morphology of non - toxic goiter , the role of auto - immunity and lipid abnormalities in overt and sub - clinical hypothyroid goiter patients. METHODS: A descriptive observational study was undertaken amongst goiter patients without thyrotoxic features comprising 50 randomly selected cases within the range of 12 - 65years. Goiter patients with thyrotoxic features , acute illness and other visceral diseases were excluded. The patients were evaluated with thyroid function tests , USG - thyroid , FNAC - thyroid , anti - TPO and lipid profile after thorough clinical examination. RESULTS : In my study , most patients were female (with male: female ratio 1:5.25 and were middle aged (betwe en age group 30 - 49years. Among all patients 60 %( i.e . 30 patients had Hashimoto’s thyroiditis , 24% (i.e. 12 patients had diffuse colloid goiter and 16% (i.e. 8 patients had nodular goiter. 52% (i.e. 26 of all patients and 76.6% (i.e. 23 of Hashimoto ’s goiter patients were anti - TPO positive. Majority of colloid goiter (i.e. 66.7% and nodular goiter (50% patients were euthyroid but majority of Hashimoto’s goiter patients were hypothyroid (65.38% overt and 33% sub - clinical. Majority of anti - TPO posit ive patients were hypothyroid (65.38% overt and 30.62% sub - clinical and majority of anti - TPO negative patients (66.67% were euthyroid. Within reference range of TSH , there was a linear increase in total serum cholesterol , LDL - cholesterol , triglyceride an d decrease in HDL - cholesterol with increase in TSH. This lipid profile changes are mainly seen in Hashimoto goiter patients . CONCLUSION : this study emphasizes the role of auto - immunity in non - toxic goiter patients especially Hashimoto’s thyroiditis patient s and lipid profile changes in those patients.

  11. Study of dose profile in TC scanning of cranium

    International Nuclear Information System (INIS)

    In this paper it was obtained a dose distribution profile in computerized tomography, when a head simulator object, cylindrical and manufactured in PMMA, were swiped by using the clinical protocol or this device routine. The doses were determined with radiochromic films placed at the four cardinal points and the Center, taking as reference one of object faces. The films were calibrated with pencil ionization chamber in a independent experiment where the obtained doses in the chamber, when a unique central cut or the object were obtained, were confronted with the gray scales on the irradiated films in a similar manner, revealing he factors of conversion mGy.Gray tones-1 which made possible the determination of doses in all the scanning

  12. Beam Studies Made with the SPS Ionization Profile Monitor

    CERN Document Server

    Ferioli, G; Koopman, J; Roncarolo, F

    2003-01-01

    During the last two years of SPS operation, investigations were pursued on the ability of the SPS ionization profile monitor prototype to fulfill different tasks. It is now established that the instrument can be used for injection matching tuning, by turn to turn recording of the beam size after the injection. Other applications concern beam size measurements on beams ranging from an individual bunch to a nominal SPS batch foreseen for injection into the LHC (288 bunches). By continuously tracking throughout the SPS acceleration cycle from 26 GeV to 450 GeV the evolution of parameters associated to the beam size, it is possible to explain certain beam behaviour. Comparisons are also made at different beam currents and monitor gains with measurements made with the wire scanners. Data are presented and discussed, and the possible implementation of new features is suggested in order to further improve the consistency of the measurements.

  13. Structural Studies of Nicotinic Acetylcholine Receptors: Using Acetylcholine-Binding Protein as a Structural Surrogate.

    Science.gov (United States)

    Shahsavar, Azadeh; Gajhede, Michael; Kastrup, Jette S; Balle, Thomas

    2016-06-01

    Nicotinic acetylcholine receptors (nAChRs) are members of the pentameric ligand-gated ion channel superfamily that play important roles in the control of neurotransmitter release in the central and peripheral nervous system. These receptors are important therapeutic targets for the development of drugs against a number of mental health disorders and for marketed smoking cessation aids. Unfortunately, drug discovery has been hampered by difficulties in obtaining sufficiently selective compounds. Together with functional complexity of the receptors, this has made it difficult to obtain drugs with sufficiently high-target to off-target affinity ratios. The recent and ongoing progress in structural studies holds promise to help understand structure-function relationships of nAChR drugs at the atomic level. This will undoubtedly lead to the design of more efficient drugs with fewer side effects. As a high-resolution structure of a nAChR is yet to be determined, structural studies are to a large extent based on acetylcholine-binding proteins (AChBPs) that despite low overall sequence identity display a high degree of conservation of overall structure and amino acids at the ligand-binding site. Further, AChBPs reproduce relative binding affinities of ligands at nAChRs. Over the past decade, AChBPs have been used extensively as models for nAChRs and have aided the understanding of drug receptor interactions at nAChRs significantly. PMID:26572235

  14. Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods.

    Science.gov (United States)

    Ataci, Nese; Arsu, Nergis

    2016-12-01

    In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6×10(5)M(-1)from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7°C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution. PMID:27367618

  15. Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

    International Nuclear Information System (INIS)

    Highlights: ► Natural and synthetic inhibitors of human phosphomevalonate kinase identified. ► Virtual screening yielded a hit rate of 15%, with inhibitor Kd’s of 10–60 μM. ► NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based 1H–15N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (Kd). Tight binding compounds with Kd’s ranging from 6–60 μM were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

  16. Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: daniel.sem@cuw.edu [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)

    2013-01-04

    Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

  17. Vertical profile of fog microphysics : a case study

    Science.gov (United States)

    Burnet, Frédéric; Brilouet, Pierre-Etienne; Mazoyer, Marie; Bourrianne, Thierry; Etcheberry, Jean-Michel; Gaillard, Brigitte; Legain, Dominique; Tzanos, Diane; Barrié, Joel; Barrau, Sébastien; Defoy, Stephan

    2016-04-01

    The occurrence and development of fogs result from the non-linear interaction of competing radiative, thermodynamic, microphysical and dynamical processes and the forecasting of their life cycle still remains a challenging issue. Several field campaigns have been carried out at the SIRTA observatory in the Paris suburb area (France). These experiments have shown that fog events exhibit large differences of the microphysical properties and various evolutions during their life cycle. To better understand relationships between the different processes and to validate numerical simulations it is necessary however to document the vertical profile of the fog microphysics. A CDP (Cloud Droplet Spectrometer) from DMT (Droplet Measurement Technology, Boulder, CO) has been modified to allow measurements of the droplet size distribution in fog layers with a tethered balloon. This instrumental set-up has been used during a field campaign during the winter 2013-214 in the Landes area in the South West of France. To validate the vertical profiles provided by the modified CDP, a mast was equipped with microphysical instruments at 2 altitude levels with an another CDP at 24 m and a Fog Monitor FM100 at 42 m. The instrumental set-up deployed during this campaign is presented. Data collected during a fog event that occurred during the night of 5-6 March 2014 are analysed. We show that microphysical properties such as droplet number concentration, LWC and mean droplet size, exhibit different time evolution during the fog life cycle depending on the altitude level. Droplet size distribution measurements are also investigated. They reveal sharp variations along the vertical close to the top of the fog layer. In addition it is shown that the shape of the size distributions at the top follows a time evolution typical of a quasi-adiabatic droplet growth.

  18. Interaction of D-LSD with binding sites in brain: a study in vivo and in vitro

    International Nuclear Information System (INIS)

    The localization of [3H]-d-lysergic acid diethylamide ([3H]LSD) binding sites in the mouse brain was compared in vivo and in vitro. Radioautography of brain sections incubated with [3H]LSD in vitro revealed substantial specific [3H]LSD binding in cortical layers III-IV and areas CA1 and dentate gyrus in hippocampus. In contrast, in brain sections from animals that received [3H]LSD in vivo, binding in hippocampus was scant and diffuse, although the pattern of labeling in cortex was similar to that seen in vitro. The low specific binding in hippocampus relative to cortex was confirmed by homogenate filtration studies of brain areas from mice that received injections of [3H]LSD. Time-course studies established that peak specific binding at ten minutes was the same in cortex and hippocampus. At all times, binding in hippocampus was about one-third of that in cortex; in contrast, the concentration of free [3H]LSD did not vary between regions. This finding was unexpected, because binding studies in vitro in membrane preparations indicated that the density and affinity of [3H]LSD binding sites were similar in both brain regions. Saturation binding studies in vivo showed that the lower amount of [3H]LSD binding in hippocampus was attributable to a lower density of sites labeled by [3H]LSD. The pharmacological identify of [3H]LSD binding sites in vivo may be relevant to the hallucinogenic properties of LSD and of other related hallucinogens

  19. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    OpenAIRE

    Hua-jin Zeng; Ran Yang; Jing You; Ling-bo Qu; Yan-jun Sun

    2016-01-01

    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly thro...

  20. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-04-21

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

  1. Study on the Interaction of Zinc Ion Binding with Human Serum Albumin using Isothermal Titration Calorimetry

    International Nuclear Information System (INIS)

    The interaction between zinc ion and human serum albumin (HSA) was investigated by nano-Watt- scale isothermal titration calorimetry (ITC). From the analysis of the ITC data, the binding characteristics and thermodynamic properties of the system were obtained and the binding mechanism was discussed. It was found that the experimental data fit well with the Langmuir's binding theory and the system behaved as a system with two classes of binding sites (high-affinity and low-affinity binding site). The binding number of high-affinity binding site (N1) is 1.40 and the binding constant (K1) is 2.72*105 L/mol. For the low-affinity binding site, the binding number (N2) is 1.55 and the binding constant (K2) is 3.78*103 L/mol. Moreover, it was indicated by the thermodynamic analysis that the binding processes of both types of binding sites were exothermic and spontaneous. The high-affinity binding was an enthalpy-entropy synergically driven process and the electrostatic interaction was the main force, while the low-affinity binding was an enthalpy driven process and this process was mainly driven by the van der Waals forces. (author)

  2. Equilibrium dialysis studies of WR-33278 and WR-1065 binding to calf thymus DNA

    International Nuclear Information System (INIS)

    Radioprotection by WR-2721, S-2-(3-aminopropylamino) ethyl phosphorothioate, is thought to involve its corresponding thiol (WR-1065) or symmetrical disulfide (WR-33278). It has been suggested that these metabolites concentrate close to the DNA target molecule. As one test of this hypothesis the authors measured the ability of these metabolites to bind or concentrate with DNA in vitro in order to achieve a high local concentration. The binding of WR-33278 (0.05-0.4mM) to calf thymus DNA (6mM, with respect to phosphate) was determined at 50, 100, and 150mM-KCl in 1mM-Tris, pH 7.0, by equilibrium dialysis. Drug levels were analyzed by derivatization with monobrombimane, and quantitated by Fluoresence HPLC, (samples were reduced with dithiothreitol prior to analysis). Preliminary studies with WR-1065 indicate that it also binds to DNA but with larger Kd values. Results suggest that concentration of WR-33278 and WR-1065 by electrostatic attraction to DNA phosphate can be a significant factor in the mechanism of radioprotection by WR-2721

  3. Binding of piano-stool Ru(II) complexes to DNA; QM/MM study.

    Science.gov (United States)

    Futera, Zdeněk; Platts, James A; Burda, Jaroslav V

    2012-10-01

    Ru(II) "piano-stool" complexes belong to group of biologically active metallocomplexes with promising anticancer activity. In this study, we investigate the reaction mechanism of [(η(6)-benzene)Ru(II)(en)(H(2)O)](2+) (en = ethylenediamine) complex binding to DNA by hybrid QM/MM computational techniques. The reaction when the Ru(II) complex is coordinated on N7-guanine from major groove is explored. Two reaction pathways, direct binding to N7 position and two-step mechanism passing through O6 position, are considered. It was found that the reaction is exothermic and the direct binding process is preferred kinetically. In analogy to cisplatin, we also explored the possibility of intrastrand cross-link formation where the Ru(II) complex makes a bridge between two adjacent guanines. Two different pathways were found, leading to a final structure with released benzene ligand. This process is exothermic; however, one pathway is blocked by relatively high initial activation barrier. Geometries, energies, and electronic properties analyzed by atoms in molecules and natural population analysis methods are discussed. PMID:22707416

  4. Study of the influence of chemical binding on resonant absorption and scattering of neutrons

    International Nuclear Information System (INIS)

    At present time the problem of taking into account of the crystalline binding in the heavy nuclei resonance range is not correctly treated in nuclear data processing codes. The present work deals separately with resonant absorption and scattering of neutrons. The influence of crystalline binding is considered for both types of reactions in the harmonic crystal frame work. The harmonic crystal model is applied to the study of resonant absorption cross sections to show the inconsistency of the free gas model widely in use in reactor neutronics. The errors due to the use of the latter were found to be non negligible. These errors should be corrected by introducing a more elaborated harmonic crystal model in codes for resonances analysis and on the nuclear data processing stage. Currently the influence of crystalline binding on transfer cross section in the resonance domain is taken into account in a naive manner using the model of the free nucleus at rest in the laboratory system. In this work I present a formalism (Uncoupled Phonon Approximation) which permits to consider in more detail the crystalline structure of the nuclear fuel. This formalism shows new features in comparison with the static model. (author)

  5. Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR.

    Science.gov (United States)

    Bartova, Simona; Pechlaner, Maria; Donghi, Daniela; Sigel, Roland K O

    2016-06-01

    Self-splicing group II introns are highly structured RNA molecules, containing a characteristic secondary and catalytically active tertiary structure, which is formed only in the presence of Mg(II). Mg(II) initiates the first folding step governed by the κζ element within domain 1 (D1κζ). We recently solved the NMR structure of D1κζ derived from the mitochondrial group II intron ribozyme Sc.ai5γ and demonstrated that Mg(II) is essential for its stabilization. Here, we performed a detailed multinuclear NMR study of metal ion interactions with D1κζ, using Cd(II) and cobalt(III)hexammine to probe inner- and outer-sphere coordination of Mg(II) and thus to better characterize its binding sites. Accordingly, we mapped (1)H, (15)N, (13)C, and (31)P spectral changes upon addition of different amounts of the metal ions. Our NMR data reveal a Cd(II)-assisted macrochelate formation at the 5'-end triphosphate, a preferential Cd(II) binding to guanines in a helical context, an electrostatic interaction in the ζ tetraloop receptor and various metal ion interactions in the GAAA tetraloop and κ element. These results together with our recently published data on Mg(II) interaction provide a much better understanding of Mg(II) binding to D1κζ, and reveal how intricate and complex metal ion interactions can be. PMID:26880094

  6. Europium chelate-loaded liposomes: a tool for the study of binding and integrity of liposomes.

    Science.gov (United States)

    Orellana, A; Laukkanen, M L; Keinänen, K

    1996-10-01

    Using the biotin-streptavidin interaction as a model, we investigated the suitability of lanthanide chelates as encapsulated liposomal labels in liposome-based binding assays. Large unilamellar phospholipid:cholesterol liposomes containing europium-DTPA chelate and biotinylated phosphatidylethanolamine were prepared by detergent dialysis. The resulting Eu-liposomes ([symbol: see text] 120 nm) bound specifically to streptavidin in microtiter wells as measured by time-resolved fluorometric assay (TRF). The intensity of fluorescence released from the bound liposomes was dependent on the concentration of biotin in the liposome membrane, the concentration of europium entrapped in the liposomes, the incubation time and the amount of liposomes used in the assay. The sensitivity of the TRF assay allowed the detection of binding of attomole quantities of liposomes. The streptavidin-immobilised liposomes subjected to porcine pancreatic phospholipase A2 (EC 3.1.1.4) and detergents displayed a dose-dependent release of the encapsulated europium. Lanthanide-chelate-liposomes should prove useful for studies addressing binding and stability of liposomes. PMID:8865811

  7. Binding of several anti-tumor drugs to bovine serum albumin: Fluorescence study

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun [College of Chemistry, Changchun Normal University, Changchun 130032 (China)], E-mail: sy_bi@sina.com; Sun Yantao [College of Chemistry, Jilin University, Changchun 130023 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Qiao Chunyu; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130023 (China); Liu Chunming [College of Chemistry, Changchun Normal University, Changchun 130032 (China)

    2009-05-15

    The interactions of mitomycin C (MMC), fluorouracil (FU), mercaptopurine (MP) and doxorubicin hydrochloride (DXR) with bovine serum albumin (BSA) were studied by spectroscopic method. Quenching of fluorescence of serum albumin by these drugs was found to be a static quenching process. The binding constants (K{sub A}) were 9.66x10{sup 3}, 2.08x10{sup 3}, 8.20x10{sup 2} and 7.50x10{sup 3} L mol{sup -1} for MMC-, FU-, MP- and DXR-BSA, respectively, at pH 7.4 Britton-Robinson buffer at 28 deg. C. The thermodynamic functions such as enthalpy change ({delta}H), entropy change ({delta}S) and Gibbs free-energy change ({delta}G) for the reactions were also calculated according to the thermodynamic equations. The main forces in the interactions of these drugs with BSA were evaluated. It was found that the interactions of MMC and FU with BSA were exothermic processes and those of MP and DXR with BSA were endothermic. In addition, the binding sites on BSA for the four drugs were probed by the changes of binding properties of these drugs with BSA in the presence of two important site markers such as ibuprofen and indomethacin. Based on the Foester theory of non-radiation energy transfer, the binding distances between the drugs and tryptophane were calculated and they were 3.00, 1.14, 2.85, and 2.79 nm for MMC, FU, MP and DXR, respectively.

  8. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding

    International Nuclear Information System (INIS)

    Highlights: • Indoleamine 2,3-dioygenase has been studied by resonance Raman spectroscopy. • Trp-binding to the enzyme induces high frequency shift of the Fe–His stretching mode. • Increased imidazolate character of histidine promotes the O–O bond cleavage step. • A fine-tuning of the reactivity of the O–O bond cleavage reaction is identified. • The results are consistent with the sequential oxygen-atom-transfer mechanism. - Abstract: Resonance Raman spectra of ligand-bound complexes including the 4-phenylimidazole complex and of free and L-Trp-bound forms of indoleamine 2, 3-dioxygenase in the ferric state were examined. Effects on the vinyl and propionate substituent groups of the heme were detected in a ligand-dependent fashion. The effects of phenyl group of 4-phenylimidazole on the vinyl and propionate Raman bands were evident when compared with the case of imidazole ligand. Substrate binding to the ferrous protein caused an upshift of the iron–histidine stretching mode by 3 cm−1, indicating an increase in negativity of the imidazole ring, which favors the O–O bond cleavage. The substrate binding event is likely to be communicated from the heme distal side to the iron–histidine bond through heme substituent groups and the hydrogen-bond network which includes water molecules, as identified in an X-ray structure of a 4-phenylimidazole complex. The results provide evidence for fine-tuning of the reactivity of O–O bond cleavage by the oxygenated heme upon binding of L-Trp

  9. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Sachiko; Hara, Masayuki [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Sugimoto, Hiroshi; Shiro, Yoshitsugu [Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Ogura, Takashi, E-mail: ogura@sci.u-hyogo.ac.jp [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)

    2013-06-20

    Highlights: • Indoleamine 2,3-dioygenase has been studied by resonance Raman spectroscopy. • Trp-binding to the enzyme induces high frequency shift of the Fe–His stretching mode. • Increased imidazolate character of histidine promotes the O–O bond cleavage step. • A fine-tuning of the reactivity of the O–O bond cleavage reaction is identified. • The results are consistent with the sequential oxygen-atom-transfer mechanism. - Abstract: Resonance Raman spectra of ligand-bound complexes including the 4-phenylimidazole complex and of free and L-Trp-bound forms of indoleamine 2, 3-dioxygenase in the ferric state were examined. Effects on the vinyl and propionate substituent groups of the heme were detected in a ligand-dependent fashion. The effects of phenyl group of 4-phenylimidazole on the vinyl and propionate Raman bands were evident when compared with the case of imidazole ligand. Substrate binding to the ferrous protein caused an upshift of the iron–histidine stretching mode by 3 cm{sup −1}, indicating an increase in negativity of the imidazole ring, which favors the O–O bond cleavage. The substrate binding event is likely to be communicated from the heme distal side to the iron–histidine bond through heme substituent groups and the hydrogen-bond network which includes water molecules, as identified in an X-ray structure of a 4-phenylimidazole complex. The results provide evidence for fine-tuning of the reactivity of O–O bond cleavage by the oxygenated heme upon binding of L-Trp.

  10. Clicked bis-PEG-peptide conjugates for studying calmodulin-Kv7.2 channel binding

    OpenAIRE

    Bonache de Marcos, María Ángeles; Alaimo, Alessandro; Malo, Covadonga; Millet, Oscar; Villarroel, Alvaro; González-Muñiz, Rosario

    2014-01-01

    The recombinant Kv7.2 calmodulin (CaM) binding site (Q2AB CaMBD) shows a high tendency to aggregate, thus complicating biochemical and structural studies. To facilitate these studies we have conceived bis-PEG-peptide CaMBD-mimetics linking helices A and B in single, easy to handle molecules. Short PEG chains were selected as spacers between the two peptide molecules, and a Cu(i)-catalyzed cycloaddition (CuAAC) protocol was used to assemble the final bis-PEG-peptide conjugate, by the convenien...

  11. Cross species comparison of C/EBPa and PPAR¿ profiles in mouse and human adipocytes reveals interdependent retention of binding sites

    OpenAIRE

    Sandelin Albin; Nielsen Ronni; Chen Yun; Jørgensen Mette; Schmidt Søren F; Mandrup Susanne

    2011-01-01

    Abstract Background The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degree of overlap and are associated with the majority of genes upregulated during differentiation of murine 3T3-L1 adipocytes. Results Here we have mapped all binding site...

  12. Experimental - theoretical study of axially compressed cold formed steel profiles

    Directory of Open Access Journals (Sweden)

    Bešević Miroslav

    2011-01-01

    Full Text Available Analysis of axially compressed steel members made of cold formed profiles presented in this paper was conducted through both experimental and numerical methods. Numerical analysis was conducted by means of "PAK" finite element software designed for nonlinear static and dynamic analysis of structures. Results of numerical analysis included ultimate bearing capacity with corresponding middle section force-deflection graphs and buckling curves. Extensive experimental investigation were also concentrated on determination of bearing capacity and buckling curves. Experiments were conducted on five series with six specimens each for slenderness values of 50, 70, 90, 110 and 120. Compressed simply supported members were analyzed on Amsler Spherical pin support with unique electronical equipment and software. Besides determination of forcedeflection curves, strains were measured in 18 or 12 cross sections along the height of the members. Analysis included comparisons with results obtained by different authors in this field recently published in international journals. Special attention was dedicated to experiments conducted on high strength and stainless steel members.

  13. A study of structural properties on profiles HMMs

    CERN Document Server

    Bernardes, Juliana S; Costa, Vitor Santos; Zaverucha, Gerson

    2007-01-01

    Motivation: Despite profile hidden Markov Models (pHMMs) being an useful tool for detection of the divergent member in protein families, they are not succefully when proteins are in Twilight zone. We have purposed a method that adding structural properties into pHMMs training phrase. To end this, we have introduced a novel sequence weighting algorithm which given a different weigth for each amino acid in the protein, the weigths are in agreement with the structural similarity of amino acid. From a same train set (aligned homology proteins) we build five pHMMs, one for each structural properties. The properties used were: primary, secondary and terciary structures, accessibility and packing residue. We named this HMMER-STRUCT tool. Results: We used the SCOP database to perform our experiments. We performed take-one-family-out cross-validation over superfamilies. MAMMOTH-mult structural tool was used to align training set proteins. Performance was evaluated through ROC curves, and through Precision/Recall curve...

  14. Spectroscopic studies of the binding of Cu(II) complexes of oxicam NSAIDs to alternating G-C and homopolymeric G-C sequences

    Science.gov (United States)

    Chakraborty, Sreeja; Bose, Madhuparna; Sarkar, Munna

    2014-03-01

    Drugs belonging to the Non-steroidal anti-inflammatory (NSAID) group are not only used as anti-inflammatory, analgesic and anti-pyretic agents, but also show anti-cancer effects. Complexing them with a bioactive metal like copper, show an enhancement in their anti-cancer effects compared to the bare drugs, whose exact mechanism of action is not yet fully understood. For the first time, it was shown by our group that Cu(II)-NSAIDs can directly bind to the DNA backbone. The ability of the copper complexes of NSAIDs namely meloxicam and piroxicam to bind to the DNA backbone could be a possible molecular mechanism behind their enhanced anticancer effects. Elucidating base sequence specific interaction of Cu(II)-NSAIDs to the DNA will provide information on their possible binding sites in the genome sequence. In this work, we present how these complexes respond to differences in structure and hydration pattern of GC rich sequences. For this, binding studies of Cu(II) complexes of piroxicam [Cu(II)-(Px)2 (L)2] and meloxicam [Cu(II)-(Mx)2 (L)] with alternating GC (polydG-dC) and homopolymeric GC (polydG-polydC) sequences were carried out using a combination of spectroscopic techniques that include UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy. The Cu(II)-NSAIDs show strong binding affinity to both polydG-dC and polydG-polydC. The role reversal of Cu(II)-meloxicam from a strong binder of polydG-dC (Kb = 11.5 × 103 M-1) to a weak binder of polydG-polydC (Kb = 5.02 × 103 M-1), while Cu(II)-piroxicam changes from a strong binder of polydG-polydC (Kb = 8.18 × 103 M-1) to a weak one of polydG-dC (Kb = 2.18 × 103 M-1), point to the sensitivity of these complexes to changes in the backbone structures/hydration. Changes in the profiles of UV absorption band and CD difference spectra, upon complex binding to polynucleotides and the results of competitive binding assay using ethidium bromide (EtBr) fluorescence indicate different binding modes in each

  15. Spatial profile of laser beam in antiresonant ring cavity: experimental study

    Science.gov (United States)

    Grabovski, Vitaly V.; Prokhorenko, Valentin I.; Yatskiv, Dmytro Y.

    1996-03-01

    This paper presents results of experimental studies of the spatial profile of the beam in lasers with an antiresonant ring. The near-field profile of the beam was measured by the pin-hole technique. In case of the active crystal placed into the ring, the beam profile was found to be Gaussian within a wide range of the pumping power. Variation of the width of the Gaussian profile is caused by the thermal lens in the active crystal. Measurements of the FWHM of the Gaussian profile demonstrated that it is proportional to the one-fourth power of the focal length of the thermal lens, as in the case of a stable cavity.

  16. Application of the novel bioluminescent ligand-receptor binding assay to relaxin-RXFP1 system for interaction studies.

    Science.gov (United States)

    Wu, Qing-Ping; Zhang, Lei; Shao, Xiao-Xia; Wang, Jia-Hui; Gao, Yu; Xu, Zeng-Guang; Liu, Ya-Li; Guo, Zhan-Yun

    2016-04-01

    Relaxin is a prototype of the relaxin family peptide hormones and plays important biological functions by binding and activating the G protein-coupled receptor RXFP1. To study their interactions, in the present work, we applied the newly developed bioluminescent ligand-receptor binding assay to the relaxin-RXFP1 system. First, a fully active easily labeled relaxin, in which three Lys residues of human relaxin-2 were replaced by Arg, was prepared through overexpression of a single-chain precursor in Pichia pastoris and in vitro enzymatic maturation. Thereafter, the B-chain N-terminus of the easily labeled relaxin was chemically cross-linked with a C-terminal cysteine residue of an engineered NanoLuc through a disulfide linkage. Receptor-binding assays demonstrated that the NanoLuc-conjugated relaxin retained high binding affinity with the receptor RXFP1 (K d = 1.11 ± 0.08 nM, n = 3) and was able to sensitively monitor binding of a variety of ligands with RXFP1. Using the novel bioluminescent binding assay, we demonstrated that three highly conserved B-chain Arg residues of relaxin-3 had distinct contributions to binding of the receptor RXFP1. In summary, our present work provides a novel bioluminescent ligand-receptor binding assay for the relaxin-RXFP1 system to facilitate their interaction studies, such as characterization of relaxin analogues or screening novel agonists or antagonists of RXFP1. PMID:26767372

  17. Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity.

    Science.gov (United States)

    Malik, Zulezwan Ab; Cobley, James N; Morton, James P; Close, Graeme L; Edwards, Ben J; Koch, Lauren G; Britton, Steven L; Burniston, Jatin G

    2013-12-01

    Two-dimensional gel electrophoresis provides robust comparative analysis of skeletal muscle, but this technique is laborious and limited by its inability to resolve all proteins. In contrast, orthogonal separation by SDS-PAGE and reverse-phase liquid chromatography (RPLC) coupled to mass spectrometry (MS) affords deep mining of the muscle proteome, but differential analysis between samples is challenging due to the greater level of fractionation and the complexities of quantifying proteins based on the abundances of their tryptic peptides. Here we report simple, semi-automated and time efficient (i.e., 3 h per sample) proteome profiling of skeletal muscle by 1-dimensional RPLC electrospray ionisation tandem MS. Solei were analysed from rats (n = 5, in each group) bred as either high- or low-capacity runners (HCR and LCR, respectively) that exhibited a 6.4-fold difference (1,625 ± 112 m vs. 252 ± 43 m, p ions, which spanned three orders of magnitude. In total, 207 proteins were analysed, which encompassed almost all enzymes of the major metabolic pathways in skeletal muscle. The most abundant protein detected was type I myosin heavy chain (RA = 5,843 ± 897) and the least abundant protein detected was heat shock 70 kDa protein (RA = 2 ± 0.5). Sixteen proteins were significantly (p ion (551.21 m/z) of the doubly-charged peptide SLGVGFATR (454.19 m/z) of residues 23-31 of FABPH. SRM was conducted on technical replicates of each biological sample and exhibited a coefficient of variation of 20%. The abundance of FABPH measured by SRM was 2.84-fold greater (p = 0.0095) in HCR muscle. In addition, SRM of FABPH was performed in vastus lateralis samples of young and elderly humans with different habitual activity levels (collected during a previous study) finding FABPH abundance was 2.23-fold greater (p = 0.0396) in endurance-trained individuals regardless of differences in age. In summary, our findings in HCR/LCR rats provide protein-level confirmation for earlier

  18. Whether age of menarche is influenced by body mass index and lipoproteins profile? a retrospective study

    OpenAIRE

    Fereidoun Azizi; Fahimeh Ramezani Tehrani; Maryam Farahmand

    2012-01-01

    Background: Menarche, a milestone in the reproductive life span of a woman, is influenced by several genetics and environmental factors. There is no consensus regarding the impact of body mass index (BMI) and lipid profiles on the age of menarche, as the results of various studies demonstrate. Objective: To investigate the correlation between age of menarche and BMI/lipoprotein profile in a community sample of Iranian girls. Materials and Methods: In the study, 370 girls, aged 10-16 years, wh...

  19. Substance P: binding properties and studies on cellular responses in guinea pig macrophages

    International Nuclear Information System (INIS)

    The neuropeptide Substance P (SP) has been recognized to modulate functional activities of inflammatory cells. The authors have previously shown that it mediates macrophage activation. In this study they examined binding characteristics of SP and searched for additional evidence of heightened metabolic activity of guinea pig peritoneal macrophages upon challenge with this peptide. Radioligand studies indicated the existence of a homogeneous class of specific binding sites with high affinity for SP on macrophages. Scatchard analysis yielded an apparent K/sub D/ of 1.9 +/- 0.4 x 10-8 M (range: 1.4 to 2.4 x 10-8 M), which was confirmed by kinetic studies. Binding was dose related, saturable, reversible, and could be inhibited by the SP antagonist (D-Pro2, D-Phe7, D-Trp9)-SP. Examination of peptide structural requirements revealed that both the COOH- and NH2-terminus contribute to receptor-ligand interaction. Other members of the tachykinin group of peptides were devoid of stimulatory action on macrophages. Cellular responses after engagement of the receptor sites by SP included downregulation of the membrane-associated enzyme 5'-nucleotidase and stimulation of synthesis and release of arachidonic acid metabolites, as well as of the lysosomal enzyme ADGase. These actions were specific as evidenced by immunoabsorption experiments. The findings demonstrate that macrophage activation afforded by SP is effected through a receptor-mediated mechanism. Liberation of proinflammatory and immunomodulating substances in response to SP may be relevant to the pathogenesis of neuroinflammatory disease

  20. Thermodynamic parameters of the binding of retinol to binding proteins and to membranes

    International Nuclear Information System (INIS)

    Retinol (vitamin A alcohol) is a hydrophobic compound and distributes in vivo mainly between binding proteins and cellular membranes. To better clarify the nature of the interactions of retinol with these phases which have a high affinity for it, the thermodynamic parameters of these interactions were studied. The temperature-dependence profiles of the binding of retinol to bovine retinol binding protein, bovine serum albumin, unilamellar vesicles of dioleoylphosphatidylcholine, and plasma membranes from rat liver were determined. It was found that binding of retinol to retinol binding protein is characterized by a large increase in entropy and no change in enthalpy. Binding to albumin is driven by enthalpy and is accompanied by a decrease in entropy. Partitioning of retinal into unilamellar vesicles and into plasma membranes is stabilized both by enthalpic and by entropic components. The implications of these finding are discussed

  1. Phenanthrene binding by humic acid–protein complexes as studied by passive dosing technique

    International Nuclear Information System (INIS)

    This work investigated the binding behavior of phenanthrene by humic acids (HA-2 and HA-5), proteins (bovine serum albumin (BSA)), lysozyme and pepsin), and their complexes using a passive dosing technique. All sorption isotherms were fitted well with Freundlich model and the binding capability followed an order of HA-5 > HA-2 > BSA > pepsin > lysozyme. In NaCl solution, phenanthrene binding to HA-BSA complexes was much higher than the sum of binding to individual HA and BSA, while there was no enhancement for HA-pepsin. Positively charged lysozyme slightly lowered phenanthrene binding on both HAs due to strong aggregation of HA-lysozyme complexes, leading to reduction in the number of binding sites. The binding enhancement by HA-BSA was observed under all tested ion species and ionic strengths. This enhancement can be explained by unfolding of protein, reduction of aggregate size and formation of HA-BSA complexes with favorable conformations for binding phenanthrene. Highlights: • Phenanthrene binding capability followed an order: HA-5>HA-2>BSA>pepsin>lysozyme. • Phenanthrene binding to HA-BSA was enhanced relative to individual HA and BSA. • Binding enhancement to HA-BSA was observed under all tested solution conditions. • The enhancement is related to BSA unfolding, size reduction and HA-BSA complexation. -- Phenanthrene binding to HA-BSA complexes is much higher than the sum to individual HA and BSA while there was no binding enhancement to HA-pepsin or HA-lysozyme

  2. The Investigation of Different Properties of Clonidine Drug Binding to Carbon Nanotube: A Theoretical Study

    OpenAIRE

    Z. Yousefian

    2014-01-01

    In this study, we investigated the binding of Clonidine Drug (C9H9Cl2N3) with zigzag single walled Carbon Nanotubes (SWCNTs) (5, 0) and a length of 5ᵒA by theoretical methods of theory (NMR,NBO, HOMO- LUMO Gap energy,…calculations) using Gaussian ­09 software package. Then, Simulation was done in MM+, AMBER and OPLS force fields by Monte Carlo method in HyperChem. Three important energy parameters – Potential Energy, Kinetic Energy and Total Energy-calculated in five different simulating temp...

  3. The Investigation of Different Properties of Clonidine Drug Binding to Carbon Nanotube: A Theoretical Study

    Directory of Open Access Journals (Sweden)

    Z. Yousefian

    2014-12-01

    Full Text Available In this study, we investigated the binding of Clonidine Drug (C9H9Cl2N3 with zigzag single walled Carbon Nanotubes (SWCNTs (5, 0 and a length of 5ᵒA by theoretical methods of theory (NMR,NBO, HOMO- LUMO Gap energy,…calculations using Gaussian ­09 software package. Then, Simulation was done in MM+, AMBER and OPLS force fields by Monte Carlo method in HyperChem. Three important energy parameters – Potential Energy, Kinetic Energy and Total Energy-calculated in five different simulating temperatures (308, 310, 312, 314 and 316 Kelvin were used for computation and good results were obtained.

  4. radiochemical studies on the binding of humic materials with toxic elements and compounds

    International Nuclear Information System (INIS)

    industrial nations produce several billion tons of waste every year . this figure will increase as both population and industrial growth increase. there are many kinds of waste, including refinery waste, which consists of hydrocarbons, heavy metals, metal catalysts and caustic solution; dredge spoils, some of which are highly polluted and cntains substances potentially hazardous to human health or the marine ecosystem; chemical waste such as insecticides, pesticides, other complex chemicals and heavy metals; radioactive waste and agricultural waste, anmd most of them are extremely hazardous and harmful to the marine ecosystem and its inhabitants.the aim of this thesis is to study the binding of humic materials with toxic elements and compounds

  5. Iron profiles and speciation of the upper water column at the Bermuda Atlantic time-series Study site: a model based sensitivity study

    Directory of Open Access Journals (Sweden)

    L. Weber

    2007-03-01

    Full Text Available A one-dimensional model of the biogeochemistry and speciation of iron is coupled with the General Ocean Turbulence Model (GOTM and a NPZD-type ecosystem model. The model is able to simulate the temporal patterns and vertical profiles of dissolved iron (dFe in the upper ocean at the Bermuda Atlantic Time-series Study site reasonably well. Subsurface model profiles strongly depend on the parameter values chosen for the loss processes for iron, colloidal aggregation and scavenging onto particles. Current estimates for these parameters result in depletion of dFe. A high stability constant of iron-binding organic ligands is required to reproduce the observed degree of organic complexation below the mixed layer. A solubility of atmospherically deposited iron higher than 2% lead to dFe concentrations incompatible with observations. Despite neglecting ultraviolet radiation, the model produces diurnal variations and mean vertical profiles of H2O2 and iron species that are in good agreement with observations.

  6. First-principles study of solute–vacancy binding in Cu

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yufei [State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240 (China); Gao, Haiyan, E-mail: gaohaiyan@sjtu.edu.cn [State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240 (China); Han, Yanfeng; Dai, Yongbing [State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240 (China); Bian, Fenggang [Shanghai Institute of Applied Physics, CAS, Shanghai 201204 (China); Wang, Jun; Sun, Baode [State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240 (China); Shanghai Key Laboratory of Advanced High-temperature Materials and Precision Forming, Shanghai Jiao Tong University, Shanghai 200240 (China)

    2014-09-01

    Highlights: • Solute–vacancy binding is a key quantity in understanding diffusion kinetics. • A large database of solute–vacancy binding energies in Cu from first-principles calculations based on density functional theory was presented in the paper. • The trends in the binding energies in terms of super cell size, solutes size and magnetic moments were analyzed. - Abstract: Solute–vacancy binding is a key quantity in understanding diffusion kinetics, and may also have a considerable impact on the hardening response in Cu alloys. However, the binding energies between solute atoms and vacancies in Cu are largely unknown and difficult to measure accurately. A large database of solute–vacancy binding energies in Cu from first-principles calculations based on density functional theory was presented in the paper. The trends in the binding energies in terms of super cell size, solutes size and magnetic moments are analyzed. The calculated binding energies agree well with experimental measurements available.

  7. Some Studies On Bacteriological Profile Of Kidney Stone

    OpenAIRE

    S. D. Deokar And D. G. Kadam

    2013-01-01

    Most of the antimicrobial susceptibility surveillance studies focus on isolates from hospitalized patients.In the present investigation a retrospective analysis of microbiological data of antimicrobial susceptibility ofbacterial Urinary Isolates of Urolithiasis from the hospitals in the Barshi town was performed. Such studies had notbeen undertaken earlier in this region. The bacteriological studies of urinary stone included samples from sixty six(66) cases of Urolithiasis. Thirty three (33) ...

  8. Binding hot-spots in an antibody-ssDNA interface: a molecular dynamics study.

    Science.gov (United States)

    Wang, Yeng-Tseng; Lee, Wen-Jay

    2012-10-30

    Simulating antigen-antibody interactions is essential for elucidating antigen-antibody mechanics. Proteins interactions are vital for elucidating antibody-ssDNA associations in immunology. Therefore, this study investigated the dissociation of the human systemic lupus erythematosus antibody-ssDNA complex structure. Dissociation (i.e. the distance between the center of mass of the ssDNA and the antibody) is also studied using the potential of mean force calculations based on molecular dynamics and the explicit water model. The MM-PBSA method is also used to prove our dissociation simulations. With 605 nanosecond molecular dynamics simulations, the results indicate that the 8 residues (i.e. Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2)), and the five inter-protein molecular hydrogen bonds may profoundly impact the antibody-ssDNA interaction, a finding which may be useful for protein engineering of this antibody-ssDNA structure. Experimental binding affinity of this antibody-ssDNA complex equals 7.00 kcal mol(-1). Our dissociation binding affinity is 7.96 ± 0.33 kcal mol(-1) and MM-PBSA binding affinity is 9.12 ± 1.65 kcal mol(-1), which is close to the experimental value. Additionally, the 8 residues Gly44 (HCDR2), Asn54 (HCDR2), Arg98 (HCDR3), Tyr100 (HCDR3), Asp101 (HCDR3), Tyr32 (LCDR1), Tyr49 (LCDR2) and Asn50 (LCDR2) may play a more significant role in developing bioactive antibody analogues. PMID:23079742

  9. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)

    2015-01-21

    The uranyl cation (UO₂²⁺) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  10. Spectroscopic, Viscositic, DNA Binding and Cytotoxic Studies of Newly Synthesized Steroidal Imidazolidines.

    Science.gov (United States)

    Dar, Ayaz Mahmood; Shamsuzzaman; Khan, Shakir

    2016-03-01

    A series of new steroidal imidazolidine derivatives (4-6) were synthesized after reacting steroidal thiosemicarbazones with chloro ethylacetate in absolute ethanol. After characterization by spectral and analytical data, the interaction studies of compounds (4-6) with DNA were carried out by UV-vis, fluorescence spectroscopy, hydrodynamic measurements, molecular docking and gel electrophoresis. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.63 × 10(3) M(-1), 1.81 × 10(3) M(-1) and 2.06 × 10(3) M(-1), respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis demonstrated that compound 4 showed strong interaction during the concentration dependent cleavage activity with pBR322 DNA. The molecular docking study suggested the intercalation of imidazolidine moiety of steroid derivative in minor groove of DNA. During in vitro cytotoxicity, compounds (4-6) revealed potential toxicity against the different human cancer cells (MTT assay). The uptake of compound 4 by MCF-7 and HeLa cells was studied by confocal microscopy which determined cell shrinkage and hence leading to the apoptosis. The results revealed that compound 4 has better prospectus to act as cancer chemotherapeutic candidate which warrants further in vivo anticancer investigations. PMID:26698876

  11. Structural studies of nucleoside analog and feedback inhibitor binding to Drosophila melanogaster multisubstrate deoxyribonucleoside kinase

    DEFF Research Database (Denmark)

    Mikkelsen, Niels Egil; Munch-Petersen, Birgitte; Eklund, Hans

    2008-01-01

    relate them to the binding of substrate and feedback inhibitors. dCTP and dGTP binds similarly as the feedback inhibitor dTTP with the base in the substrate site. All investigated nucleoside analogs bind similarly as the pyrimidine substrates with many interactions in common. In contrast, the base of d...

  12. Cohort profile: the English longitudinal study of ageing.

    Science.gov (United States)

    Steptoe, Andrew; Breeze, Elizabeth; Banks, James; Nazroo, James

    2013-12-01

    The English Longitudinal Study of Ageing (ELSA) is a panel study of a representative cohort of men and women living in England aged ≥50 years. It was designed as a sister study to the Health and Retirement Study in the USA and is multidisciplinary in orientation, involving the collection of economic, social, psychological, cognitive, health, biological and genetic data. The study commenced in 2002, and the sample has been followed up every 2 years. Data are collected using computer-assisted personal interviews and self-completion questionnaires, with additional nurse visits for the assessment of biomarkers every 4 years. The original sample consisted of 11 391 members ranging in age from 50 to 100 years. ELSA is harmonized with ageing studies in other countries to facilitate international comparisons, and is linked to financial and health registry data. The data set is openly available to researchers and analysts soon after collection (http://www.esds.ac.uk/longitudinal/access/elsa/l5050.asp). PMID:23143611

  13. Clinical Profile of Extraocular Muscle Palsy: A Retrospective Study

    Directory of Open Access Journals (Sweden)

    Suman Adhikari, BOptom

    2013-12-01

    Full Text Available Background: The sixth cranial nerve has been found to be the most commonly affected in previous studies of cranial nerve palsies. This study was carried out to determine the most common nerve involved in extraocular muscle (EOM palsies and the most common cause of EOM palsy in Nepal.Methods: The diagnosed cases of third, fourth, or sixth nerve palsy for 10 years (2000-2010 at the B.P. Koirala Lions Center for Ophthalmic Studies outpatient department were included in the study. A retrospective review of patients’ records was performed, and the causes of EOM palsy were grouped as: vascular, trauma, tumor,aneurysm, undetermined, and others. Recovery of the palsy was evaluated by reviewing the records of the patients who were followed up one month after the initial visit.Results: A total of 838 patients was included in the study. The average patient age was 37 years. The sixth nerve was most commonly affected (n=458, 54.65%, and the most common etiology was undetermined (n=408, 48.68%. Among the cases where the cause of palsy was known, the largest number of patients had trauma (n=188, 16.46%.Conclusion: It was concluded that in Nepal, the most commonly affected cranial nerve is the sixth nerve, in accordance with the other studies done in the past in different parts of the world. Most of the cases of cranial nerve palsy were found to have no specific cause and were not associated with diagnosed systemic disease.

  14. Binding Studies of Natural Product Berberine with DNA G-Quadruplex

    Directory of Open Access Journals (Sweden)

    Nagendra K. Sharma

    2011-01-01

    Full Text Available Problem statement: The ends of chromosome had highly repetitive short G and C-rich sequences of DNA. These sequences were known to form stable tetraplex type of secondary structures which help to maintain gene integratity after cell divison. Approach: Any reagent which controls the random cell division would be useful to design anticancer drugs. Therefore a many natural and synthesized molecules which stabilized tetraplex structures are targeted as anticancer drug entities. Results: Among them, Berberine hydrochloride natural product and its analogues are well studies as G-quadruplex stabilizing agent. In this report, DNA sequence 5’-G3-C5-G3-3’ has been designed which has probability to form i-motif and G-qua druplex types of secondary structures. Herein we studied the interaction between this DNA strands and Berberine hydrochloride by 1H-NMR techniques and UV in two different PH (4.7 and 7.4 conditions. Conclusion/Recommendations: Our preliminary results showed that Berberine bind with this DNA strand in both pH conditions which is further supported by UV melting experiments. In future this sequence can be used as probe to screen out tetraplex binding natural products which help to generate new anticancer drugs.

  15. Structure and stability of copper clusters: A tight-binding molecular dynamics study

    International Nuclear Information System (INIS)

    In this paper we propose a tight-binding molecular dynamics with parameters fitted to first-principles calculations on the smaller clusters and with an environment correction, to be a powerful technique for studying large transition-metal/noble-metal clusters. In particular, the structure and stability of Cun clusters for n=3-55 are studied by using this technique. The results for small Cun clusters (n=3-9) show good agreement with ab initio calculations and available experimental results. In the size range 10≤n≤55 most of the clusters adopt icosahedral structure which can be derived from the 13-atom icosahedron, the polyicosahedral 19-, 23-, and 26-atom clusters, and the 55-atom icosahedron, by adding or removing atoms. However, a local geometrical change from icosahedral to decahedral structure is observed for n=40-44 and return to the icosahedral growth pattern is found at n=45 which continues. Electronic 'magic numbers' ( n=2, 8, 20, 34, 40) in this regime are correctly reproduced. Due to electron pairing in highest occupied molecular orbitals (HOMOs), even-odd alternation is found. A sudden loss of even-odd alternation in second difference of cluster binding energy, HOMO-LUMO (LUMO, lowest unoccupied molecular orbital) gap energy and ionization potential is observed in the region n∼40 due to structural change there. Interplay between electronic and geometrical structure is found

  16. Structural, vibrational, NMR, quantum chemical, DNA binding and protein docking studies of two flexible imine oximes

    Indian Academy of Sciences (India)

    YUNUS KAYA

    2016-09-01

    Two flexible imine oxime molecules, namely, 3-(pyridin-2-ylmethylimino)-butan-2-one oxime (HL¹) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL²) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, three stable molecules and the most stable conformer were determined for the both imine oximes. The spectroscopic properties such as vibrational and NMR were calculated for the most stable conformer of the HL¹ and HL². The calculation results were applied to simulate infrared spectra of the title compounds, which show good agreement with observed spectra. In addition, the stable three molecules of the both imine oximes have been used to carry out DNA binding and protein docking studies with DNA and protein structures (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligands inside the DNA and protein cavity.

  17. Binding of the neuroleptic drug, gabapentin, to bovine serum albumin: Insights from experimental and computational studies

    International Nuclear Information System (INIS)

    The interaction between antiepileptic drug, gabapentin (GP), and bovin serum albumin (BSA) was studied by spectroscopic and computational methods. The native fluorescence of BSA was quenched by GP. Stern–Volmer quenching constant was calculated at different temperatures which suggested a static mechanism. The association constant (Ka) was calculated from fluorescence quenching studies, which increased with temperature rising. GP competed well with warfarine for hydrophobic subdomain IIA (Sudlow's site I) on the protein. Enthalpy and entropy changes during the interaction of GP with BSA were obtained using van't Hoff plot, which showed an entropy-driven process and involvement of hydrophobic forces (ΔH>0 and ΔS>0). Synchronous fluorescence measurements of BSA solution in the presence of GP showed a considerable blue shift when Δλ=15 nm, therefore, GP interacts with tyrosine-rich sites on BSA. Optimized docked model of BSA–GP mixture confirmed the experimental results. -- Highlights: • Interaction of gabapentin and bovine serum albumin (BSA) is investigated by spectroscopic techniques. • Gabapentin can quench the fluorescence of BSA through a static quenching procedure. • The binding of gabapentin to BSA is driven mainly by hydrophobic interactions. • Subdomain IIA (Sudlow's site I) of BSA is found to be the main binding site for gabapentin. • Molecular docking modeling confirmed the experimental results

  18. High-throughput screening of monoclonal antibodies against plant cell wall glycans by hierarchical clustering of their carbohydrate microarray binding profiles

    DEFF Research Database (Denmark)

    Moller, Isabel; Marcus, Susan E.; Haeger, Ash;

    2007-01-01

    Antibody-producing hybridoma cell lines were created following immunisation with a crude extract of cell wall polymers from the plant Arabidopsis thaliana. In order to rapidly screen the specificities of individual monoclonal antibodies (mAbs), their binding to microarrays containing 50 cell wall...... investigated using subsequent immunochemical and biochemical analyses and two novel mAbs are described in detail. mAb LM13 binds to an arabinanase-sensitive pectic epitope and mAb LM14, binds to an epitope occurring on arabinogalactan-proteins. Both mAbs display novel patterns of recognition of cell walls in...... plant materials....

  19. Immunological properties of prolactin and studies on a gonadotropin binding inhibitor

    International Nuclear Information System (INIS)

    The physiological role of prolactin in horses has not yet been well defined. With the availability of highly purified ePRL for inducing antibody formation in rabbits and for radiolabeling with Na125I, a very sensitive (0.4-0.6 ng/ml) and highly specific homologous RIA for ePRL was developed. A heterologous RIA using 125I-labeled ovine PRL and anti-ePRL antiserum was also developed and compared to the homologous RIA for ePRL. Of the two systems, it is concluded that this homologous RIA system is more suitable and more reliable for measuring prolactin concentration in horse serum samples. Until now, biochemical information on PRL has not been available for reptilian species. Sea turtle (Chelonia mydas) prolactin was purified from pituitary extracts by selective precipitation, DEAE-cellulose chromatography and gel filtration. Similar to other species of PRL, sea turtle PRL is a 22,000-24,000 daltons protein and contains a high content of glutamic acid, aspartic acid, serine and leucine, the N-terminal amino acid residue. Gonadotropin (FSH) binding inhibitor was partially purified from sheep testes by ammonium sulfate fractionation and ion exchange chromatography. The FSH-BI (molecular weight: 50,000 daltons, estimated by gel filtration) contains a protein moiety necessary for binding inhibitory activity. The inhibition of the binding of 125I-labeled ovine FSH to its receptor by the FSH-BI is not competitive. Both in vivo and in vitro biological studies of FSH-BI preparations in rats indicated various effects on FSH and LH activities at the gonadal level. These findings suggest a physiological role for FSH-BI in the regulation of reproduction

  20. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    International Nuclear Information System (INIS)

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg2+. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg2+, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics

  1. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhongshan [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom); College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Xiang, Quanju [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Department of Microbiology, College of Resource and Environment Science, Sichuan Agriculture University, Yaan 625000 (China); Zhu, Xiaofeng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Dong, Haohao [Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); He, Chuan [School of Electronics and Information, Wuhan Technical College of Communications, No. 6 Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065 (China); Wang, Haiyan; Zhang, Yizheng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Wang, Wenjian, E-mail: Wenjian166@gmail.com [Laboratory of Department of Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080 (China); Dong, Changjiang, E-mail: C.Dong@uea.ac.uk [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom)

    2014-09-26

    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  2. Tissue-Specific Metabolic Profile Study of Moringa oleifera L. Using Nuclear Magnetic Resonance Spectroscopy

    OpenAIRE

    Mahmud, Iqbal; Chowdhury, Kamal; Boroujerdi, Arezue

    2014-01-01

    Moringa oleifera, an important multipurpose crop, is rich in various phytochemicals: flavonoids, antioxidants, vitamins, minerals and carotenes. The purpose of this study was to profile the groups of metabolites in leaf and stem tissues of M. oleifera. Various sugars, amino acids, and organic acid derivatives were found in all of the M. oleifera tissues with different profiles/peak intensities depending on the tissue. 1D proton nuclear magnetic resonance (NMR) was applied for collecting metab...

  3. A study for profiling mathematics teachers regarding factors affecting promotion of students' metacognition

    OpenAIRE

    Şeker, Vuslat; Ader, Engin

    2015-01-01

    The main objective of this study was to describe mathematics teachers' profiles on factors affecting their promotion of students' metacognition through developing profiling tools. In the light of this aim, four factors from the Framework for Analysing Mathematics Teaching for the Advancement of Metacognition-FAMTAM-(Ader, 2009) were used. The factors were (1) teachers' conceptu-alization of metacognition, (2) teachers' perceptions of students' features and needs, (3) distribution of mathemati...

  4. Profile and perceptions of biogas as automobile fuel : A study of Svensk Biogas

    OpenAIRE

    Larsson, Anneli

    2008-01-01

    From an environmental- and health perspective, biogas and other biomass-based fuels have several advantages; nevertheless the majority of motorists fill their cars with petroleum-based fuels. This thesis is designed to explore the profile of biogas in relation to its perceptions. It is a study concerning the communication between the biogas producing company Svensk Biogas and their biogas users and non biogas users. To obtain a thorough understanding of the profile and perceptions of biogas a...

  5. Study of the cavitating instability on a grooved Venturi profile

    CERN Document Server

    Danlos, Amélie; Ravelet, Florent; Coutier-Delgosha, Olivier; Bakir, Farid

    2012-01-01

    Cavitation is a limiting phenomenon in many domains of fluid mechanics. Instabilities of a partial cavity developed on an hydrofoil, a converging-diverging step or in an inter-blade channel in turbomachinery, have already been investigated and described in many previous works. The aim of this study is to evaluate a passive control method of the sheet cavity. According to operating conditions, cavitation can be described by two different regimes: an unstable regime with a cloud cavitation shedding and a stable regime with only a pulsating sheet cavity. Avoiding cloud cavitation can limit structure damages since a pulsating sheet cavity is less agressive. The surface condition of a converging-diverging step, like a Venturi-type obstacle, is here studied as a solution for a passive control of the cavitation. This study discusses the effect of an organized roughness, in the shape of longitudinal grooves, on the developed sheet cavity. Analyzes conducted with Laser Doppler Velocimetry, visualisations and pressure ...

  6. BACTERIOLOGICAL PROFILE OF SURGICAL PERITONITIS: A PROSPECTIVE OBSERVATIONAL STUDY

    Directory of Open Access Journals (Sweden)

    Manju

    2015-09-01

    Full Text Available Peritonitis is defined as inflammation of peritoneum that lines the abdominal cavity and the organs contained therein. In Surgical practice we most often encounter cases of peritonitis which are mostly secondary to hollow viscous perforation. Purpose of our study is to find out which type of peritonitis is more common in our institute, which is the most common bacteria isolated from peritoneal fluid and which antibiotic is it most sensitive to. We studied 104 cases o f age group 16 and above of both sex who presented with clinical features of peritonitis. Peritoneal fluid was obtained and sent for culture and sensitivity. Peritoneal fluid culture was positive in 55.76% cases. The incidence of culture positivity increas ed with duration of presentation. Gastro duodenal perforation was the most common etiological factor for peritonitis found in 42.86% cases followed by ileal perforation. E. c oli was the most common bacteria isolated in study group followed by klebsiella. M ost of the cultures were monomicrbial. E. coli was sensitive to amikacin, imipenem and meropenem (100%. So in our study Gram negative infection is more common in surgical peritonitis. Identification of bacteria and its sensitivity to the antibiotics is he lpful to avoid injudicious use of antibiotics in surgical peritonitis. Proper choice of antibiotics along with surgical management and proper resuscitation in cases of surgical peritonitis can reduces mortality and morbidity associated with these high risk cases

  7. Profiling families enrolled in food allergy immunotherapy studies.

    LENUS (Irish Health Repository)

    DunnGalvin, Audrey

    2009-09-01

    Little is known about specific psychological factors that affect parents\\' decisions to take part in clinical studies. We examined factors, related to health-related quality of life (HRQoL), that may influence parents\\' decision to allow their children to participate in research on clinical food allergy.

  8. Profiling Families Enrolled in Food Allergy Immunotherapy Studies

    NARCIS (Netherlands)

    DunnGalvin, Audrey; Chang, Wen Chin; Laubach, Susan; Steele, Pamela H.; Dubois, Anthony E. J.; Burks, A. Wesley; Hourihane, Jonathan O'B.

    2009-01-01

    BACKGROUND: Little is known about specific psychological factors that affect parents' decisions to take part in clinical studies. We examined factors, related to health-related quality of life (HRQoL), that may influence parents' decision to allow their children to participate in research on clinica

  9. Students from Australian Universities Studying Abroad: A Demographic Profile

    Science.gov (United States)

    Nerlich, Steve

    2015-01-01

    Australia is one of many countries to encourage its students to study abroad and hence develop a global perspective. Traditionally, students who have pursued this option represented a relatively privileged and demographically narrow group. More recently, governments and other agencies have been offering funding support with the aim of…

  10. Some Studies On Bacteriological Profile Of Kidney Stone

    Directory of Open Access Journals (Sweden)

    S. D. Deokar And D. G. Kadam

    2013-08-01

    Full Text Available Most of the antimicrobial susceptibility surveillance studies focus on isolates from hospitalized patients.In the present investigation a retrospective analysis of microbiological data of antimicrobial susceptibility ofbacterial Urinary Isolates of Urolithiasis from the hospitals in the Barshi town was performed. Such studies had notbeen undertaken earlier in this region. The bacteriological studies of urinary stone included samples from sixty six(66 cases of Urolithiasis. Thirty three (33 samples showed presence of bacteria namely Klebsiella pneumoniae,Pseudomonas aeruginosa, Proteus vulgaris, Escherichia coli, Aeromonas spp. and Staphylococcus saprophyticus.In twenty eight (28 infected stone cases the organisms isolated from crushed stone were same, while five (5 casesof culture positive stones were found different microorganisms. Biochemical identification study was performed asper the standard methods. The problem of Urolithiasis was found more in males than females.The relation betweenUTI & urinary stones was analyzed in present study, out of Sixty-six UTI(66 cases studied,in thirty-three (50%cases an infection induced stones in which eight cases (12.12% from female and twenty five (37.87% cases frommale. Infection induced stones were not detected in the female age group below fifteen. Three (3 cases of infectioninduced stones were detected in male group below 15. In case of middle age group (16 to 45 infection inducedurinary stones were five(5 in female and seventeen(17 in male, while above 46 age group one(01 in female andfive(05 in male. Sixty-six cases were reported including 18 female cases (27.27% & 48 male cases (72.73%. Thehigh incidence (50% of infection-induced stones seen in the present study is in close agreement with observation ofVargas et al & Benu Dewan et al .The commonest pathogens recovered from pre-operative urine culture and stonecultures were Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus vulgaris, Aeromonas

  11. PROFILE OF OCULAR TRAUMA IN UTTARAKHAND, A HOSPITAL BASED STUDY.

    Directory of Open Access Journals (Sweden)

    Renu Dhasmana

    2013-01-01

    Full Text Available Background: Although ocular trauma is preventable public health problem throughout the world it is still one of the common causes of ophthalmic morbidity and monocular blindness. There are no published studies on pattern and severity of ocular trauma in Uttarakhand. The present study analyzes the pattern and visual outcome of ocular trauma in this region. Methods: Study design: Prospective hospital-based study. Settings: Patients of ocular trauma presenting to Ophthalmology OPD and emergency department of Himalayan Institute of Medical Sciences, Dehradun. Participants: All ocular injury patients seen for the first time during the period January to December 2008. Results: A total of 88 patients, and 103 eyes, were studied. Men had two fold higher rate of ocular injury than women. The mean age of presentation was 31.2 + 13.6 years (range: 6 - 80 years. The predominant age group of patients was 21-40 years, 55.29 % (n = 47. Eye injuries related to road traffic accident were seen in 37.86% of eyes. Industrial workers were more frequently involved in ocular trauma (23.86%. Closed globe injuries were noted in 55 eyes (53.39% and open globe injuries were noted in 40 eyes (38.83%. Eight eyes (7.76% suffered from chemical injuries. The initial presenting visual acuity of patients with blunt ocular trauma was better than penetrating injury. Eye with better visual acuity at presentation had better visual prognosis at 6 months. Conclusion: Ocular injuries were common in young males. Road traffic accidents related eye injuries were noted in significant number of cases. Strict implementation of traffic rules, health education and preventive strategies may help to decrease the occurrence of ocular injuries.

  12. Binding equilibrium study of phosphotungstic acid and HSA or BSA with UV spectrum, fluorescence spectrum and equilibrium dialysis

    Institute of Scientific and Technical Information of China (English)

    黄瑾; 袁余洲; 梁宏

    2002-01-01

    The binding equilibrium between phosphotungstic acid (H7[P(W2O7)6]@XH2O;PTA) and human serum albumin (HSA) or bovine serum albumin (BSA) has been studied by UV-Vis, fluorescence spectroscopies and equilibrium dialysis. It has been observed that UV absorption enhanced and the fluorescence quenched as the PTA binding to HSA or BSA at physiological pH 7.43( ± 0.02). The Scatchard analysis indicated that there exists a strong binding site of PTA in both HSA and BSA, and the successive stability constants of these two systems are obtained by nonlinear least-squares methods fitting Bjerrum formula.

  13. Homology Modeling Study of Bovine μ-Calpain Inhibitor-Binding Domains

    Directory of Open Access Journals (Sweden)

    Han-Ha Chai

    2014-05-01

    Full Text Available The activated mammalian CAPN-structures, the CAPN/CAST complex in particular, have become an invaluable target model using the structure-based virtual screening of drug candidates from the discovery phase to development for over-activated CAPN linked to several diseases, such as post-ischemic injury and cataract formation. The effect of Ca2+-binding to the enzyme is thought to include activation, as well as the dissociation, aggregation, and autolysis of small regular subunits. Unfortunately, the Ca2+-activated enzyme tends to aggregate when provided as a divalent ion at the high-concentration required for the protease crystallization. This is also makes it very difficult to crystallize the whole-length enzyme itself, as well as the enzyme-inhibitor complex. Several parameters that influence CAPN activity have been investigated to determine its roles in Ca2+-modulation, autoproteolysis, phosphorylation, and intracellular distribution and inhibition by its endogenous inhibitor CAST. CAST binds and inhibits CAPN via its CAPN-inhibitor domains (four repeating domains 1–4; CAST1–4 when CAPN is activated by Ca2+-binding. An important key to understanding CAPN1 inhibition by CAST is to determine how CAST interacts at the molecular level with CAPN1 to inhibit its protease activity. In this study, a 3D structure model of a CAPN1 bound bovine CAST4 complex was built by comparative modeling based on the only known template structure of a rat CAPN2/CAST4 complex. The complex model suggests certain residues of bovine CAST4, notably, the TIPPKYQ motif sequence, and the structural elements of these residues, which are important for CAPN1 inhibition. In particular, as CAST4 docks near the flexible active site of CAPN1, conformational changes at the interaction site after binding could be directly related to CAST4 inhibitory activity. These functional interfaces can serve as a guide to the site-mutagenesis in research on bovine CAPN1 structure

  14. Chemical profile of crude oils in support of toxicity studies

    International Nuclear Information System (INIS)

    Acute and chronic exposure of fish to oil spills causes toxic effects at all life stages. Eighty per cent of the polycyclic aromatic hydrocarbons (PAHs) in oils are alkylated PAH compounds, requiring a specialized analysis for fingerprinting oil fractions. Fingerprinting provides important information for oil spill response to prevent exposure of fish to the most toxic oils. It helps determine the best control and remediation option. This study focused on characterizing the alkylphenanthrene class of PAH because it causes embryo-larval toxicity. The bioavailability of alkylphenanthrene was determined through a linear correlation between the capacity factor and LogP values in Mesa crude and ANS crude oils. The study makes it possible to predict the ecological risk of oil spills in aquatic ecosystems

  15. Cohort Profile: the Health and Retirement Study (HRS)

    OpenAIRE

    Sonnega, Amanda; Faul, Jessica D; Ofstedal, Mary Beth; Kenneth M. Langa; Phillips, John WR; David R Weir

    2014-01-01

    The Health and Retirement Study (HRS) is a nationally representative longitudinal survey of more than 37 000 individuals over age 50 in 23 000 households in the USA. The survey, which has been fielded every 2 years since 1992, was established to provide a national resource for data on the changing health and economic circumstances associated with ageing at both individual and population levels. Its multidisciplinary approach is focused on four broad topics—income and wealth; health, cognition...

  16. Cohort Profile: The Skin Cancer After Organ Transplant Study

    OpenAIRE

    Madeleine, Margaret M; Johnson, Lisa G.; Daling, Janet R.; Schwartz, Stephen M.; Carter, Joseph J.; Berg, Daniel; Nelson, Karen; Davis, Connie L.; Galloway, Denise A.

    2012-01-01

    The Skin Cancer after Organ Transplant (SCOT) study was designed to investigate the link between genus beta human papillomavirus (HPV) and squamous cell skin cancer (SCSC). We focused on a population receiving immunosuppressive therapy for extended periods, transplant patients, as they are at extremely high risk for developing SCSC. Two complementary projects were conducted in the Seattle area: (i) a retrospective cohort with interview data from 2004 recipients of renal or cardiac transplants...

  17. Urodynamic profile in myelopathies: A follow-up study

    Directory of Open Access Journals (Sweden)

    Gupta Anupam

    2009-01-01

    Full Text Available Aims: To study the significance of filling cystometry in assessment and management of neurogenic bladder in myelopathies and correlate neurological recovery and bladder management in the follow up. Study Design: Retrospective analysis of reports of filling cystometry in patients with traumatic and non-traumatic myelopathy. Setting: Neuro-rehabilitation unit of a tertiary care university hospital. Methods: The study was carried out between September 2005 and June 2006 and included all subjects with myelopathy who underwent filling cystometry. ASIA impairment scale was used to assess neurological status during admission as well as in the follow up. Bladder management was advised based on the cystometric findings. Neurological recovery and mode of bladder management were correlated during the follow up after a minimum of 6 months. Results: Fifty-two subjects (38 males, 14 females, mean age 33.26 ± 14.66 years (10-80 underwent filling cystometry. Twenty patients had cervical, 24 had thoracic and 8 had lumbar myelopathy. Cystometric findings were overactive detrusor observed in 43 patients, (21 had detrusor sphincter dyssynergia (DSD, 22 without DSD and areflexic/underactive detrusor in 9. Post-void residual (>15% of voided urine was significant in 27 patients. Twenty-three patients (44% reported for follow up (16 males, 7 females after a mean duration of 9.04 ± 2.44 months (6-15 months. Neurological recovery was seen in 61% cases, while 1 patient showed deterioration. Only 26% patients reported change in bladder management during follow up. Correlation between neurological recovery and bladder management was found to be insignificant ( P > 0.05 using spearman correlation co-efficient. Conclusions: Filling cystometry is valuable for assessment and management of neurogenic bladder after myelopathy. No significant relationship was observed between neurological recovery and neurogenic bladder management in the follow up in the present study.

  18. Study on the Credit Risk in Societies with Agricultural Profile

    Directory of Open Access Journals (Sweden)

    Jenica POPESCU

    2015-09-01

    Full Text Available The credit risk is one of the most important risks the banks face in their daily work and it has a direct impact on bank performance. In the current context, a bank has available a variety of options to determine capital requirements, to decrease the credit risk. This study aims to analyze the correlation of the main indicators of creditworthiness of firms and the credit risk, that a bank will take giving credit to these firms.

  19. Gene expression profiling in molecular studies of hormone actions

    OpenAIRE

    Ståhlberg, Nina

    2003-01-01

    Although the link between hormones and their physiological effects have been known for a long time, large pieces are still missing in our understanding of how these extracellular signals induce their effects at the cellular level. Signal transduction studies have gathered plenty of information about hormone signaling, but the complex network of interactions between different hormones, signaling pathways and cell types is still not completely understood. Advances in genome re...

  20. Cohort profile: the Cambridge Baby Growth Study (CBGS)

    OpenAIRE

    Prentice, P.; Acerini, C. L.; Eleftheriou, A.; Hughes, I A; Ong, K K; Dunger, D B

    2015-01-01

    The Cambridge Baby Growth Study has been supported by the European Union Framework V, the World Cancer Research Foundation International, the Medical Research Council, the NIHR Cambridge Comprehensive Biomedical Research Centre, the Newlife Foundation for disabled children, the Mothercare Group Foundation, Mead Johnson Nutrition, the Evelyn Trust, the Wellbeing of Women, Diabetes UK and a collaborative research grant from the European Society for Paediatric Endocrinology.

  1. Cohort Profile: The Nicotine Dependence in Teens (NDIT) Study.

    Science.gov (United States)

    O'Loughlin, Jennifer; Dugas, Erika N; Brunet, Jennifer; DiFranza, Joseph; Engert, James C; Gervais, Andre; Gray-Donald, Katherine; Karp, Igor; Low, Nancy C; Sabiston, Catherine; Sylvestre, Marie-Pierre; Tyndale, Rachel F; Auger, Nathalie; Auger, Nathalie; Mathieu, Belanger; Tracie, Barnett; Chaiton, Michael; Chenoweth, Meghan J; Constantin, Evelyn; Contreras, Gisèle; Kakinami, Lisa; Labbe, Aurelie; Maximova, Katerina; McMillan, Elizabeth; O'Loughlin, Erin K; Pabayo, Roman; Roy-Gagnon, Marie-Hélène; Tremblay, Michèle; Wellman, Robert J; Hulst, Andraeavan; Paradis, Gilles

    2015-10-01

    The Nicotine Dependence in Teens (NDIT) study is a prospective cohort investigation of 1294 students recruited in 1999-2000 from all grade 7 classes in a convenience sample of 10 high schools in Montreal, Canada. Its primary objectives were to study the natural course and determinants of cigarette smoking and nicotine dependence in novice smokers. The main source of data was self-report questionnaires administered in class at school every 3 months from grade 7 to grade 11 (1999-2005), for a total of 20 survey cycles during high school education. Questionnaires were also completed after graduation from high school in 2007-08 and 2011-12 (survey cycles 21 and 22, respectively) when participants were aged 20 and 24 years on average, respectively. In addition to its primary objectives, NDIT has embedded studies on obesity, blood pressure, physical activity, team sports, sedentary behaviour, diet, genetics, alcohol use, use of illicit drugs, second-hand smoke, gambling, sleep and mental health. Results to date are described in 58 publications, 20 manuscripts in preparation, 13 MSc and PhD theses and 111 conference presentations. Access to NDIT data is open to university-appointed or affiliated investigators and to masters, doctoral and postdoctoral students, through their primary supervisor (www.nditstudy.ca). PMID:25022274

  2. A Study on Sustainable Innovation Profile of Turkey

    Directory of Open Access Journals (Sweden)

    Pelin Vardarlier

    2015-12-01

    Full Text Available Innovation is the only way of solution to achieve sustainable growth, social welfare and employment in a country. This study principally focuses on the relationship between growth and innovation in the light of information derived from a general literature review about definition, sources and risks of innovation, and measurement of innovation performance. Then, the contributions of innovative capability on economic growth and employment as well as innovation systems on a country basis have been discussed, and accordingly, actions to be taken, including a shift in paradigm, for a growth-innovation-national innovation system and its sustainability have been addressed. In addition, current innovation performance indicators of Turkey have been discussed in the light of a scope which is outlined in the initial sections of the study, and the change in such performance indicators between 1998 and 2009 has been examined. After analysis of the above mentioned criteria and comparisons against practices in developed countries and communities, suggestions have been made about the activities to be carried out in order to make Turkey’s current innovation system “sustainable”, to support and improve innovation. In the study, a research application has been conducted using the content analysis method on the “President’s Message” letters of 158 state and foundation universities that are located in Turkey and that have a website, and the importance accorded to innovation by the universities has been determined.

  3. A Study on Sustainable Innovation Profile of Turkey

    Directory of Open Access Journals (Sweden)

    Pelin Vardarlier

    2015-10-01

    Full Text Available Innovation is the only way of solution to achieve sustainable growth, social welfare and employment in a country.This study principally focuses on the relationship between growth and innovation in the light of information derived from a general literature review about definition, sources and risks of innovation, and measurement of innovation performance. Then, the contribution of innovative capability on economic growth and employment as well as innovation systems on a country basis have been discussed, and accordingly, actions to be taken, including a shift in paradigm, for a growth-innovation-national innovation system and its sustainability have been addressed. In addition, current innovation performance indicators of Turkey have been discussed in the light of a scope which is outlined in the initial sections of the study, and the change in such performance indicators between 1998 and 2009 has been examined. After analysis of the above mentioned criteria and comparisons against practices in developed countries and communities, suggestions have been made about the activities to be carried out in order to make Turkey’s current innovation system “sustainable”, to support and improve innovation.In the study, a research application has been conducted using the content analysis method on the “President’s Message” letters of 158 state and foundation universities that are located in Turkey and that have a website, and the importance accorded to innovation by the universities has been determined. 

  4. Ellipsometric studies of synthetic albumin-binding chitosan-derivatives and selected blood plasma proteins

    Science.gov (United States)

    Sarkar, Sabyasachi

    This dissertation summarizes work on the synthesis of chitosan-derivatives and the development of ellipsometric methods to characterize materials of biological origin. Albumin-binding chitosan-derivatives were synthesized via addition reactions that involve amine groups naturally present in chitosan. These surfaces were shown to have an affinity towards human serum albumin via ELISA, UV spectroscopy and SDS PAGE. Modified surfaces were characterized with IR ellipsometry at various stages of their synthesis using appropriate optical models. It was found that spin cast chitosan films were anisotropic in nature. All optical models used for characterizing chitosan-derivatives were thus anisotropic. Chemical signal dependence on molecular structure and composition was illustrated via IR spectroscopic ellipsometry (IRSE). An anisotropic optical model of an ensemble of Lorentz oscillators were used to approximate material behavior. The presence of acetic acid in spin-cast non-neutralized chitosan samples was thus shown. IRSE application to biomaterials was also demonstrated by performing a step-wise chemical characterizations during synthesis stages. Protein adsorbed from single protein solutions on these modified surfaces was monitored by visible in-situ variable wavelength ellipsometry. Based on adsorption profiles obtained from single protein adsorption onto silicon surfaces, lumped parameter kinetic models were developed. These models were used to fit experimental data of immunoglobulin-G of different concentrations and approximate conformational changes in fibrinogen adsorption. Biomaterial characterization by ellipsometry was further extended to include characterization of individual protein solutions in the IR range. Proteins in an aqueous environment were characterized by attenuated total internal reflection (ATR) IR ellipsometry using a ZnSe prism. Parameterized dielectric functions were created for individual proteins using Lorentz oscillators. These

  5. A Descriptive Study on the Neonatal Morbidity Profile of Autism Spectrum Disorders, Including a Comparison with Other Neurodevelopmental Disorders

    Science.gov (United States)

    Atladóttir, H. Ó.; Schendel, D. E.; Parner, E. T.; Henriksen, T. B.

    2015-01-01

    The aim of this study was to describe the profile of specific neonatal morbidities in children later diagnosed with autism spectrum disorder (ASD), and to compare this profile with the profile of children with hyperkinetic disorder, cerebral palsy, epilepsy or intellectual disability. This is a Danish population based cohort study, including all…

  6. A STUDY ON THE MYCOLOGICAL PROFILE OF ONYCHOMYCOSIS

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    Saroj

    2012-12-01

    Full Text Available ABSTRACT: BACKGROUND: Onychomycosis refers to fungal infection of nails w ith various etiological agents, involving dermatophytes, yeasts and moulds. It constitutes an important health problem because of its rising prevalence and u nder-diagnosis especially in developing countries. AIMS: To analyse the mycological and cultural characteri stics of onychomycosis with respect to the various etiological agents. SETTINGS AND DESIGN: Nail samples collected from patients attending the dermatology clinic of Dr B.R Ambedkar medical college were processed in the microbiology department of Dr B.R Ambedkar medic al college. MATERIALS AND METHODS: Nail clippings and subungual scrapings of patients wi th onychomycosis were subjected to KOH preparation. Culture was done on Sab ouraud’s dextrose agar medium and Sabouraud’s dextrose agar with 5% chloramphenicol an d cycloheximide. Species identification was done by colony characteristics, pigment productio n, slide culture and LPCB stain. RESULTS: Out of 98 cases, 73 showed the growth of fungus, a mounting to 74.50% positivity. Among those 73 cases, the infective fungal agents pr edominantly were dermatophytes (54.80%, and the rest were due to yeasts (23.30% and moulds(22% . Among the different species, Trichophyton rubrum (43.84% accounted for the majority of dermatophytes; candida albicans (16.44% was the predominant yeast; and as pergillus niger (16.44% the commonest mould. The age group most commonly affected was 16-3 0yrs and males were commonly affected in our study. CONCLUSION: The present study highlights the need for microbiol ogical confirmation in case of onychomycosis for appropriate management of onychomycosis cases and further epidemiological study

  7. Study on the binding of colloidal zinc oxide nanoparticles with bovine serum albumin

    Science.gov (United States)

    Kathiravan, A.; Paramaguru, G.; Renganathan, R.

    2009-09-01

    The interaction between colloidal zinc oxide (ZnO) nanoparticles and bovine serum albumin (BSA) was studied by using absorption, fluorescence, Fourier transform infrared, synchronous and time resolved fluorescence spectroscopic measurements. The apparent association constant has been deduced ( Kapp = 1.1 × 10 4 M -1) from the absorption spectral changes of BSA-colloidal ZnO nanoparticles using Benesi-Hildebrand equation. Addition of colloidal ZnO nanoparticles effectively quenched the intrinsic fluorescence of BSA. The number of binding sites ( n = 1.06) and apparent binding constant ( K = 2.5 × 10 4 M -1) were calculated by relevant fluorescence data. Based on Forster's non-radiation energy transfer theory, distance between the donor (BSA) and acceptor (ZnO) ( r0 = 2.88 nm) as well as the critical energy transfer distance ( R0 = 2.49 nm) has also been calculated. The interaction between colloidal ZnO and BSA occurs through static quenching mechanism. The effect of colloidal ZnO nanoparticles on the conformation of BSA has been analyzed by means of UV-visible absorption spectra and synchronous fluorescence spectra.

  8. DNA binding studies of 3, 5, 6-trichloro-2-pyridinol pesticide metabolite.

    Science.gov (United States)

    Kashanian, Soheila; Shariati, Zohreh; Roshanfekr, Hamideh; Ghobadi, Sirous

    2012-07-01

    3, 5, 6-Trichloro-2-pyridinol (TCP) is a stable metabolite of two major pesticides, Chlopyrifos insecticide and Triclopyr herbicide, which are widely used in the world. The potential health hazard associated with TCP is identified due to its high affinity to the DNA molecule. Therefore, in this study, the interaction of native calf thymus DNA with TCP has been investigated using spectrophotometric, circular dichroism (CD), spectrofluorometric, viscometric and voltametric techniques. It was found that TCP molecules could interact with DNA via a groove-binding mode, as evidenced by hyperchromism, with no red shift in the UV absorption band of TCP, no changes in K(b) values in the presence of salt, no significant changes in the specific viscosity and CD spectra of DNA, and a decrease in peak currents with no shift in the voltamogram. In addition, TCP is able to release Hoechst 33258, a strong groove binder, in the DNA solutions. The results are indicative of the groove-binding mode of TCP to DNA. PMID:22519761

  9. Study of Binding Interaction between Pif80 Protein Fragment and Aragonite

    Science.gov (United States)

    Du, Yuan-Peng; Chang, Hsun-Hui; Yang, Sheng-Yu; Huang, Shing-Jong; Tsai, Yu-Ju; Huang, Joseph Jen-Tse; Chan, Jerry Chun Chung

    2016-08-01

    Pif is a crucial protein for the formation of the nacreous layer in Pinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of β-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization.

  10. Protein profile study of the cervical cancer using HPLC-LIF

    Science.gov (United States)

    Sujatha; Rai, Lavanya; Krishnanand, B. R.; Mahato, K. K.; Kartha, V. B.; C, Santhosh

    2006-02-01

    Optical methods and proteomics investigations are becoming promising approaches for early detection of many diseases, which remain clinically silent for long periods. We have used efficient High Performance Liquid Chromatography (HPLC) separation combined with highly sensitive laser induced fluorescence detection of proteins present in clinical samples for diagnostic applications in cervical cancer. The protein profile and the fluorescence of individual proteins were simultaneously recorded using our HPLC-LIF system. Protein profiles (Chromatogram) of serum from normal male and female volunteers with and without tobacco habits, and malignant serum samples were studied. Protein profiles were also recorded for lysates of exfoliated cells collected from Pap smear of normal and cancer patients. The protein profile patterns were subjected to Principal component Analysis. Discrimination of normal and malignant samples were achieved with very high sensitivity and specificity.

  11. Study of radiation exposure profiles in interventional radiology professionals

    International Nuclear Information System (INIS)

    Interventional Radiology is the radiology area that provides the highest dose values to the medical staff. Recent surveys show that personal dosimeters may underestimate the radiation dose values in interventional physicians, especially in the extremities and crystalline. The objective of this work was to study the exposure levels to radiation from medical staff in different interventional radiology procedures. Therefore, thermoluminescent dosimeters type LiF: Mg, Ti (TLD-100) were used positioned in the main interventional physician and an assistant in the following locations: some inches below the crystalline, thyroid, chest, gonads, hand and foot. By comparing the values obtained with the annual reference dose levels in workers, maximum numbers of annual procedures were found. Altogether, there were 23 procedures evaluated: 10 diagnostics, 9 angioplasties and 4 stents. The maximum number of annual procedures were estimated by discounting the percentages of attenuation of radiological protection. For procedures of the type diagnosis, angioplasty and stent for the main interventionist, the maximum number of annual procedures were 641, 445 and 113 respectively, while for the interventionists assistants were 930, 1202 and 215 respectively. As each interventionist body region is subject to different levels of exposure, detailed studies of exposure in each region provide better conclusions about what actions are necessary to ensure radiological protection professionals

  12. A STUDY OF EFFECT OF LEKHANIYA MAHAKASHAYA ON LIPID PROFILE

    Directory of Open Access Journals (Sweden)

    Kumar Naresh

    2012-12-01

    Full Text Available Many of the heart diseases are closely associated with rise in the level of serum lipids, the condition known as ‘hyperlipidaemia’ which further leads to atherosclerosis. In Ayurvedic view, hyperlipidaemia could be considered analogous with increased dusht medo dhatu in the body which is caused by hypo functioning of medo-dhaatwaghi. According to Sharangdhara, any drug possessing laghu and tikshana properties, katu vipaka and ushana virya performs lekhan karma i.e. curretive and absorptive action on Dosha, Dhatu and Mala. Along with lekhan karma, owing to above said attributes, these drugs improve strength of agni particularly Jathragni and dhaatwagni which further reduces and ultimately stops production of Dhust Medo Dhatu in the body. The Lekhaniya Mahakashaya, mentioned in Charaka Samhita possesses above mentioned characteristics. The only need was to prove its hypolipidaemic effect in human body by conducting clinical trials. The present study proved this fact.

  13. STUDY OF SINGLE-LOBED CIRCULAR POLARIZATION PROFILES IN THE QUIET SUN

    Energy Technology Data Exchange (ETDEWEB)

    Sainz Dalda, A. [Stanford-Lockheed Institute for Space Research, Stanford University, HEPL, 466 Via Ortega, Stanford, CA 94305-4085 (United States); Martinez-Sykora, J.; Title, A. [Lockheed Martin Solar and Astrophysics Laboratory, 3176 Porter Dr., Palo Alto, CA 94304 (United States); Bellot Rubio, L., E-mail: asdalda@stanford.edu, E-mail: asainz@lmsal.com [Instituto de Astrofisica de Andalucia, CSIC, Apdo. 3004, 18080 Granada (Spain)

    2012-03-20

    The existence of asymmetries in the circular polarization (Stokes V) profiles emerging from the solar photosphere has been known since the 1970s. These profiles require the presence of a velocity gradient along the line of sight (LOS), possibly associated with gradients of magnetic field strength, inclination, and/or azimuth. We have focused our study on the Stokes V profiles showing extreme asymmetry in the form of only one lobe. Using Hinode spectropolarimetric measurements, we have performed a statistical study of the properties of these profiles in the quiet Sun. We show their spatial distribution, their main physical properties, how they are related with several physical observables, and their behavior with respect to their position on the solar disk. The single-lobed Stokes V profiles occupy roughly 2% of the solar surface. For the first time, we have observed their temporal evolution and have retrieved the physical conditions of the atmospheres from which they emerged using an inversion code implementing discontinuities of the atmospheric parameters along the LOS. In addition, we use synthetic Stokes profiles from three-dimensional magnetoconvection simulations to complement the results of the inversion. The main features of the synthetic single-lobed profiles are in general agreement with the observed ones, lending support to the magnetic and dynamic topologies inferred from the inversion. The combination of all these different analyses suggests that most of the single-lobed Stokes V profiles are signals coming from the magnetic flux emergence and/or submergence processes taking place in small patches in the photosphere of the quiet Sun.

  14. Binding of Cu(II) ions to peptides studied by fluorescence spectroscopy and isothermal titration calorimetry.

    Science.gov (United States)

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech

    2016-01-15

    Steady-state and time-resolved fluorescence quenching measurements supported by Isothermal Titration Calorimetry (ITC) were used to study the interactions of Cu(2+) with four peptides. Two of them were taken from the N-terminal part of the FBP28 protein (formin binding protein) WW domain: Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr-NH2 (D9) and its mutant Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr-NH2 (D9_M) as well as two mutated peptides from the B3 domain of the immunoglobulin binding protein G derived from Streptococcus: Asp-Val-Ala-Thr-Tyr-Thr-NH2 (J1) and Glu-Val-Ala-Thr-Tyr-Thr-NH2 (J2). The measurements were carried out at 298.15K in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution with a pH of 6. The fluorescence of all peptides was quenched by Cu(2+) ions. The stoichiometry, conditional stability constants and thermodynamic parameters for the interactions of the Cu(2+) ions with D9 and D9_M were determined from the calorimetric data. The values of the conditional stability constants were additionally determined from fluorescence quenching measurements and compared with those obtained from calorimetric studies. There was a good correlation between data obtained from the two techniques. On the other hand, the studies revealed that J1 and J2 do not exhibit an affinity towards metal ions. The obtained results prove that fluorescence quenching experiments may be successfully used in order to determine stability constants of complexes with fluorescent ligands. Finally, based on the obtained results, the coordinating properties of the peptides towards the Cu(2+) ions are discussed. PMID:26363471

  15. Inhibition of [(11)C]mirtazapine binding by alpha(2)-adrenoceptor antagonists studied by positron emission tomography in living porcine brain

    DEFF Research Database (Denmark)

    Smith, Donald F.; Dyve, Suzan; Minuzzi, Luciano;

    2006-01-01

    We have developed [(11)C]mirtazapine as a ligand for PET studies of antidepressant binding in living brain. However, previous studies have determined neither optimal methods for quantification of [(11)C]mirtazapine binding nor the pharmacological identity of this binding. To obtain that informati...... brain. Synapse 59:463-471, 2006. (c) 2006 Wiley-Liss, Inc....

  16. Upregulated GABA inhibitory function in AD/HD children with Child Behavior Checklist–Dysregulation Profile: 123I-iomazenil SPECT study

    Directory of Open Access Journals (Sweden)

    Shinichiro eNagamitsu

    2015-06-01

    Full Text Available The Child Behavior Checklist–Dysregulation Profile (CBCL-DP refers to a pattern of elevated scores on the Attention Problems, Aggression, and Anxiety/Depression subscales of the Child Behavior Checklist. The aim of the present study was to investigate the potential role of GABA inhibitory neurons in children with attention deficit/hyperactivity disorder (AD/HD and dysregulation assessed with a dimensional measure. Brain single photon emission computed tomography (SPECT was performed in 35 children with AD/HD using 123I-iomazenil, which binds with high affinity to benzodiazepine receptors. Iomazenil binding activities were assessed with respect to the presence or absence of a threshold CBCL-DP (a score ≥210 for the sum of the three subscales Attention Problems, Aggression, and Anxiety/Depression. We then attempted to identify which CBCL-DP subscale explained the most variance with respect to SPECT data, using age, sex, and history of maltreatment as covariates. Significantly higher iomazenil binding activity was seen in the posterior cingulate cortex (PCC of AD/HD children with a significant CBCL-DP. The Anxiety/Depression subscale on the CBCL had significant effects on higher iomazenil binding activity in the left superior frontal, middle frontal, and temporal regions, as well as in the PCC. The present brain SPECT findings suggest that GABAergic inhibitory neurons may play an important role in the neurobiology of the CBCL-DP, in children with ADHD.

  17. X-ray diffraction study of the binding of the antisickling agent 12C79 to human hemoglobin

    International Nuclear Information System (INIS)

    The hemoglobin binding site of the antisickling agent 12C79 has been determined by x-ray crystallography. 12C79 is recognized as one of the first molecules to reach clinical trials that was designed, de novo, from x-ray-determined atomic coordinates of a protein. Several previous attempts to verify the proposed Hb binding sites via crystallographic studies have failed. Using revised experimental procedures, the authors obtained 12C79-deoxhemoglobin crystals grown after reaction with oxyhemoglobin and cyanoborohydride reduction to stabilize the Schiff base linkage. The difference electron-density Fourier maps show that two 12C79 molecules bind covalently to both symmetry-related N-terminal amino groups of the hemoglobin α chains. This is in contrast to the original design that proposed the binding of one drug molecule that spans the molecular dyad to interact with both N-terminal α-amino groups

  18. Investigations of acetaminophen binding to bovine serum albumin in the presence of fatty acid: Fluorescence and 1H NMR studies

    Science.gov (United States)

    Bojko, B.; Sułkowska, A.; Maciążek-Jurczyk, M.; Równicka, J.; Sułkowski, W. W.

    2009-04-01

    The binding of acetaminophen to bovine serum albumin (BSA) was studied by the quenching fluorescence method and the proton nuclear magnetic resonance technique ( 1H NMR). For fluorescence measurements 1-anilino-9-naphthalene sulfonate (ANS) hydrophobic probe was used to verify subdomain IIIA as acetaminophen's likely binding site. Three binding sites of acetaminophen in subdomain IIA of bovine serum albumin were found. Quenching constants calculated by the Stern-Volmer modified method were used to estimate the influence of myristic acid (MYR) on the drug binding to the albumin. The influence of [fatty acid]/[albumin] molar ratios on the affinity of the protein towards acetaminophen was described. Changes of chemical shifts and relaxation times of the drug indicated that the presence of MYR inhibits interaction in the AA-albumin complex. It is suggested that the elevated level of fatty acids does not significantly influence the pharmacokinetics of acetaminophen.

  19. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host–Guest Binding Study

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei

    2016-06-17

    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 x 103 M-1) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity.

  20. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host-Guest Binding Study.

    Science.gov (United States)

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei

    2016-06-17

    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 × 10(3) M(-1)) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity. PMID:27267936

  1. The Binding of Iron to Perineuronal Nets: A Combined Nuclear Microscopy and Moessbauer Study

    Energy Technology Data Exchange (ETDEWEB)

    Morawski, M. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Reinert, T. [Universitaet Leipzig, Fakultaet fuer Physik und Geowissenschaften (Germany); Brueckner, G. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Wagner, F. E. [Technische Universitaet Muenchen, Physik-Department E15 (Germany); Arendt, T. H. [Universitaet Leipzig, Paul Flechsig Institute fuer Hirnforschung (Germany); Troeger, W., E-mail: troeger@physik.uni-leipzig.de [Universitaet Leipzig, Fakultaet fuer Physik und Geowissenschaften (Germany)

    2004-12-15

    A specialized form of extracellular matrix (ECM) surrounds subpopulations of neurons termed 'perineuronal nets' (PNs). These PNs form highly anionic charged structures in the direct microenvironment of neurons, assumed to be involved in local ion homeostasis since they are able to scavenge and bind redox-active iron ions. The quantity and distribution of iron-charged PNs of the extracellular matrix in the rat brain areas of the cortex and the red nucleus was investigated using the powerful combination of Particle-Induced X-ray Emission (PIXE) and Moessbauer spectroscopy. These studies reveal that the iron is bound to the PNs as Fe(III). PNs in both brain regions accumulate up to three to five times more Fe{sup 3+} than any other tissue structure in dependency on the applied Fe concentration with local amount maximums of 480 mmol/l Fe at PNs.

  2. The Binding of Iron to Perineuronal Nets: A Combined Nuclear Microscopy and Moessbauer Study

    International Nuclear Information System (INIS)

    A specialized form of extracellular matrix (ECM) surrounds subpopulations of neurons termed 'perineuronal nets' (PNs). These PNs form highly anionic charged structures in the direct microenvironment of neurons, assumed to be involved in local ion homeostasis since they are able to scavenge and bind redox-active iron ions. The quantity and distribution of iron-charged PNs of the extracellular matrix in the rat brain areas of the cortex and the red nucleus was investigated using the powerful combination of Particle-Induced X-ray Emission (PIXE) and Moessbauer spectroscopy. These studies reveal that the iron is bound to the PNs as Fe(III). PNs in both brain regions accumulate up to three to five times more Fe3+ than any other tissue structure in dependency on the applied Fe concentration with local amount maximums of 480 mmol/l Fe at PNs.

  3. A longitudinal study of serum cobalamins and its binding proteins in lactating women

    DEFF Research Database (Denmark)

    Mørkbak, A L; Ramlau-Hansen, C H; Møller, U K; Henriksen, T B; Møller, Jan; Nexø, E

    2006-01-01

    OBJECTIVE: To examine longitudinal changes in serum cobalamins, transcobalamin (TC) and haptocorrin (HC) during lactation and to investigate the influence of vitamin B12 supplementation on these parameters. DESIGN: A 9-month follow-up study. SUBJECTS AND METHODS: Lactating mothers (N=89) including...... 23 supplemented with vitamin B12 (1-18 microg/daily), 41 partly supplemented and 25 not supplemented. Blood samples collected 3 weeks (baseline) and 4 and 9 months post-partum were analysed for cobalamins, TC and HC. Both the total concentration and the cobalamin-saturated form (holo) of TC and HC...... were analysed. RESULTS: No significant differences were observed in serum cobalamins or its binding proteins related to supplementation with vitamin B12 or the duration of lactation. Serum cobalamins remained unchanged from 3 weeks to 9 months post-partum. Total TC (holoTC) (median+/-s.e. pmol...

  4. Optical Nanofiber Integrated into Optical Tweezers for In Situ Fiber Probing and Optical Binding Studies

    Directory of Open Access Journals (Sweden)

    Ivan Gusachenko

    2015-07-01

    Full Text Available Precise control of particle positioning is desirable in many optical propulsion and sorting applications. Here, we develop an integrated platform for particle manipulation consisting of a combined optical nanofiber and optical tweezers system. We show that consistent and reversible transmission modulations arise when individual silica microspheres are introduced to the nanofiber surface using the optical tweezers. The observed transmission changes depend on both particle and fiber diameter and can be used as a reference point for in situ nanofiber or particle size measurement. Thence, we combine scanning electron microscope (SEM size measurements with nanofiber transmission data to provide calibration for particle-based fiber assessment. This integrated optical platform provides a method for selective evanescent field manipulation of micron-sized particles and facilitates studies of optical binding and light-particle interaction dynamics.

  5. A molecular dynamics study of chloride binding by the cryptand SC24

    Science.gov (United States)

    Owenson, B.; MacElroy, R. D.; Pohorille, A.

    1988-01-01

    The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.

  6. Changing Occupational Profiles in the Hotel Industry: Case Studies in France, Italy and Spain. Synthesis Report.

    Science.gov (United States)

    Gatti, Mario; Grazia Mereu, Maria; Tagliaferro, Claudio

    Changing occupational profiles in the hotel industry in France, Italy, and Spain were examined in case studies that included interviews with hotel managers, human resource managers, and individuals employed in hotel occupations identified as new or entailing new skills. The study focused on the following topics: (1) changes in the hotel industry…

  7. A Profile of an Effective Teacher of English: A Qualitative Study from Poland

    Science.gov (United States)

    Werbinska, Dorota

    2009-01-01

    This paper presents and discusses a research study aimed at defining the profile of an effective Polish teacher of English. The study, which is qualitative in nature, has been conducted among English language teachers in Poland who are considered excellent in their professional environment. Their kinds of knowledge and their beliefs about the…

  8. A study to evaluate cephalometric hard tissue profile of Tamil population for orthognathic surgery

    OpenAIRE

    Nachiappan, S; Tharanikumar, S.; Chandran, Ajay; Anusudha, P.; Nandini, G. D.; Balasubramaniam, Murali

    2015-01-01

    The primary aim of this study is to compare, the cephalometric hard tissue profile values and analysis between Tamil and Caucasian population. The study also aims to create a better understanding in the facial proportions of Tamil Nadu population and to have better diagnosis and treatment planning for orthognathic surgery for Tamil population in Tamil Nadu.

  9. Co(III and Ni(II Complexes Containing Bioactive Ligands: Synthesis, DNA Binding, and Photocleavage Studies

    Directory of Open Access Journals (Sweden)

    M. C. Prabhakara

    2007-02-01

    Full Text Available DNA binding and photocleavage characteristics of a series of mixed ligand complexes of the type [M(bpy2qbdp](PF6n⋅xH2O (where M=Co(III or Ni(II, bpy=2.2′-bipryidine, qbdp = Quinolino[3,2-b]benzodiazepine, n=3 or 2 and x=5 or 2 have been investigated. The DNA binding property of the complexes with calf thymus DNA has been investigated by using absorption spectra, viscosity measurements, as well as thermal denaturation studies. Intrinsic binding constant (Kb has been estimated under similar set of experimental conditions. Absorption spectral studies indicate that the Co(III and Ni(II complexes intercalate between the base pairs of the CT-DNA tightly with intrinsic DNA binding constant of 1.3×106 and 3.1×105 M-1 in Tris-HCl buffer containing 50 mM NaCl, respectively. The proposed DNA binding mode supports the large enhancement in the relative viscosity of DNA on binding to quinolo[3,2-b]benzodiazepine. The oxidative as well as photo-induced cleavage reactions were monitered by gel electrophoresis for both complexes. The photocleavage experiments showed that the cobalt(III complex can cleave pUC19 DNA effectively in the absence of external additives as an effective inorganic nuclease.

  10. Studies on the hyaluronate binding properties of newly synthesized proteoglycans purified from articular chondrocyte cultures

    Energy Technology Data Exchange (ETDEWEB)

    Sandy, J.D.; Plaas, A.H.

    1989-06-01

    Primary cultures of rabbit articular chondrocytes have been maintained for 10 days and labeled with (35S)sulfate, (3H)leucine, and (35S)cysteine in pulse-chase protocols to study the structure and hyaluronate binding properties of newly synthesized proteoglycan monomers. Radiolabeled monomers were purified from medium and cell-layer fractions by dissociative CsCl gradient centrifugation with bovine carrier monomer, and analyzed for hyaluronate binding affinity on Sepharose CL-2B in 0.5 M Na acetate, 0.1% Triton X-100, pH 6.8. Detergent was necessary to prevent self-association of newly synthesized monomers during chromatography. Monomers secreted during a 30-min pulse labeling with (35S)sulfate had a low affinity relative to carrier. Those molecules released into the medium during the first 12 h of chase remained in the low affinity form whereas those retained by the cell layer rapidly acquired high affinity. In cultures where more than 90% of the preformed cell-layer proteoglycan was removed by hyaluronidase digestion before radiolabeling the newly synthesized low affinity monomers also rapidly acquired high affinity if retained in the cell layer. Cultures labeled with amino acid precursors were used to establish the purity of monomer preparations and to isolate core proteins for study. Leucine- or cysteine-labeled core proteins derived from either low or high affinity monomer preparations migrated as a single major species on sodium dodecyl sulfate-polyacrylamide gel electrophoresis with electrophoretic mobility very similar to that of core protein derived from extracted proteoglycan monomer. Purified low affinity monomers were converted to the high affinity form by treatment at pH 8.6; however, this change was prevented by guanidinium-HCl at concentrations above 0.8 M.

  11. Effect of tetrahydrocurcumin on insulin receptor status in type 2 diabetic rats: studies on insulin binding to erythrocytes

    Indian Academy of Sciences (India)

    Pidaran Murugan; Leelavinothan Pari; Chippada Appa Rao

    2008-03-01

    Curcumin is the most active component of turmeric. It is believed that curcumin is a potent antioxidant and anti-inflammatory agent. Tetrahydrocurcumin (THC) is one of the major metabolites of curcumin, and exhibits many of the same physiological and pharmacological activities as curcumin and, in some systems, may exert greater antioxidant activity than curcumin. Using circulating erythrocytes as the cellular mode, the insulin-binding effect of THC and curcumin was investigated. Streptozotocin (STZ)–nicotinamide-induced male Wistar rats were used as the experimental models. THC (80 mg/kg body weight) was administered orally for 45 days. The effect of THC on blood glucose, plasma insulin and insulin binding to its receptor on the cell membrane of erythrocytes were studied. Mean specific binding of insulin was significantly lowered in diabetic rats with a decrease in plasma insulin. This was due to a significant decrease in mean insulin receptors. Erythrocytes from diabetic rats showed a decreased ability for insulin–receptor binding when compared with THC-treated diabetic rats. Scatchard analysis demonstrated that the decrease in insulin binding was accounted for by a decrease in insulin receptor sites per cell, with erythrocytes of diabetic rats having less insulin receptor sites per cell than THC-treated rats. High affinity (Kd1), low affinity (Kd2) and kinetic analyses revealed an increase in the average receptor affinity of erythrocytes from THC-treated rats compared with those of diabetic rats. These results suggest that acute alteration of the insulin receptor on the membranes of erythrocytes occurred in diabetic rats. Treatment with THC significantly improved specific insulin binding to the receptors, with receptor numbers and affinity binding reaching near-normal levels. Our study suggests the mechanism by which THC increases the number of total cellular insulin binding sites resulting in a significant increase in plasma insulin. The effect of THC is

  12. Alteration in plasma lipid profile in oral submucous fibrosis patients: A case control study

    Directory of Open Access Journals (Sweden)

    Pramod Kumar

    2013-01-01

    Full Text Available Background: Lipids are major cell membrane components essential for various biological functions including cell growth and division of normal and malignant tissue. They are also required for maintenance of structural and functional integrity of all biological membranes. Alteration in the plasma lipid profile has been associated with a variety of cancers and precancerous conditions including those of the head and neck region. Aim: The present study aimed to evaluate the alteration in plasma lipid profile in oral submucous fibrosis (OSF patients. Materials and Methods: A total of 30 patients were included in the study, 20 with oral submucous fibrosis and 10 healthy controls. Fasting plasma lipid profile including Total Cholesterol (TC, Very Low Density Lipoproteins (VLDL, Low Density Lipoproteins (LDL, High Density Lipoproteins (HDL and Tri-Glycerides (TG were measured using semiautomatic analyser. The data obtained were analysed using independent sample ′t′ test. Results: A statistically significant decrease in plasma total cholesterol, LDL and HDL was observed in patients with OSMF as compared to the controls, but it was not statistically significant for VLDL and TG values. Conclusion: The results of the present study show that there is an inverse relationship between lipid profile and the presence of oral submucous fibrosis. Hence, alteration in plasma lipid profile may have a diagnostic role in the future and can be used as a biochemical indicator to detect the initial changes seen in the neoplastic process..

  13. TOLNET – A Tropospheric Ozone Lidar Profiling Network for Satellite Continuity and Process Studies

    Directory of Open Access Journals (Sweden)

    Newchurch Michael J.

    2016-01-01

    Full Text Available Ozone lidars measure continuous, high-resolution ozone profiles critical for process studies and for satellite validation in the lower troposphere. However, the effectiveness of lidar validation by using single-station data is limited. Recently, NASA initiated an interagency ozone lidar observation network under the name TOLNet to promote cooperative multiple-station ozone-lidar observations to provide highly timeresolved (few minutes tropospheric-ozone vertical profiles useful for air-quality studies, model evaluation, and satellite validation. This article briefly describes the concept, stations, major specifications of the TOLNet instruments, and data archiving.

  14. TOLNET - A Tropospheric Ozone Lidar Profiling Network for Satellite Continuity and Process Studies

    Science.gov (United States)

    Newchurch, Michael J.; Kuang, Shi; Leblanc, Thierry; Alvarez, Raul J.; Langford, Andrew O.; Senff, Christoph J.; Burris, John F.; McGee, Thomas J.; Sullivan, John T.; DeYoung, Russell J.; Al-Saadi, Jassim; Johnson, Matthew; Pszenny, Alex

    2016-06-01

    Ozone lidars measure continuous, high-resolution ozone profiles critical for process studies and for satellite validation in the lower troposphere. However, the effectiveness of lidar validation by using single-station data is limited. Recently, NASA initiated an interagency ozone lidar observation network under the name TOLNet to promote cooperative multiple-station ozone-lidar observations to provide highly timeresolved (few minutes) tropospheric-ozone vertical profiles useful for air-quality studies, model evaluation, and satellite validation. This article briefly describes the concept, stations, major specifications of the TOLNet instruments, and data archiving.

  15. Lysine-functionalized nanodiamonds: synthesis, physiochemical characterization, and nucleic acid binding studies

    Directory of Open Access Journals (Sweden)

    Kaur R

    2012-07-01

    . These modified NDs formed highly stable aqueous dispersions with a zeta potential of 49 mV and particle size of approximately 20 nm. The functionalized NDs were found to be able to bind plasmid DNA and small interfering RNA by forming nanosized "diamoplexes".Conclusion: The lysine-substituted ND particles generated in this study exhibit stable aqueous formulations and show potential for use as carriers for genetic materials.Keywords: disaggregation, spectroscopy, dispersion, electrophoresis, size, zeta potential

  16. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun

    2015-06-11

    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  17. Single-pulse and profile-variability study of PSR J1022+1001

    Science.gov (United States)

    Liu, K.; Karuppusamy, R.; Lee, K. J.; Stappers, B. W.; Kramer, M.; Smits, R.; Purver, M. B.; Janssen, G. H.; Perrodin, D.

    2015-05-01

    Millisecond pulsars (MSPs) are known as highly stable celestial clocks. Nevertheless, recent studies have revealed the unstable nature of their integrated pulse profiles, which may limit the achievable pulsar timing precision. In this article, we present a case study on the pulse-profile variability of PSR J1022+1001. We have detected approximately 14 000 subpulses (components of single pulses) in 35-h long observations, mostly located in the trailing component of the integrated profile. Their flux densities and fractional polarization suggest that they represent the bright end of the energy distribution in ordinary emission mode and are not giant pulses. The occurrence of subpulses in the leading and trailing components of the integrated profile is shown to be correlated. For subpulses from the latter, a preferred pulse width of approximately 0.25 ms has been found. Using simultaneous observations from the Effelsberg 100-m telescope and the Westerbork Synthesis Radio Telescope, we have found that the integrated profile varies on a time-scale of a few tens of minutes. We show that improper polarization calibration and diffractive scintillation cannot be the sole reason for the observed instability. In addition, we demonstrate that timing residuals generated from averages of the detected subpulses are dominated by phase jitter and we place an upper limit of ˜700 ns on jitter noise, based on continuous 1-min integrations.

  18. Validation of Association between Breastfeeding Duration, Facial Profile, Occlusion, and Spacing: A Cross-sectional Study

    Science.gov (United States)

    Sharma, Mohit; Nehra, Karan; Jayan, Balakrishna; Poonia, Anish; Bhattal, Hiteshwar

    2016-01-01

    ABSTRACT Introduction: This cross-sectional retrospective study was designed to assess the relationships among breastfeeding duration, nonnutritive sucking habits, convex facial profile, nonspaced dentition, and distoclusion in the deciduous dentition. Materials and methods: A sample of 415 children (228 males, 187 females) aged 4 to 6 years from a mixed Indian population was clinically examined by two orthodontists. Information about breastfeeding duration and nonnutritive sucking habits was obtained by written questionnaire which was answered by the parents. Results: Chi-square test did not indicate any significant association among breastfeeding duration, convex facial profile, and distoclusion. Statistically significant association was observed between breastfeeding duration and nonspaced dentition and also between breastfeeding duration and nonnutritive sucking habits. Nonnutritive sucking habits had a statistically significant association with distoclusion and convex facial profile (odds ratio 7.04 and 4.03 respectively). Nonnutritive sucking habits did not have a statistically significant association with nonspaced dentition. Conclusion: The children breastfed 6 months duration. It can also be hypothesized that nonnutritive sucking habits may act as a dominant variable in the relationship between breastfeeding duration and occurrence of convex facial profile and distoclusion in deciduous dentition. How to cite this article: Agarwal SS, Sharma M, Nehra K, Jayan B, Poonia A, Bhattal H. Validation of Association between Breastfeeding Duration, Facial Profile, Occlusion, and Spacing: A Cross-sectional Study. Int J Clin Pediatr Dent 2016;9(2):162-166. PMID:27365941

  19. TO STUDY ASSOCIATION BETWEEN LIPID PROFILE IN VEGETARIANS AND NON - VEGETARIANS IN THE LOCAL POPULATION

    Directory of Open Access Journals (Sweden)

    Seemadevi

    2015-04-01

    Full Text Available BACKGROUND: To Study Association b etween Lipid Profile i n Vegetarians a nd Non - Vegetarians in t he Local Population . MATERIALS AND METHODS: Descriptive study was conducted in the area Chittur from April 2014 to April 2015. One hundred and fifty (75 vegetarians and 75 non - vegetarians healthy individuals, aged 30 – 60 years we re studied in the central lab o f Karuna Medical College. Overnight fasting venous blood samples were collected for estimating. Fasting Blood Sugar (FBS, Serum Alanine Transaminase (ALT and , Serum lipid profile. RESULTS: The mean age of the study subjects was 38 and 37 of the vegetarians and non - vegetarians respectively with normal serum ALT. The vegetarians subjects had signifi cantly lower mean serum Total Cholesterol (TC [mean difference (95% CI] [ - 0 . 42 ( - 0 . 78, - 0 . 06] and LDL [ - 0 . 45 ( - 0 . 75, - 0 . 15] compared to non - vegetarians . However, triglyceride, HDL, FBS, were identical . In Pearson’s correlation, consumption of vegetable diet significantly correlated with serum TC, LDL. CONCLUSION: I n our study the vegetarian study have a lower lipid profile status as compared to the non - vegetarian subjects. Therefore consumption of a vegetarian diet has to be encouraged . KEYWORDS: Chittu r; Vegetarian; Non Vegetarian Lipid Profile .

  20. Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate

    Science.gov (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya

    2015-08-01

    A new binuclear O-bridged Cu(II) complex with 4-chlorophenyl acetate and 2,2‧-bipyridine has been synthesized and characterized using FT-IR, powder and single crystal XRD and electrochemical solution studies. The results revealed that the two penta-coordinated Cu(II) centers are linked by two carboxylate ligands in end-on bonding fashion. The coordination geometry is slightly distorted square pyramidal (SP) with bridging oxygen atoms occupying the apical position and other ligands lying in the equatorial plane. The striking difference in Cu-O bond distance of the bridging oxygen atom in the complex may be responsible for the SP geometry of Cu(II) ion. The complex gave rise to metal centered irreversible electro-activity where one electron Cu(II)/Cu(III) oxidation process and a single step two electron Cu(II)/Cu(0) reduction process was observed. The redox processes were found predominantly adsorption controlled. The values of diffusion coefficient and heterogeneous rate constant for oxidation process were 6.98 × 10-7 cm2 s-1 and 4.60 × 10-5 cm s-1 while the corresponding values for reduction were 5.30 × 10-8 cm2 s-1 and 5.41 × 10-6 cm s-1, respectively. The formal potential and charge transfer coefficient were also calculated. The DNA-binding ability was explored through cyclic voltammetry and UV-Visible spectroscopy. Diminution in the value of Do for oxidation indicated the binding of the complex with DNA corresponding to Kb = 8.58 × 104 M-1. UV-Visible spectroscopy yielded ε = 49 L mol-1 cm-1 and Kb = 2.96 × 104 M-1. The data of both techniques support each other. The self-induced redox activation of the complex, as indicated by cyclic voltammetry heralds its potential applications in redox catalysis and anticancer activity.

  1. Identification of a novel series of BET family bromodomain inhibitors: binding mode and profile of I-BET151 (GSK1210151A).

    Science.gov (United States)

    Seal, Jonathan; Lamotte, Yann; Donche, Frédéric; Bouillot, Anne; Mirguet, Olivier; Gellibert, Françoise; Nicodeme, Edwige; Krysa, Gael; Kirilovsky, Jorge; Beinke, Soren; McCleary, Scott; Rioja, Inma; Bamborough, Paul; Chung, Chun-Wa; Gordon, Laurie; Lewis, Toni; Walker, Ann L; Cutler, Leanne; Lugo, David; Wilson, David M; Witherington, Jason; Lee, Kevin; Prinjha, Rab K

    2012-04-15

    A novel series of quinoline isoxazole BET family bromodomain inhibitors are discussed. Crystallography is used to illustrate binding modes and rationalize their SAR. One member, I-BET151 (GSK1210151A), shows good oral bioavailability in both the rat and minipig as well as demonstrating efficient suppression of bacterial induced inflammation and sepsis in a murine in vivo endotoxaemia model. PMID:22437115

  2. A comparative study of fatty acid profiles of fat in commercial Spanish suckling kids and lambs

    Directory of Open Access Journals (Sweden)

    Alberto Horcada

    2014-04-01

    Full Text Available Fatty acid profiles are a major contributor to meat quality in small ruminants. Nevertheless, while fatty acid profiles from suckling lambs have been extensively studied they are virtually unknown in suckling kids. Fatty acid profiles of intramuscular and kidney knob fat depots of suckling kids were compared with fatty acid profiles of lambs with a quality label in the Spanish market. Forty suckling kids from Blanca Celtibérica (BC, Moncaína (Mo, Negra Serrana (NS and Murciano Granadina (MG breeds and 20 Churra male suckling lambs labelled with ‘Lechazo de Castilla y León’ Protected Geographic Indication were slaughtered at commercial live weights (12 kg. In both depots differences in the unsaturated fatty acid profile were observed between breeds. The most pronounced differences were observed between meat goat breeds (BC, Mo and NS and lambs, whilst a greater similarity in the fatty acid profile was observed between kids from dairy goat breeds (MG and lambs. The lowest polyunsaturated fatty acid content was observed in meat goat breeds (approximately 21 to 22% of total fatty acids detected in the intramuscular fat. No significant differences in atherogenic index and desirable fatty acid content (range 68 to 70% of total fatty acids detected were observed. However, a more favourable (lower than 8.07 n-6/n-3 ratio was observed in meat goat breeds. The use of fatty acid profiles from intramuscular and kidney knob fat could be proposed as a tool to differentiate goat kids and lambs. The fact that intramuscular fat from suckling kids and lambs shows appropriate lipid nutritional indices and their low carcass fatness indicate that moderate consumption of suckling kid and lamb meat may contribute to an overall balanced diet for humans.

  3. Studying the evolution of transcription factor binding events using multi-species ChIP-Seq data.

    Science.gov (United States)

    Zheng, Wei; Zhao, Hongyu

    2013-03-01

    Recent technology advances make it possible to collect whole-genome transcription factor binding (TFB) profiles from multiple species through the ChIP-Seq data. This provides rich information to understand TFB evolution. However, few rigorous statistical models are available to infer TFB evolution from these data. We have developed a phylogenetic tree based method to model the on/off rates of TFB events. There are two unique features of our method compared to existing models. First, we mask nucleotide substitutions and focus on INDEL disruption of TFB events, which are rarer evolution events and more appropriate for divergent species and non-coding regulatory regions. Second, we correct for ascertainment bias in ChIP-Seq data by maximizing likelihood conditional on the observed (incomplete) data. Simulations show that our method works well in model selection and parameter estimation when there are sufficient aligned TFB events. When this method is applied to a ChIP-Seq data set with five vertebrates, we find that the instantaneous transition rates to INDELs are higher in TFB regions than in homologous non-binding regions. This is driven by an excess of alignment columns showing binding in one species but gaps in all other species. When we compare the inferred transition rates between the conserved and non-conserved regions, as expected, the conserved regions are estimated to have lower transition rates. The R package TFBphylo that implements the described model can be downloaded from http://bioinformatics.med.yale.edu/. PMID:23446869

  4. Mass Spectrometric Studies of Non-Covalent Binding Interactions Between Metallointercalators and DNA

    Science.gov (United States)

    Urathamakul, Thitima; Talib, Jihan; Beck, Jennifer L.; Ralph, Stephen F.

    Over the past 2 decades there has been increasing interest in metal complexes that bind non-covalently to DNA, driven in part by a host of potential applications for molecules that can accomplish this task with high affinity and selectivity. As a result many workers have used a wide variety of experimental techniques, several of which are discussed in other chapters of this book, to unravel the details of the precise intermolecular interactions involved. Here we discuss one of the most recent additions to the armory of techniques used by chemists to interrogate metal complex/DNA interactions. For the majority of its existence mass spectrometry (MS) has proven to be of enormous advantage to chemists by virtue of its ability to provide the molecular weights of compounds as well as structural information via fragmentation patterns. However, the high energies associated with many earlier MS techniques which result in fragmentation of covalent bonds, prevent its application for studying weaker intermolecular interactions. The advent of soft ionisation methods such as matrix assisted laser desorption ionisation (MALDI) and electrospray ionisation (ESI) has revolutionised mass spectrometric analysis of biomolecules, by allowing these normally fragile molecules to be introduced into the gas phase for analysis with minimal, if any, fragmentation. It was then recognised that ESI-MS, in particular, might be suitable for investigating non-covalent interactions between small molecules and either proteins or nucleic acids. This was confirmed by a number of early studies involving organic intercalators and minor groove binding ligands, prompting our interest in evaluating ESI-MS as a tool for studying non-covalent interactions between metal complexes and DNA. This chapter contains a discussion of the basic principles behind ESI-MS that enable it to introduce representative samples of solutions containing metal complexes and DNA into the gas phase for analysis. This will be

  5. Equilibrium studies of skin-like pressure and current-density profiles

    International Nuclear Information System (INIS)

    During the last few years considerable attention has been devoted to the study of turbulent heating as a heating method for large plasma volumes. In TORTUR - and other related experiments - the application of a heating pulse leads to anomalous heating without macroscopic plasma deformation. Immediately after the heating pulse is applied, the discharge is usually characterized by hollow pressure and current profiles that at the end of the pulse have filled up and have evolved into normal tokamak-like parabolic profiles. Since the plasma properties are such that, even on the μs timescale, MHD equilibrium can be established, we investigated the properties of a class of MHD equilibria that give rise to such characteristic pressure and current profiles. For this investigation a computer code for toroidal ideal MHD equilibria was rewritten and improved. The improvement of the code consists in employing a Moebius transformation, which maps the plane of the cross-section onto a plane in which the magnetic axis coincides with the origin of the coordinate system. This results in a code that can easily handle concave pressure and current profiles. The profiles obtained by means of this code show good agreement with the experimentally measured ones. The use of the mapping has resulted in a code with an improvement of convergence for high-beta cases

  6. Radiolabelling of phoneutria nigriventer spider toxin (Tx1): a tool to study its binding site

    International Nuclear Information System (INIS)

    The neurotoxin Tx1, isolated from the venom of the South American spider Phoneutria nigriventer produces tail elevation and spastic paralysis of posterior limbs after intracerebral ventricular injection in mice. Tx1 also produces ileum contraction in bioassay. We have investigated the binding of radioiodinated-Tx1 (125 I-Tx1) on the preparation of myenteric plexus-longitudinal muscle membrane from guinea pig ileum (MPLM) as a tool to characterize the interaction of this neurotoxin with its site. The neurotoxin Tx1 was radioiodinated with Na125 I by the lactoperoxidase method. 125 I-Tx1 specifically binds to a single class of noninteracting binding sites of high affinity (Kd= 3.5 x 10-10 M) and low capacity (1.2 pmol/mg protein). The specific binding increased in parallel with the protein concentration. In competition experiments the ligands of ionic channels used (sodium, potassium and calcium) did not affect the binding of 125 I-Tx1 to MPLM neither did the cholinergic ligands (hemicholinium-3, hexamethonium, d-tubocurarine and atropine). Another neurotoxin (Tx2-6, one of the isoforms of Tx2 pool) decreased toxin with MPLM and showed that toxin has a specific and saturable binding site in guinea pig ileum and this binding site appears to be related to the Tx2 site. (author)

  7. Adolescent Risk Behaviors: Studying Typical and Atypical Individuals via Multidimensional Scaling Profile Analysis

    Science.gov (United States)

    Dong, Yang; Ding, Cody

    2012-01-01

    Within the framework of problem behavior theory, the purpose of this study was to examine risk behavior profiles of typical and atypical adolescents and the differential outcomes of well-beings for these individuals in the United States. Based on the data from the survey of Health Behavior of School-Aged Children by World Health Organization,…

  8. A Study on the Intelligence Profiles of Taiwan Indigenous Students: The Case of Second Grade Pupils

    Science.gov (United States)

    Liu, Wei-Yu; Teele, Sue

    2009-01-01

    This paper attempts to develop an intelligence-fair assessment tool to explore the intelligence profiles of 15 second grade Amis pupils. This study was conducted in an elementary school in Taiwan with a largely Amis population of lower socioeconomic status. The results illustrate that the most developed intelligence for eight pupils was musical…

  9. On depth profiling of hydrogen and helium isotopes and its application to ion-implantation studies

    International Nuclear Information System (INIS)

    The thesis is divided into two parts, the first being a general review of the experimental methods for depth profiling of light isotopes, where ion beams are used. In the second part, studies of ion implantation of hydrogen and helium isotopes, applying the techniques discussed in the first part, are described. The paper summarizes recent experimental results and discusses recent developments. (Auth.)

  10. Significance of mannose-binding lectin deficiency and nucleotide-binding oligomerization domain 2 polymorphisms in Staphylococcus aureus bloodstream infections: a case-control study.

    Directory of Open Access Journals (Sweden)

    Michael Osthoff

    Full Text Available BACKGROUND: Pathways coordinated by innate pattern recognition receptors like mannose-binding lectin (MBL and nucleotide-binding oligomerization domain 2 (NOD2 are among the first immune responses to Staphylococcus aureus (S. aureus bloodstream infections (BSI in animal models, but human data are limited. Here, we investigated the role of MBL deficiency and NOD2 mutations in the predisposition to and severity of S. aureus BSI. PATIENTS AND METHODS: A matched case-control study was undertaken involving 70 patients with S. aureus BSI and 70 age- and sex-matched hospitalized controls. MBL levels, MBL2 and NOD2 polymorphisms were analyzed. RESULTS: After adjusting for potential confounders, MBL deficiency (<0.5 µg/ml was found less frequently in cases than controls (26 vs. 41%, OR 0.4, 95% confidence interval (CI 0.20-0.95, p=0.04 as were low producing MBL genotypes (11 vs. 23%, OR 0.2, 95% CI 0.08-0.75, p=0.01, whereas NOD2 polymorphisms were similarly distributed. Cases with NOD2 polymorphisms had less organ dysfunction as shown by a lower SOFA score (median 2.5 vs. 4.5, p=0.02, whereas only severe MBL deficiency (<0.1 µg/ml was associated with life-threatening S. aureus BSI (OR 5.6, 95% CI 1.25-24.85, p=0.02. CONCLUSIONS: Contrary to animal model data, our study suggests MBL deficiency may confer protection against acquiring S. aureus BSI. NOD2 mutations were less frequently associated with multi-organ dysfunction. Further human studies of the innate immune response in S. aureus BSI are needed to identify suitable host targets in sepsis treatment.

  11. A STUDY ON CLINICAL, LABORATORY PROFILE AND OUTCOME OF DENGUE FEVER

    OpenAIRE

    Vanamali; Venugopal; Yeshwanth; Dilip

    2013-01-01

    ABSTRACT: BACKGROUND AND OBJECTIVES : In recent days there is an alarming increase in the incidence of dengue fever and has emerged as a serious international public health threat with almost half of the world's population at risk for infection . Very few studies have been conducted in this part of our country and hence this study was undertaken to study the clinical picture, la boratory profile and outcome of dengue fever in and around khammam. MATERIAL...

  12. Binding kinetics of magnetic nanoparticles on latex beads and yeast cells studied by magnetorelaxometry

    International Nuclear Information System (INIS)

    The ion exchange mediated binding of magnetic nanoparticles (MNP) to modified latex spheres and yeast cells was quantified using magnetorelaxometry. By fitting subsequently recorded relaxation curves, the kinetics of the binding reactions was extracted. The signal of MNP with weak ion exchanger groups bound to latex and yeast cells scales linearly with the concentration of latex beads or yeast cells whereas that of MNP with strong ion exchanger groups is proportional to the square root of concentration. The binding of the latter leads to a much stronger aggregation of yeast cells than the former MNP

  13. Klebsiella 'modifying factor': binding studies with HLA-B27+ and B27- lymphocytes.

    OpenAIRE

    Trapani, J A; McKenzie, I. F.

    1985-01-01

    On the basis that extracts of some klebsiella organisms bind selectively to the lymphocytes of HLA-B27+ individuals and induce the appearance of new antigens, attempts were made to detect the binding of klebsiella products to HLA-B27+ and B27- lymphocytes by a number of different techniques. Firstly, blocking of the binding of two different HLA-B27 specific monoclonal antibodies to HLA-B27+ lymphocytes has been examined following exposure of the lymphocytes to a cell-free culture filtrate fro...

  14. Theoretical Study of Sequence Selectivity and Preferred Binding Mode of Psoralen with DNA

    Directory of Open Access Journals (Sweden)

    Patricia Saenz-Méndez

    2007-01-01

    Full Text Available Psoralen interaction with two models of DNA was investigated using molecular mechanics and molecular dynamics methods. Calculated energies of minor groove binding and intercalation were compared in order to define a preferred binding mode for the ligand. We found that both binding modes are possible, explaining the low efficiency for monoadduct formation from intercalated ligands. A comparison between the interaction energy for intercalation between different base pairs suggests that the observed sequence selectivity is due to favorable intercalation in 5′-TpA in (ATn sequences.

  15. Studies on the actin-binding protein HS1 in platelets

    Directory of Open Access Journals (Sweden)

    Auger Jocelyn M

    2007-11-01

    Full Text Available Abstract Background The platelet cytoskeleton mediates the dramatic change in platelet morphology that takes place upon activation and stabilizes thrombus formation. The Arp2/3 complex plays a vital role in these processes, providing the protrusive force for lamellipodia formation. The Arp2/3 complex is highly regulated by a number of actin-binding proteins including the haematopoietic-specific protein HS1 and its homologue cortactin. The present study investigates the role of HS1 in platelets using HS1-/- mice. Results The present results demonstrate that HS1 is not required for platelet activation, shape change or aggregation. Platelets from HS1-/- mice spread normally on a variety of adhesion proteins and have normal F-actin and Arp2/3 complex distributions. Clot retraction, an actin-dependent process, is also normal in these mice. Platelet aggregation and secretion is indistinguishable between knock out and littermates and there is no increase in bleeding using the tail bleeding assay. Conclusion This study concludes that HS1 does not play a major role in platelet function. It is possible that a role for HS1 is masked by the presence of cortactin.

  16. 1HNMR study of methotrexate serum albumin (MTX SA) binding in rheumatoid arthritis

    Science.gov (United States)

    Sułkowska, A.; Maciążek-Jurczyk, M.; Bojko, B.; Równicka, J.; Sułkowski, W. W.

    2008-11-01

    Rheumatoid arthritis (RA) is an immunologically depended disease. It is characterized by a chronic, progressive inflammatory process. Methotrexate (4-amino-10-methylfolic acid, MTX) is the modifying drug used to treat RA. The aim of the presented studies is to determine the low affinity binding site of MTX in bovine (BSA) and human (HSA) serum albumin with the use of proton nuclear magnetic resonance ( 1HNMR) spectroscopy. The analysis of 1HNMR spectra of MTX in the presence of serum albumin (SA) allows us to observe the interactions between aromatic rings of the drug and the rings of amino acids located in the hydrophobic subdomains of the protein. On the basis of the chemical shifts σ [ppm] and the relaxation times T1 [s] of drug protons the hydrophobic interaction between MTX-SA and the stoichiometric molar ratio of the complex was evaluated. This work is a part of a spectroscopic study on MTX-SA interactions [A. Sułkowska, M. Maciążek, J. Równicka, B. Bojko, D. Pentak, W.W. Sułkowski, J. Mol. Struct. 834-836 (2007) 162-169].

  17. DNA-binding, cytotoxicity, cellular uptake, apoptosis and photocleavage studies of Ru(II) complexes.

    Science.gov (United States)

    N Deepika; C Shobha Devi; Y Praveen Kumar; K Laxma Reddy; P Venkat Reddy; D Anil Kumar; Surya S Singh; S Satyanarayana

    2016-07-01

    Two Ru(II) complexes [Ru(phen)2bppp](ClO4)2 (1) and [Ru(phen)27-Br-dppz](ClO4)2 (2) [phen=1,10 phenanthroline, 7-Br-dppz=7-fluorodipyrido[3,2-a:2',3'-c]phenazine, bppp=11-bromo-pyrido[2',3':5,6]pyrazino[2,3-f] [1,10]phenanthroline] have been synthesized and characterized by elemental analysis, ES-MS, (1)H-NMR, (13)C-NMR and IR. The in vitro cytotoxicity of the complexes examined against a panel of cancer cell lines (HeLa, Du145 and A549) by MTT method, both complexes show prominent anticancer activity against various cancer cells. Live cell imaging study and flow cytometric analysis demonstrate that both the complexes 1 and 2 could cross the cell membrane accumulating in the nucleus. Further, flow cytometry experiments showed that the cytotoxic Ru(II) complexes 1 and 2 induced apoptosis of HeLa tumor cell lines. Photo induced DNA cleavage studies have been performed and results indicate that both the complexes efficiently photo cleave pBR322 DNA. The binding properties of two complexes toward CT-DNA were investigated by various optical methods and viscosity measurements. The experimental results suggested that both Ru(II) complexes can intercalate into DNA base pairs. The complexes were docked into DNA-base pairs using the GOLD docking program. PMID:27107334

  18. DNA-binding studies and biological activities of new nitrosubstituted acyl thioureas

    Science.gov (United States)

    Tahir, Shaista; Badshah, Amin; Hussain, Raja Azadar; Tahir, Muhammad Nawaz; Tabassum, Saira; Patujo, Jahangir Ali; Rauf, Muhammad Khawar

    2015-11-01

    Four new nitrosubstituted acylthioureas i.e. 1-acetyl-3-(4-nitrophenyl)thiourea (TU1), 1-acetyl-3-(2-methyl-4-nitrophenyl)thiourea (TU2), 1-acetyl-3-(2-methoxy-4-nitrophenyl)thiourea (TU3) and 1-acetyl-3-(4-chloro-3-nitrophenyl)thiourea (TU4) have been synthesized and characterized (by C13 and H1 nuclear magnetic resonance, Fourier transform infrared spectroscopy and single crystal X-ray diffraction). As a preliminary investigation of the anti-cancer potencies of the said compounds, DNA interaction studies have been carried out using cyclic voltammetry and UV-vis spectroscopy along with verification from computational studies. The drug-DNA binding constants are found to be in the order, KTU3 9.04 × 106 M-1 > KTU4 8.57 × 106 M-1 > KTU2 6.05 × 106 M-1 > KTU1 1.16 × 106 M-1. Furthermore, the antioxidant, cytotoxic, antibacterial and antifungal activities have been carried out against DPPH (1,1-diphenyl-2-dipicrylhydrazyl), Brine shrimp eggs, gram positive (Micrococcus luteus, Staphylococcus aureus) and gram negative (Bordetella bronchiseptica, Salmonella typhimurium, Enterobacter aerogens) and fungal cultures (Aspergillus fumigatus, Mucor species, Aspergillus niger, Aspergillus flavus) respectively.

  19. RNA targeting by small molecule alkaloids: Studies on the binding of berberine and palmatine to polyribonucleotides and comparison to ethidium

    Science.gov (United States)

    Islam, Md. Maidul; Suresh Kumar, Gopinatha

    2008-03-01

    The binding affinity, energetics and conformational aspects of the interaction of isoquinoline alkaloids berberine and palmatine to four single stranded polyribonucleotides polyguanylic acid [poly(G)], polyinosinic acid [poly(I)], polycytidylic acid [poly(C)] and polyuridylic acid [poly(U)] were studied by absorption, fluorescence, isothermal titration calorimetry and circular dichroism spectroscopy and compared with ethidium. Berberine, palmatine and ethidium binds strongly with poly(G) and poly(I) with affinity in the order 10 5 M -1 while their binding to poly(C) and poly(U) were very weak or practically nil. The same conclusions have also emerged from isothermal titration calorimetric studies. The binding of all the three compounds to poly(C) and poly(I) was exothermic and favored by both negative enthalpy change and positive entropy change. Conformational change in the polymer associated with the binding was observed in poly(I) with all the three molecules and poly(U) with ethidium but not in poly(G) and poly(C) revealing differences in the orientation of the bound molecules in the hitherto different helical organization of these polymers. These fundamental results may be useful and serve as database for the development of futuristic RNA based small molecule therapeutics.

  20. Bovine Chymosin: A Computational Study of Recognition and Binding of Bovine κ-Casein

    DEFF Research Database (Denmark)

    Palmer, David S.; Christensen, Anders Uhrenholt; Sørensen, Jesper; Celik, Leyla; Qvist, Karsten Bruun; Schiøtt, Hanne Birgit

    2010-01-01

    Bovine chymosin is an aspartic protease that selectively cleaves the milk protein κ-casein. The enzyme is widely used to promote milk clotting in cheese manufacturing. We have developed models of residues 97-112 of bovine κ-casein complexed with bovine chymosin, using ligand docking, conformational...... search algorithms, and molecular dynamics simulations. In agreement with limited experimental evidence, the model suggests that the substrate binds in an extended conformation with charged residues on either side of the scissile bond playing an important role in stabilizing the binding pose. Lys111 and...... Lys112 are observed to bind to the N-terminal domain of chymosin displacing a conserved water molecule. A cluster of histidine and proline residues (His98-Pro99-His100-Pro101-His102) in κ-casein binds to the C-terminal domain of the protein, where a neighboring conserved arginine residue (Arg97) is...

  1. Study on the Binding Mode of a Co(Ⅱ) Complex with DNA

    Institute of Scientific and Technical Information of China (English)

    ZHOU Qing-Hua; YANG Pin

    2005-01-01

    The mode of binding of CoLCl2, here L=bis(2-benzimidazolylmethyl)amine, with calf thymus DNA has been investigated by fluorescence measurements, equilibrium dialysis, viscosity experiments and gel electrophoresis. The complex was found to bind but weakly to DNA, with binding constant of 1.96× 104 L/mol determind at 20 ℃ in a solution containing 5 mmol/L Tris-HCl (pH 7.1) and 50 mmol/L NaCl. Polyelectrolyte theory was applied to analyse these values. Viscosity experiments show that binding did not alter the relative viscosity of DNA with any complexes to an appreciable extent. Electrophoresis test displayed that the compound could not cleave the DNA.These results show that the complex is essentially electrostatically bound to DNA.

  2. STD NMR spectroscopy: a case study of fosfomycin binding interactions in living bacterial cells

    Energy Technology Data Exchange (ETDEWEB)

    Milagre, Cintia D.F.; Cabeca, Luis Fernando; Martins, Lucas G.; Marsaioli, Anita J., E-mail: anita@iq [Universidade Estadual de Campinas (IQ/UNICAMP), SP (Brazil). Inst. de Quimica

    2011-07-01

    A saturation transfer difference (STD) NMR experiment was successfully employed to observe the binding interactions of fosfomycin resistant and non-resistant bacterial strains using living cell suspensions, without the need for isotopic labelling of the ligand or receptor. (author)

  3. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties. PMID:27444879

  4. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.

    Science.gov (United States)

    Du, Juan; Wang, Xue; Dong, Chun-Hai; Yang, Jian Ming; Yao, Xiao Jun

    2016-01-01

    Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin) or polymeric form (F-actin). Members of the actin-depolymerizing factor (ADF)/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1) in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1-actin complex, we constructed a homology model of the AtADF1-actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA) methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin. PMID:27414648

  5. Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies.

    Science.gov (United States)

    Vertessy, B G; Harmat, V; Böcskei, Z; Náray-Szabó, G; Orosz, F; Ovádi, J

    1998-11-01

    The modulatory action of Ca2+-calmodulin on multiple targets is inhibited by trifluoperazine, which competes with target proteins for calmodulin binding. The structure of calmodulin crystallized with two trifluoperazine molecules is determined by X-ray crystallography at 2.74 A resolution. The X-ray data together with the characteristic and distinct signals obtained by circular dichroism in solution allowed us to identify the binding domains as well as the order of the binding of two trifluoperazine molecules to calmodulin. Accordingly, the binding of trifluperazine to the C-terminal hydrophobic pocket is followed by the interaction of the second drug molecule with an interdomain site. Recently, we demonstrated that the two bisindole derivatives, vinblastine and KAR-2 [3"-(beta-chloroethyl)-2",4"-dioxo-3, 5"-spirooxazolidino-4-deacetoxyvinblastine], interact with calmodulin with comparable affinity; however, they display different functional effects [Orosz et al. (1997) British J. Pharmacol. 121, 955-962]. The structural basis responsible for these effects were investigated by circular dichroism and fluorescence spectroscopy. The data provide evidence that calmodulin can simultaneously accommodate trifluoperazine and KAR-2 as well as vinblastine and KAR-2, but not trifluoperazine and vinblastine. The combination of the binding and structural data suggests that distinct binding sites exist on calmodulin for vinblastine and KAR-2 which correspond, at least partly, to that of trifluoperazine at the C-terminal hydrophobic pocket and at an interdomain site, respectively. This structural arrangement can explain why these drugs display different anticalmodulin activities. Calmodulin complexed with melittin is also able to bind two trifluoperazine molecules, the binding of which appears to be cooperative. Results obtained with intact and proteolytically cleaved calmodulin reveal that the central linker region of the protein is indispensable for simultanous interactions

  6. Geometry, Energy, and Some Electronic Properties of Carbon Polyprismanes: Ab Initio and Tight-Binding Study

    OpenAIRE

    Konstantin P. Katin; Shostachenko, Stanislav A.; Avkhadieva, Alina I.; Mikhail M. Maslov

    2015-01-01

    We report geometry, energy, and some electronic properties of [n,4]- and [n,5]prismanes (polyprismanes): a special type of carbon nanotubes constructed from dehydrogenated cycloalkane C4- and C5-rings, respectively. Binding energies, interatomic bonds, and the energy gaps between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) have been calculated using density functional approach and nonorthogonal tight-binding model for the systems up to thir...

  7. Crystallographic studies on B12 binding proteins in eukaryotes and prokaryotes

    OpenAIRE

    Sukumar, Narayanasami

    2013-01-01

    The x-ray crystal structures of several important vitamin B12 binding proteins that have been solved in recent years have enhanced our current understanding in the vitamin B12 field. These structurally diverse groups of B12 binding proteins perform various important biological activities, both by transporting B12 as well as catalyzing various biological reactions. An in-depth comparative analysis of these structures was carried out using PDB coordinates of a carefully chosen database of B12 b...

  8. A Study on the Presence of Ferritin-binding Proteins in Fetal Horse Plasma

    OpenAIRE

    Hashimoto, Masafumi; NAMBO, Yasuo; Kondo, Takashi; Watanabe, Kiyotaka; Orino, Koichi

    2011-01-01

    In mammal circulation, ferritin-binding proteins (FBPs) are thought to be involved in clearance of circulating ferritin after complex formation with it through receptor-mediated uptake. However, there is no report on fetal FBP in fetal circulation. Although iron concentrations of fetal horse plasma were higher than those of adult horse plasma, plasma ferritin concentrations and ferritin-binding activities were found to be significantly lower in fetus than in adult. FBPs were purified from fet...

  9. Study of an intense proton beam profiler based on laser absorption

    International Nuclear Information System (INIS)

    Among the challenges of high current proton accelerators, the development of new beam diagnostics is of major importance. The main difficulty for these instruments, is the beam power which deteriorates any instruments used to catch it. The chosen detectors are therefore 'non-interceptive systems. After an introduction concerning characteristics of the used accelerator (chapter I), parameters defining a beam of particles are presented (chapter II). Among these ones, the profile is an important beam characteristic for its transport. After the description of the different types of beam profilers, their problematic application to intense beams is discussed. New physical phenomena have to be used for profilers. Thus, we have prospected optical luminescence phenomena. The light produced during the interaction of protons with the residual gas and/or locally injected is a source of informations on beam characteristics. In chapters III and IV, there is an experimental and theoretical analysis of the luminescence. Chapter V is a direct application of spectroscopic measurements to estimate the output of protons with a non-interceptive technique. With the spectral analysis, the idea of a profiler based on laser absorption is developed. This presentation is both theoretical and experimental (chapters 6 and 7). The laser absorption needs the use of metastable states we define in the chapter 6. The evolution of the metastable states, with time and space, has been rigorously studied to discuss the concept of an optical profiler. Chapter VII presents all the necessary instrumentation for the use of a laser and the first measurements with the beam. At the thesis end, the first recorded profile is presented. An experimental critic is presented with a description of the different sources of errors and the proposed cures. (author)

  10. Computational study of the binding modes of caffeine to the adenosine A2A receptor.

    Science.gov (United States)

    Liu, Yuli; Burger, Steven K; Ayers, Paul W; Vöhringer-Martinez, Esteban

    2011-12-01

    Using the recently solved crystal structure of the human adenosine A(2A) receptor, we applied MM/PBSA to compare the binding modes of caffeine with those of the high-affinity selective antagonist ZM241385. MD simulations were performed in the environment of the lipid membrane bilayer. Four low-energy binding modes of caffeine-A(2A) were found, all of which had similar energies. Assuming an equal contribution of each binding mode of caffeine, the computed binding free energy difference between caffeine and ZM241385 is -2.4 kcal/mol, which compares favorably with the experimental value, -3.6 kcal/mol. The configurational entropy contribution of -0.9 kcal/mol from multiple binding modes of caffeine helps explain how a small molecule like caffeine can compete with a significantly larger molecule, ZM241385, which can form many more interactions with the receptor. We also performed residue-wise energy decomposition and found that Phe168, Leu249, and Ile274 contribute most significantly to the binding modes of caffeine and ZM241385. PMID:21970461

  11. GABA binding to an insect GABA receptor: a molecular dynamics and mutagenesis study.

    Science.gov (United States)

    Ashby, Jamie A; McGonigle, Ian V; Price, Kerry L; Cohen, Netta; Comitani, Federico; Dougherty, Dennis A; Molteni, Carla; Lummis, Sarah C R

    2012-11-21

    RDL receptors are GABA-activated inhibitory Cys-loop receptors found throughout the insect CNS. They are a key target for insecticides. Here, we characterize the GABA binding site in RDL receptors using computational and electrophysiological techniques. A homology model of the extracellular domain of RDL was generated and GABA docked into the binding site. Molecular dynamics simulations predicted critical GABA binding interactions with aromatic residues F206, Y254, and Y109 and hydrophilic residues E204, S176, R111, R166, S176, and T251. These residues were mutated, expressed in Xenopus oocytes, and their functions assessed using electrophysiology. The data support the binding mechanism provided by the simulations, which predict that GABA forms many interactions with binding site residues, the most significant of which are cation-π interactions with F206 and Y254, H-bonds with E204, S205, R111, S176, T251, and ionic interactions with R111 and E204. These findings clarify the roles of a range of residues in binding GABA in the RDL receptor, and also show that molecular dynamics simulations are a useful tool to identify specific interactions in Cys-loop receptors. PMID:23200041

  12. Biologically active monoiodinated alpha-MSH derivatives for receptor binding studies using human melanoma cells

    International Nuclear Information System (INIS)

    Three different monoiodinated radioligands of alpha-MSH (alpha-melanocyte-stimulating hormone) were compared in a binding assay with human D10 melanoma cells: [Tyr(125I)2]-alpha-MSH, [Tyr(125I)2,NIe4]-alpha-MSH, and [Tyr(125I)2,NIe4,D-Phe7]-alpha-MSH. They were prepared either by the classical chloramine T method or by the Enzymobead method. A simple and rapid purification scheme was developed consisting of a primary separation on reversed-phase C18 silica cartridges immediately after the iodination, followed by HPLC purification before each binding experiment. Biological testing of the three radioligands showed that they all retained high melanotropic activity in the B16 melanin assay and the Anolis melanophore assay. However, in human D10 melanoma cells, [Tyr(125I)2,NIe4]-alpha-MSH led to a high degree of non-specific binding to the cells which could not be displaced by excess alpha-MSH and only partially by [NIe4]-alpha-MSH. The [Tyr(125I)2,NIe4,D-Phe7]-alpha-MSH tracer gave similar results but with a much lower proportion of non-specific binding. On the other hand, [Tyr(125I)2]-alpha-MSH proved to be an excellent radioligand whose non-specific binding to the D10 cells was not higher than 20% of the total binding

  13. Binding of 2',3'-cyclic nucleotide 3'-phosphodiesterase to myelin: an in vitro study.

    Science.gov (United States)

    De Angelis, D A; Braun, P E

    1996-06-01

    The binding of 2', 3'-cyclic nucleotide 3'-phosphodiesterase isoform 1 (CNP1) to myelin and its association with cytoskeletal elements of the sheath have been characterized with in vitro synthesized polypeptides and purified myelin. We have previously shown that the cysteine residue present in the carboxy-terminal CXXX box of CNP1 is isoprenylated, and that both C15 farnesyl and C20 geranylgeranyl isoprenoids can serve as substrates for the modification. Here, we have mutated the CXXX box to obtain selectively farnesylated CNP1 or geranyl- geranylated CNP1 and found that these two modified forms of CNP1 behave identically in all of the assays performed. Isoprenylation is essential but not sufficient for the binding of in vitro synthesized CNP1 to purified myelin, because a control nonmyelin protein is isoprenylated, yet unable to bind to myelin. In our assay, membrane-bound CNP1 partitions quantitatively into the nonionic detergent-insoluble phase of myelin, suggesting that CNP1 binds to cytoskeletal elements within myelin. However, isoprenylated CNP1 fails to bind to the cytoskeletal matrix isolated from myelin by detergent treatment, implying that both detergent-soluble and insoluble myelin components are involved in the binding of CNP1. A model for the interactions between CNP1 and myelin is presented, consistent with models proposed for other isoprenylated proteins. PMID:8632178

  14. Long-term aerosol study on continental scale through EARLINET vertical profiles

    Science.gov (United States)

    Mona, Lucia; Pappalardo, Gelsomina; Linne, Holger; Wandinger, Ulla

    2015-04-01

    Lidar techniques offer the opportunity for investigating the aerosol vertical profiles, which is an important information for climatological, meteorological and air quality issues. EARLINET (European Aerosol Research Lidar Network) has been providing aerosol optical properties vertical profiles over Europe since May 2000. Long-term aerosol observations performed within EARLINET allows a climatological study of aerosol properties over Europe. All EARLINET stations perform almost simultaneously measurements three times per week following a scheduling established in 2000. Besides these climatological measurements, additional measurements are performed in order to monitor special events (as volcanic eruptions and desert dust intrusion), for satellite data evaluation and integrated studies and during intensive measurements campaigns. Aerosol optical properties vertical profiles are freely available at www.earlinet.org and through ACRIS data center http://www.actris.net/. This data are currently published on the CERA database with an associated doi number. Based mainly on Raman technique, EARLINET stations typically provide direct measurement of extinction profiles, and therefore of the aerosol optical depth (AOD), a key parameter for understanding the aerosol role on radiation budget. The free troposphere contribution to AOD and altitude of lofted layers are provided thanks to the vertical profiling capability of lidar technique. The representativeness of EARLINET regular scheduling for climatological studies is investigating through the comparison with AERONET and MODIS measurements. We find that the regular measurements schedule is typically sufficient for climatological studies. In addition lidar punctual measurements are representative for a larger area (1°x1°) in a climatological sense. Long term analysis of EARLINET profiles shows that the AOD in generally decreasing over Europe in agreement with both passive-sensors and in situ measurements. Mean vertical

  15. Characterization of histamine receptors in isolated pig basilar artery by functional and radioligand binding studies

    International Nuclear Information System (INIS)

    Histamine receptors in pig basilar arteries were investigated in vitro by radioligand binding assays and by measuring the contractile and relaxant responses to histamine. Histamine and 2-pyridyethylamine (H1-agonist) induced concentration-dependent contractions, whereas impromidine (H2-agonist) induced concentration-dependent relaxations. These responses were independent of the presence of endothelial cells. Diphenhydramine (H1-antagonist) partially reversed the histamine-induced contractions to relaxations. Cimetidine (Hα2-antagonist) potentiated the contraction in a concentration-dependent manner. In the presence of cimetidine, the pEC50 value of histamine for the contraction was 6.30, and diphenhydramine competitively antagonized the histamine-induced contractions (pA2, 7.77). In the presence of diphenhydramine, the pEC50 value of histamine for the relaxation was 5.93, and cimetidine competitively antagonized the histamine-induced relaxations (pA2, 6.62). In the binding studies, the Kd value of [3H]mepyramine was 2.1 nM and the Bmax value was 95.6 fmol/mg protein. A competition experiment with diphenhydramine showed that the pKi value (7.51) was similar to the pA2 value. The Kd value for [3H]cimetidine was 126.0 nM and the Bmax value was 459.8 fmol/mg protein. The pKd (6.90) for [3H]cimetidine was similar to the pA2 for cimetidine. The Hill coefficients for these experiments were not significantly different from unity. The present findings indicate that the number of H1-receptors, in terms of the Bmax value for [3H]mepyramine, is smaller than that of H2-receptors, in terms of the Bmax value for [3H]cimetidine. However, the contractile response to histamine is predominantly mediated through stimulation of H1-receptors on vascular smooth muscle cells in pig basilar artery

  16. 1H NMR studies of insulin: histidine residues, metal binding, and dissociation in alkaline solution

    International Nuclear Information System (INIS)

    The shifts of the H2 histidine B5 and B10 resonances of 2-Zn insulin hexamer were followed in 2H2O by 1H NMR spectroscopy at 270 MHz from pH 9.85 to 7. The two resonances present at high pH, previously assigned to H2 histidine B5 and B10 residues, moved slightly downfield and split into four resonances at pH 8.95 and also at pH 7. By use of a paramagnetic broadening probe (Mn2+) and the addition of Zn2+ to metal-free insulin, it was deduced that the four resonances arose from histidines B10 and B5 in two different magnetic environments, probably either bound to Zn2+ or not bound to Zn2+. The pK' values of the B5 and B10 histidines were determined in 60% 2H2O-40% dioxan, in which insulin was soluble throughout the pH range, to be 7.1 and 6.8, respectively at 37 degrees C. Studies at higher pH indicated that at a concentration level suitable for 1H NMR (approximately 1 mM) at 37 degrees C in 2H2O the 2-Zn hexamer was largely dissociated to dimer at pH 10.3 and to monomer at pH 10.8. Addition of paramagnetic shift probe Ni2+ to metal-free insulin caused changes to the spectrum similar to those produced on addition of diamagnetic Zn2+. Addition of Co2+ gave a different result, but there was no paramagnetic shift of the H2 histidine B10 resonance, probably because of rapid exchange at the binding site. Addition of Cd2+ and of Cd2+ and Ca2+ produced changes that were similar to each other but were different from those observed on addition of Zn2+, probably due to the binding of Cd2+ and Ca2+ at glutamate B13

  17. Single pulse and profile variability study of PSR J1022+1001

    CERN Document Server

    Liu, K; Lee, K J; Stappers, B W; Kramer, M; Smits, R; Purver, M B; Janssen, G H; Perrodin, D

    2015-01-01

    Millisecond pulsars (MSPs) are known as highly stable celestial clocks. Nevertheless, recent studies have revealed the unstable nature of their integrated pulse profiles, which may limit the achievable pulsar timing precision. In this paper, we present a case study on the pulse profile variability of PSR J1022+1001. We have detected approximately 14,000 sub-pulses (components of single pulses) in 35-hr long observations, mostly located at the trailing component of the integrated profile. Their flux densities and fractional polarisation suggest that they represent the bright end of the energy distribution in ordinary emission mode and are not giant pulses. The occurrence of sub-pulses from the leading and trailing components of the integrated profile is shown to be correlated. For sub-pulses from the latter, a preferred pulse width of approximately 0.25 ms has been found. Using simultaneous observations from the Effelsberg 100-m telescope and the Westerbork Synthesis Radio Telescope, we have found that the int...

  18. Comparative study of the electron density profiles in the compact torus plasma merging experiments

    International Nuclear Information System (INIS)

    Following two previous papers on the comparative studies of the electron density distributions for a single compact torus (CT) and a spherical tokamak (ST), and for the a single ST and a merged ST, a comparative study on the dynamics of the electron density profile and after the CT and ST plasma merging process was performed. The sharpness of the peak in the electron density profile around the mid-plane just after the merging of CT with a low safety factor (q value) such as RFP or spheromak is found to be related to the speed of the magnetic axis during the plasma merging process. It is also found that the electron density gradient near the plasma edge in a high q ST is larger than that of a low q CT. High q ST is found to be provided with the magnetic structure which is able to sustain a large thermal pressure by a strong j x B force. Despite these differences in the electron density profile between CT and ST during merging, the confinement characteristics evaluated from the number of electrons confined within the magnetic separatrix after the completion of the merging is almost similar between in the merging CT and in the merging ST. For all configurations, the electron density profiles after the completion of the merging are analogous to those of the corresponding single configuration produced without the merging process. (author)

  19. Profiling the Buzz Agent: Product Referral and the Study of Social Community and Brand Attachment

    Directory of Open Access Journals (Sweden)

    Danny Pimentel Claro

    2015-04-01

    Full Text Available The buzz agent is any consumer perceived by others as a source of product referral. Previous literature in word of mouth (WOM has looked into characteristics of individuals who successfully persuade others to choose a brand. While there have been studies in this field, the literature is still scattered and little has been done to profile the consumer playing the buzz-agent role. We aim to deepen our understanding about the consumer who must be recruited as a buzz agent by a firm in a WOM marketing (WOMM initiative. The proposed profile is comprised of three key characteristics: the consumer’s position in the social community, nature of ties in the community and brand attachment. We tested our hypotheses with a survey of 542 consumers from a controlled population. Rather than relying on self-reported questions about referral behavior, we asked respondents in the population to name the individuals to whom the respondents go to obtain information to help pick a brand. This accurately pinpoints which individuals fit the profile of a buzz agent. Results show that buzz agents are popular in their social community (friends and tech experts, carry dissimilar brands as target consumers and are product experts. Our study identifies a profile of consumers that helps firms select buzz agents for WOMM initiatives.

  20. Preparation of 99Tcm-Annexin V and in vitro study of its binding characteristics in dopaminergic apoptotic neurons

    International Nuclear Information System (INIS)

    Objective: The aims of this study were two. One was to find out an optimal method for 99Tcm-Annexin V preparation and the other was to investigate the binding characteristics of 99Tcm-Annexin V in dopaminergic apoptotic neurons in vitro. Methods: For 99Tcm-Annexin V preparation, hydrazine nicotinamide (HYNIC), a bifunctional chelating agent was used. Product was purified by Sephadex G-25 column chromatography and analyzed with instant thin layer chromatography (ITLC). To test the binding characteristics in dopaminergic apoptotic neurons in vitro, a rat pheoehromocytoma cell line (PC12) treated with l-methyl-4-phenylpyridinium (MPP+) was used. Tests including time-temperature binding, saturable bind- ing, competition binding between dopaminergic apoptotic neurons and 99Tcm-HYNIC-Annexin V and dose- dependent MPP+ studies were performed and evaluated. Results: The labeling rate of 99Tcm was (64.56 ± 6.23)%. The specific activity of 99Tcm-HYNIC-Annexin V was (3.7-74)xl05 kBq/mg protein. The radiochemical purity was (93.6±2.48)% and was >90% after 4 hours storage at room temperature. Seat- chard plotting suggested that the concentrations of Kd was (7.16±1.78) nmol/L, and Bmax was (178.73± 32.62) fmoL/106 ceils. Conclusions: The preliminary results show that an optimal 99Tcm-HYNIC-Annexin V preparation method can be provided. The 99Tcm-HYNIC-Annexin V prepared in our laboratory has good receptor-binding activity and may possibly be a potential drug in studying the apoptotic phenomenon in Parkin- son's disease at early stage in an animal model. (authors)

  1. A comparative study on lifestyle and metabolic profile in normal and obese individuals

    OpenAIRE

    Revathi R, Swetha S, MeghalathaTS, Arunakumari R

    2013-01-01

    Background/Aim: The aim of the present study was to evaluate the lifestyle and metabolic profiles in normal and obese. Material and Methods: A cross sectional study design was employed. Information on body weight, height, body fat, food choices, diet and physical activity behavior were collected by a questionnaire among 100 obese adults aged 18-35 years and compared with healthy individuals as controls. Blood samples were collected to analyze blood glucose, heamoglobin and total cholesterol....

  2. Study of the aging of fermented of yacon (Smallanthus sonchifolius) and sensory profile and acceptance

    OpenAIRE

    Camila Cheker Brandão; Eduardo Ramirez Asquieri; Shireen Attaran; Clarissa Damiani

    2014-01-01

    Yacon is considered a functional food due to its the fructooligosaccharide (FOS) content, however its perishability and low production volume is a problem. The aim of this study was to analyze the changes in aging during one year of storage and conduct sensory analysis of fermented of yacon. For one year total acidity, volatile acidity, free and total sulfur dioxide, reducing sugars, sucrose, phenols and FOS and its antioxidant power were studied. At the end of aging a sensory profile and acc...

  3. A Study of Cancer Patients' Personality Profile and it's Comparison with that of Normal Persons

    OpenAIRE

    M. Imani; Sh. Zeinali; Asvadi Kermani, I.; P. Ashraphian; R Shabanloei

    2010-01-01

    Introduction & Objective: This study compared the personality profile of cancer patients with that of normal persons. The aim was identifying personality traits related to people who suffered from cancer, and helping them to cope with the situation and adjust with life.Materials & Methods: This research was a casual comparative study. For this purpose 100 persons were selected from hematology and oncology center and asked to complete (NEO) personality inventory. Then 94 persons were selecte...

  4. Profiling postgraduate workplace-based assessment implementation in Ireland: a retrospective cohort study

    OpenAIRE

    Barrett, Aileen; Galvin, Rose; Steinert, Yvonne; Scherpbier, Albert; O’Shaughnessy, Ann; Walsh, Gillian; Horgan, Mary

    2016-01-01

    In 2010, workplace-based assessment (WBA) was formally integrated as a method of formative trainee assessment into 29 basic and higher specialist medical training (BST/HST) programmes in six postgraduate training bodies in Ireland. The aim of this study is to explore how WBA is being implemented and to examine if WBA is being used formatively as originally intended. A retrospective cohort study was conducted and approved by the institution’s Research Ethics Committee. A profile of WBA require...

  5. Morbidity Profile of Stone Crusher Workers with Special Reference to Respiratory Morbidity: A Cross Sectional Study

    OpenAIRE

    Narkhede Vinod, Likhar Swarna, Mishra Mahesh K

    2012-01-01

    Background: The occupational environment at the stone crushing sites poses a potential health hazard to the workers. Exposure to heavy dust concentration from stone crushers, may produce several diseases. Methods: The present study was aimed to assess the morbidity profile of workers working in stone crusher industry. A cross-sectional study was carried out among the workers of the stone crushers located in Ratua at a distance of 23 km to the north of Bhopal city. The total workers working in...

  6. Profile of risk factors associated with suicide attempts: A study from Orissa, India

    OpenAIRE

    Kar, Nilamadhab

    2010-01-01

    Context: Periodic systematic profiling of suicidal risk factors in developing countries is an established need. Aims: It was intended to study the risk factors associated with suicide attempts in Orissa, one of the most economically compromised states of India. Settings and Design: Cross-sectional study in a general hospital. Materials and Methods: Consecutive 149 suicide attempters were evaluated for psychosocial, situational, and clinical risk factors using the Risk Rescue Rating scale, Sui...

  7. Asthma characteristics and biomarkers from the Airways Disease Endotyping for Personalized Therapeutics (ADEPT) longitudinal profiling study

    OpenAIRE

    Silkoff, P. E.; Strambu, I.; Laviolette, M.; Singh, D; FitzGerald, J M; Lam, S.; Kelsen, S.; Eich, A.; Ludwig-Sengpiel, A.; hupp, G. C; Backer, V.; Porsbjerg, C.; Girodet, P. O.; P. Berger; Leigh, R

    2015-01-01

    Background Asthma is a heterogeneous disease and development of novel therapeutics requires an understanding of pathophysiologic phenotypes. The purpose of the ADEPT study was to correlate clinical features and biomarkers with molecular characteristics, by profiling asthma (NCT01274507). This report presents for the first time the study design, and characteristics of the recruited subjects. Methods Patients with a range of asthma severity and healthy non-atopic controls were enrolled. The ast...

  8. [Comparative study of variola virus and monkeypox virus interferon-gamma-binding].

    Science.gov (United States)

    Nepomniashchikh, T S; Lebedev, L R; Riazankin, I A; Pozdniakov, S G; Gileeva, I P; Shchelkunov, S N

    2005-01-01

    DNA fragments containing genes for coding IFN-gamma-binding proteins (IFNgammaBPs) of variola virus (VARV) and monkeypox virus (MPXV) were obtained from viral genomes using PCR. Isolated genes coding desired proteins were expressed in the insect Sf21 cells using baculovirus expression system. Secreted recombinant IFNgammaBPs were isolated from culture medium of infected Sf21 cells through affinity chromatography procedure. SDS-PAAG and Western blot analysis of culture medium of infected insect cells and preparations of purified recombinant IFNgammaBPs indicated that recombinant viral proteins were dimerized even in the absence of ligand (hIFNgamma) unlike their cell (eucaryotic) analogs. Biological activity of the recombinant IFNgammaBPs were studied in the test of protective effect inhibition of hIFNgamma on L68 cells infected with murine encephalomyocarditis virus. It was shown that recombinant IFNgammaBPs had dose-dependent IFNgamma-inhibiting activity. A possibility of the elaboration of new therapeutics for anti-hIFNgamma therapy on the base of IFNgammaBPs is discussed. PMID:16358743

  9. Perturbed angular correlation studies of Hf binding to cyanocobalamin (vitamin B12)

    International Nuclear Information System (INIS)

    Gamma ray perturbed angular correlation (PAC) experiments have been carried out with 181Hf labeled cyanocobalamin. Evidence is presented which strongly indicates that Hf binds to vitamin B12 at the phosphate group linking the sugar residue to a side chain of the corrin ring system. Analysis of the time-differential PAC spectra for the crystalline Hf--B12 complex indicates a static electric quadrupole interaction at the Hf nucleus, corresponding to the electric field gradient generated by the chemical bonding. The magnitudes of the derived interaction parameters are similar to those found in Hf phosphate compounds. In aqueous solution, the Hf--B12 complex exhibits PAC spectra which appear to originate from two sources. Approximately 3/4 of the Hf nuclei experience a static electric quadrupole interaction with the same characteristic interaction frequency as in the solid, but with an increased asymmetry parameter. Approximately 1/4 of the Hf signal strength is attributable to a time-dependent quadrupole interaction with a relaxation constant indicative of an effective molecular entity comparable in size to the B12 molecule. This effect may be related to molecular motion in the solution. These results demonstrate the utility of the PAC experimental method for the study of macromolecular species in both the solid and solution forms, and opens possibilities for obtaining new information concerning the structure, orientation, and behavior of macromolecules

  10. Histochemical detection of sugar residues in lizard teeth (Liolaemus gravenhorsti: a lectin-binding study

    Directory of Open Access Journals (Sweden)

    MARCELA FUENZALIDA

    2000-01-01

    Full Text Available The structural diversity of the many oligosaccharide chains of surface glycoconjugates renders them likely candidates for modulators of cell-interactions, cellular movements, differentiation, and cellular recognition. A selection of different lectins was used to investigate the appearance of cellular distribution and changes in sugar residues during tooth development in the polyphyodont lizard, Liolaemus gravenhorsti. Lectins from three groups were used: (1 N-acetylgalactosamine specificity: BS-1, PNA, RCA-120; (2 N-acetylglucosamine specificity: ECA; and (3 fucose specificity: UEA 1 and LTA.. Digital images were processed using Scion Image. Grayscale graphics in each image were obtained. The lectins used showed a strong, wide distribution of the L-fucose and N-acetylgalactosamine at the cell surface and in the cytoplasm of multinucleate odontoclast cell, while mononuclear odontoclast cells showed no binding, suggesting some roles that the residues sugar might play in the resorption of dentine or with multinucleation of odontoclast after the attachment to the dentine surface in this polyphyodont species. Further studies must be planned to determine the specific identities of these glycoconjugates,and to elucidate the roles played by these sugar residues in the complex processes related to odontogenesis in polyphyodont species.

  11. Fluorescence correlation spectroscopy to study antibody binding and stoichiometry of complexes

    Science.gov (United States)

    Swift, Kerry M.; Matayoshi, Edmund D.

    2008-02-01

    FCS (fluorescence correlation spectroscopy) was used to study the association at the single molecule level of tumor necrosis factor alpha (TNF-α) and two of its protein antagonists Humira (TM) (adalimumab), a fully humanized monoclonal antibody, and Enbrel (TM) (etanercept), a soluble form of the TNF receptor. Single molecule approaches potentially have the advantage not only of enhanced sensitivity, but also of observing at equilibrium the details that would otherwise be lost in classical ensemble experiments where heterogeneity is averaged. We prepared fluorescent conjugates of the protein drugs and their biological target, the trimeric soluble form of TNF-α. The bivalency of adalimumab and the trimeric nature of TNF-α potentially allow several forms of associative complexes that may differ in stoichiometry. Detailed knowledge of this reaction may be relevant to understanding adalimumab's pharmacological properties. Our FCS data showed that a single trimeric TNF-α can bind up to three adalimumab molecules. Under some conditions even larger complexes are formed, apparently the result of cross-linking of TNF-α trimers by adalimumab. In addition, distinct differences between Humira and Enbrel were observed in their association with TNF-α.

  12. Proton and tritium NMR relaxation studies of peptide inhibitor binding to bacterial collagenase: Conformation and dynamics

    International Nuclear Information System (INIS)

    The interaction of succinyl-Pro-Ala, a competitive inhibitor of Achromobacter iophagus collagenase, with the enzyme was studied by longitudinal proton and tritium relaxation. Specific deuterium and tritium labeling of the succinyl part at vicinal positions allowed the measurement of the cross-relaxation rates of individual proton or tritium spin pairs in the inhibitor-enzyme complex as well as in the free inhibitor. Overall correlation times, internuclear distances, and qualitative information on the internal mobility in Suc1 (as provided by the generalized order parameter S2) could be deduced by the comparison of proton and tritium cross-relaxation of spin pairs at complementary positions in the -CH2- CH2- moiety as analyzed in terms of the model-free approach by Lipari and Szabo. The conformational and motional parameters of the inhibitor in the free and enzyme-bound state were directly compared by this method. The measurement of proton cross-relaxation in the Ala residue provided additional information on the inhibitor binding. The determination of the order parameter in different parts of the inhibitor molecule in the bound state indicates that the succinyl and alanyl residues are primarily involved in the interaction with the enzyme activity site. The succinyl moiety, characterized in solution by the conformational equilibrium among the three staggered rotamers--i.e., trans: 50%; g+: 20%; g-: 30%--adopted in the bound state the unique trans conformation

  13. Kinetics and thermodynamics of glycans and glycoproteins binding to Holothuria scabra lectin: a fluorescence and surface plasmon resonance spectroscopic study.

    Science.gov (United States)

    Gowda, Nagaraj M; Gaikwad, Sushama M; Khan, M Islam

    2013-11-01

    Holothuria scabra produces a monomeric lectin (HSL) of 182 kDa. HSL showed strong antibacterial activity and induced bacterial agglutination under in vitro conditions, indicating its role in animals' innate immune responses. Very few lectins have been reported from echinoderms and none of these lectins have been explored in detail for their sugar-binding kinetics. Affinity, kinetics and thermodynamic analysis of glycans and glycoproteins binding to HSL were studied by fluorescence and surface plasmon resonance spectroscopy. Lectin binds with higher affinity to O-linked than N-linked asialo glycans, and the affinities were relatively higher than that for sialated glycans and glycoproteins. T-antigen α-methyl glycoside was the most potent ligand having the highest affinity (Ka 8.32 ×10(7) M(-1)). Thermodynamic and kinetic analysis indicated that the binding of galactosyl Tn-antigen and asialo glycans is accompanied by an enthalpic contribution in addition to higher association rate coupled by low activation energy for the association process. Presence of sialic acid or protein matrix inhibits binding. Higher affinity of HSL for O-glycans than N-glycans had biological implications; since HSL specifically recognizes bacteria, which have mucin or O-glycan cognate on their cell surfaces and play a major role in animal innate immunity. Since, HSL had higher affinity to T-antigen, makes it a useful tool for cancer diagnostic purpose. PMID:23736907

  14. Stability, protein binding and clearance studies of [99mTc]DTPA. Evaluation of a commercially available dry-kit

    DEFF Research Database (Denmark)

    Rehling, M

    1988-01-01

    quality of a commercial [99mTc]DTPA preparation (C.I.S., France) with reference to stability, protein binding and accuracy of the determined plasma clearance values as a measure of GFR. The stability of the preparations was studied by thin-layer chromatography, the in vitro protein binding by Sephadex...... filtration after incubation with human serum albumin and in vivo protein binding by filtration of human plasma. The accuracy of the plasma clearance values was investigated by comparison with the simultaneously measured plasma clearance of [51Cr]EDTA. There was no detectable free pertechnetate or hydrolysed...... reduced technetium in eight vials five and six hours after the preparation. The in vitro protein binding 10 (20), 120 and 300 min after the preparation of eight vials was 2.3% (0.8%), 0.2% and 0.1%, respectively. The in vivo protein binding in 12 patients 5, 90 and 180 min after the injection was 0.3%, 0...

  15. Synthesis and crystal structure elucidation of new copper(II)-based chemotherapeutic agent coupled with 1,2-DACH and orthovanillin: Validated by in vitro DNA/HSA binding profile and pBR322 cleavage pathway.

    Science.gov (United States)

    Zaki, Mehvash; Afzal, Mohd; Ahmad, Musheer; Tabassum, Sartaj

    2016-08-01

    New copper(II)-based complex (1) was synthesized and characterized by analytical, spectroscopic and single crystal X-ray diffraction. The in vitro binding studies of complex 1 with CT DNA and HSA have been investigated by employing biophysical techniques to examine the binding propensity of 1 towards DNA and HSA. The results showed that 1 avidly binds to CT DNA via electrostatic mode along with the hydrogen bonding interaction of NH2 and CN groups of Schiff base ligand with the base pairs of DNA helix, leads to partial unwinding and destabilization of the DNA double helix. Moreover, the CD spectral studies revealed that complex 1 binds through groove binding interaction that stabilizes the right-handed B-form of DNA. Complex 1 showed an impressive photoinduced nuclease activity generating single-strand breaks in comparison with the DNA cleavage activity in presence of visible light. The mechanistic investigation revealed the efficiency of 1 to cleave DNA strands by involving the generation of reactive oxygen species. Furthermore, the time dependent DNA cleavage activity showed that there was gradual increase in the amount of NC DNA on increasing the photoexposure time. However, the interaction of 1 and HSA showed that the change of intrinsic fluorescence intensity of HSA was induced by the microenvironment of Trp residue. PMID:27289445

  16. Contribution of 238U-234U-230Th to the mineralogical and geochemical study of alteration profiles. The case of two African lateritic profiles

    International Nuclear Information System (INIS)

    In weathering profiles, water-rock interactions generate chemical fluxes from continents to oceans, as dissolved elements or particles. Laterites cover one third of the continents' surface and their formation processes are discussed. It is proposed to study such profiles to decipher their formation and evolution and to recognize the active weathering processes affecting them. Whole rock samples were analysed as well as fine clay fractions (238U-234U-230Th disequilibria in characterising recent mobilities were particularly considered. Two laterites were studied: a ferri-crete from Burkina Faso, and a latosol from Cameroon. The superposed petrographical horizons of lateritic profiles derive from different weathering conditions of the bedrock, and not from a continuous and progressive weathering process. The autochthonous formation of the ferruginous caps is evidenced by mineralogical and geochemical arguments. Remobilization and redistribution of chemical elements occur during the evolution of the profiles, as shown by the lanthanide distribution, which also modifies the signature of long period isotopic systems. Recent, or present, chemical mobilities affect the whole profiles, as evidenced by the 238U-234U-230Th disequilibria. The characteristics of U mobilization processes can be evaluated by use of radioactive decay equations for simple systems affected by a single U mobilization process and then evolving as closed systems. In the case of open systems affected by both U leaching and U input, an appropriate modelling allow to estimate the characteristics of U mobilities (flux, variations). The 238U-234U-230Th disequilibria are useful to detect and characterise the recent chemical mobilities affecting the weathering profiles. It appears that several processes presently affect each horizon of the lateritic profiles, and thus participate to the exported chemical fluxes. (author)

  17. Reductions in [3H]nicotinic acetylcholine binding in Alzheimer's disease and Parkinson's disease: an autoradiographic study

    International Nuclear Information System (INIS)

    In Alzheimer's disease (AD) and Parkinson's disease (PD), dysfunction in the basal forebrain cholinergic system is accompanied by a consistent loss of presynaptic cholinergic markers in cortex, but changes in cholinergic receptor binding sites are poorly understood. In the present study, we used receptor autoradiography to map the distribution of nicotinic [3H]acetylcholine binding sites in cortices of individuals with AD and PD and matched control subjects. In both diseases, a profound loss of nicotinic receptors occurs in all cortical layers, particularly the deepest layers

  18. Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Guillermo Salgado-Moran

    2013-01-01

    Full Text Available The binding of ethambutol to the C-terminal domain of the arabinosyltransferase from Mycobacterium tuberculosis was studied. The analysis was performed using an in silico approach in order to find out, by docking calculations and energy descriptors, the conformer of Ethambutol that forms the most stable complex with the C-terminal domain of arabinosyltransferase. The complex shows that location of the Ethambutol coincides with the cocrystallization ligand position and that amino acid residues ASH1051, ASN740, ASP1052, and ARG1055 should be critical in the binding of Ethambutol to C-terminal domain EmbC.

  19. A sensitive flow cytometric methodology for studying the binding of L. chagasi to canine peritoneal macrophages

    Directory of Open Access Journals (Sweden)

    Mosser David M

    2005-05-01

    Full Text Available Abstract Background The Leishmania promastigote-macrophage interaction occurs through the association of multiple receptors on the biological membrane surfaces. The success of the parasite infection is dramatically dependent on this early interaction in the vertebrate host, which permits or not the development of the disease. In this study we propose a novel methodology using flow cytometry to study this interaction, and compare it with a previously described "in vitro" binding assay. Methods To study parasite-macrophage interaction, peritoneal macrophages were obtained from 4 dogs and adjusted to 3 × 106 cells/mL. Leishmania (Leishmania chagasi parasites (stationary-phase were adjusted to 5 × 107 cells/mL. The interaction between CFSE-stained Leishmania chagasi and canine peritoneal macrophages was performed in polypropylene tubes to avoid macrophage adhesion. We carried out assays in the presence or absence of normal serum or in the presence of a final concentration of 5% of C5 deficient (serum from AKR/J mice mouse serum. Then, the number of infected macrophages was counted in an optical microscope, as well as by flow citometry. Macrophages obtained were stained with anti-CR3 (CD11b/CD18 antibodies and analyzed by flow citometry. Results Our results have shown that the interaction between Leishmania and macrophages can be measured by flow cytometry using the fluorescent dye CFSE to identify the Leishmania, and measuring simultaneously the expression of an important integrin involved in this interaction: the CD11b/CD18 (CR3 or Mac-1 β2 integrin. Conclusion Flow cytometry offers rapid, reliable and sensitive measurements of single cell interactions with Leishmania in unstained or phenotypically defined cell populations following staining with one or more fluorochromes.

  20. Multi-tracer study on in vivo and in vitro binding of trace elements with mouse liver DNA

    International Nuclear Information System (INIS)

    In vivo, semi-in vivo and in vitro binding of a series of trace elements (Be, Sc, Mn, Co, Zn, As, Se, Rb, Sr, Y, Zr, Tc, Ru and Rh) is studied by the multi-tracer technique. The corresponding nuclides in the multi-tracer solution used are 7Be, 46Sc, 54Mn, 58Co, 65Zn, 74As, 75Se, 83Rb, 85Sr, 88Y, 88Zr, 95Tcm, 103Ru and 102Rhm. It is found that most elements bound mouse liver DNA in vivo except As, Ru and Rh. In the semi-in vivo experiment, only elements Rh and As are not observed to be bound with DNA. In the in vitro experiment, DNA bound with all elements, among which Rb, Se, Zr, Ru and As showed very slight binding. In comparison, the binding in vitro is the strongest, semi-in vivo the medium and in vivo the weakest

  1. Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ.

    Science.gov (United States)

    Subramani, Vinod Kumar; Kim, Doyoun; Yun, Kyunghee; Kim, Kyeong Kyu

    2016-07-01

    The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity. PMID:27265117

  2. BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.

    OpenAIRE

    Morigen; Wang Junbai

    2009-01-01

    Abstract Background We have incorporated Bayesian model regularization with biophysical modeling of protein-DNA interactions, and of genome-wide nucleosome positioning to study protein-DNA interactions, using a high-throughput dataset. The newly developed method (BayesPI) includes the estimation of a transcription factor (TF) binding energy matrices, the computation of binding affinity of a TF target site and the corresponding chemical potential. Results The method was successfully tested on ...

  3. Molecular modeling study on the allosteric inhibition mechanism of HIV-1 integrase by LEDGF/p75 binding site inhibitors.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HIV-1 integrase (IN is essential for the integration of viral DNA into the host genome and an attractive therapeutic target for developing antiretroviral inhibitors. LEDGINs are a class of allosteric inhibitors targeting LEDGF/p75 binding site of HIV-1 IN. Yet, the detailed binding mode and allosteric inhibition mechanism of LEDGINs to HIV-1 IN is only partially understood, which hinders the structure-based design of more potent anti-HIV agents. A molecular modeling study combining molecular docking, molecular dynamics simulation, and binding free energy calculation were performed to investigate the interaction details of HIV-1 IN catalytic core domain (CCD with two recently discovered LEDGINs BI-1001 and CX14442, as well as the LEDGF/p75 protein. Simulation results demonstrated the hydrophobic domain of BI-1001 and CX14442 engages one subunit of HIV-1 IN CCD dimer through hydrophobic interactions, and the hydrophilic group forms hydrogen bonds with HIV-1 IN CCD residues from other subunit. CX14442 has a larger tert-butyl group than the methyl of BI-1001, and forms better interactions with the highly hydrophobic binding pocket of HIV-1 IN CCD dimer interface, which can explain the stronger affinity of CX14442 than BI-1001. Analysis of the binding mode of LEDGF/p75 with HIV-1 IN CCD reveals that the LEDGF/p75 integrase binding domain residues Ile365, Asp366, Phe406 and Val408 have significant contributions to the binding of the LEDGF/p75 to HIV1-IN. Remarkably, we found that binding of BI-1001 and CX14442 to HIV-1 IN CCD induced the structural rearrangements of the 140 s loop and oration displacements of the side chains of the three conserved catalytic residues Asp64, Asp116, and Glu152 located at the active site. These results we obtained will be valuable not only for understanding the allosteric inhibition mechanism of LEDGINs but also for the rational design of allosteric inhibitors of HIV-1 IN targeting LEDGF/p75 binding site.

  4. Interaction of phenylbutazone and colchicine in binding to serum albumin in rheumatoid therapy: 1H NMR study

    Science.gov (United States)

    Maciążek-Jurczyk, M.; Sułkowska, A.; Bojko, B.; Równicka-Zubik, J.; Sułkowski, W. W.

    2009-09-01

    The monitoring of drug concentration in blood serum is necessary in multi-drug therapy. Mechanism of drug binding with serum albumin (SA) is one of the most important factors which determine drug concentration and its transport to the destination tissues. In rheumatoid diseases drugs which can induce various adverse effects are commonly used in combination therapy. Such proceeding may result in the enhancement of those side effects due to drug interaction. Interaction of phenylbutazone and colchicine in binding to serum albumin and competition between them in gout has been studied by proton nuclear magnetic resonance ( 1H NMR) technique. The aim of the study was to determine the low affinity binding sites, the strength and kind of interaction between serum albumin and drugs used in combination therapy. The study of competition between phenylbutazone and colchicine in binding to serum albumin points to the change of their affinity to serum albumin in the ternary systems. This should be taken into account in multi-drug therapy. This work is a subsequent part of the spectroscopic study on Phe-COL-SA interactions [A. Sułkowska, et al., J. Mol. Struct. 881 (2008) 97-106].

  5. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    Energy Technology Data Exchange (ETDEWEB)

    Bijari, Nooshin [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Shokoohinia, Yalda [Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza; Ranjbar, Samira; Parvaneh, Shahram [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Moieni-Arya, Maryam [Student Research Committee, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2013-11-15

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp{sub 214} residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes.

  6. In Silico and in Vitro Study of Binding Affinity of Tripeptides to Amyloid β Fibrils: Implications for Alzheimer's Disease.

    Science.gov (United States)

    Viet, Man Hoang; Siposova, Katarina; Bednarikova, Zuzana; Antosova, Andrea; Nguyen, Truc Trang; Gazova, Zuzana; Li, Mai Suan

    2015-04-23

    Self-assembly of Aβ peptides into amyloid aggregates has been suggested as the major cause of Alzheimer's disease (AD). Nowadays, there is no medication for AD, but experimental data indicate that reversion of the process of amyloid aggregation reduces the symptoms of disease. In this paper, all 8000 tripeptides were studied for their ability to destroy Aβ fibrils. The docking method and the more sophisticated MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) method were employed to calculate the binding affinity and mode of tripeptides to Aβ fibrils. The ability of these peptides to depolymerize Aβ fibrils was also investigated experimentally using atomic force microscopy and fluorescence spectroscopy (Thioflavin T assay). It was shown that tripeptides prefer to bind to hydrophobic regions of 6Aβ9-40 fibrils. Tripeptides WWW, WWP, WPW and PWW were found to be the most potent binders. In vitro experiments showed that tight-binding tripeptides have significant depolymerizing activities and their DC50 values determined from dose-response curves were in micromolar range. The ability of nonbinding (GAM, AAM) and weak-binding (IVL and VLA) tripeptides to destroy Aβ fibrils was negligible. In vitro data of tripeptide depolymerizing activities support the predictions obtained by molecular docking and all-atom simulation methods. Our results suggest that presence of multiple complexes of heterocycles forming by tryptophan and proline residues in tripeptides is crucial for their tight binding to Aβ fibrils as well as for extensive fibril depolymerization. We recommend PWW for further studies as it has the lowest experimental binding constant. PMID:25815792

  7. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    International Nuclear Information System (INIS)

    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp214 residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes

  8. Profile of Nigerians with diabetes mellitus - Diabcare Nigeria study group (2008: Results of a multicenter study

    Directory of Open Access Journals (Sweden)

    Sunday Chinenye

    2012-01-01

    Full Text Available Background: Diabetes Mellitus is the commonest endocrine-metabolic disorder in Nigeria similar to the experience in other parts of the world. The aim was to assess the clinical and laboratory profile, and evaluate the quality of care of Nigerian diabetics with a view to planning improved diabetes care. Materials and Methods: In a multicenter study across seven tertiary health centers in Nigeria, the clinical and laboratory parameters of diabetic out-patients were evaluated. Clinical parameters studied include type of diabetes, anthropometry, and blood pressure (BP status, chronic complications of diabetes, and treatment types. Laboratory data assessed included fasting plasma glucose (FPG, 2-h post-prandial (2-HrPP glucose, glycated hemoglobin (HbA1c, urinalysis, serum lipids, electrolytes, urea, and creatinine. Results: A total of 531 patients, 209 (39.4% males and 322 (60.6% females enrolled. The mean age of the patients was 57.1 ± 12.3 years with the mean duration of diabetes of 8.8 ± 6.6 years. Majority (95.4% had type 2 diabetes mellitus (DM compared to type 1 DM (4.6%, with P < 0.001. The mean FPG, 2-HrPP glucose, and HbA1c were 8.1 ± 3.9 mmol/L, 10.6 ± 4.6 mmol/L, and 8.3 ± 2.2%, respectively. Only 170 (32.4% and 100 (20.4% patients achieved the ADA and IDF glycemic targets, respectively. Most patients (72.8% did not practice self-monitoring of blood glucose. Hypertension was found in 322 (60.9%, with mean systolic BP 142.0 ± 23.7 mmHg, and mean diastolic BP 80.7 ± 12.7 mmHg. Diabetic complications found were peripheral neuropathy (59.2%, retinopathy (35.5%, cataracts (25.2%, cerebrovascular disease (4.7%, diabetic foot ulcers (16.0%, and nephropathy (3.2%. Conclusion: Most Nigerian diabetics have suboptimal glycemic control, are hypertensives, and have chronic complications of DM. Improved quality of care and treatment to target is recommended to reduce diabetes-related morbidity and mortality.

  9. Clinical and psychosocial profile of HIV orphans in Northern Karnataka – a longitudinal study

    Directory of Open Access Journals (Sweden)

    Mahesh.V

    2013-07-01

    Full Text Available Background India currently has an estimated 220,000 children infected by HIV/AIDS and is home to the largest number of AIDS Orphans only next to South Africa in the world. The pandemic not only deprives Orphans of their rights to enjoy a good or a normal childhood, but it also has deleterious effects on their chances of survival or well-being. Thus the future of these children orphaned by the AIDS epidemic addresses a key social issue. Hence this study was done with the objectives, to assess the Demographic profile, Clinical profile and psycho-social profile of HIV Orphans. Methods A Longitudinal study on 82 HIV orphans in the age group 5 to 15yrs was conducted after obtaining informed consent from their caregivers for duration of one year from at Anti retroviral therapy (ART centre KIMS, Hubli. Clinical profile was assessed by WHO staging of HIV, Child Behavior Checklist (CBCL was used to assess Psycho-Social Profile. Chi-square test, paired t test are the tests of significance for qualitative and quantitative variables respectively. Results Mother to Child was the most common mode of transmission in majority of cases i.e 97%. Among the orphans 60% of them were deprived of mother’s care i.e Double orphans and maternal orphans. Majority of subjects i.e 29 (35.4% were in stage 2 of WHO clinical staging. 27(32.9% were in mild immunosuppression at 350 to 499 Absolute lymphocytic count and CD4% in the range of 20 to 25% in 26(31.7%. A statistically significant increase of psychosocial problem in orphans was observed during the follow-up. Conclusion It can be concluded that during the follow-up Psycho-social problems increased in Orphans significantly.

  10. A comparative study of MR imaging profile of titanium pedicle screws

    International Nuclear Information System (INIS)

    Objective: We compared the MR imaging profile of three different types of titanium pedicle screw implants in common usage in a human cadaveric model. We additionally compared the change in temperature during imaging among three constructs. Material and Methods: Titanium-based lumbar pedicle screw/rod constructs from three manufacturers were implanted sequentially in a human cadaveric spine. MR imaging was then performed using both conventional spin-echo sequences and advanced imaging pulse sequences. Changes in tissue temperature were also measured during imaging to assess differences among the various implants. MR images were compared in a blinded fashion by two neuro radiologists. Results: No significant differences in imaging profile were noted between the three types of titanium implants with regards to their MR artifact profile. Fast spin-echo sequences led to a decrease in perceptible MR artifacts. Moreover, there were no significant differences in temperature increase among the three manufacturers (mean increase 0.5 deg C) during imaging. Conclusion: Slight differences in the percentage of titanium among the three pedicle screw systems does not appear to result in artifact differences during MR imaging. Therefore, with regard to imaging profile considerations, the three systems studied should be considered interchangeable

  11. Proton NMR studies of aliphatic ligand binding to human plasminogen kringle 4

    International Nuclear Information System (INIS)

    A detailed 1H NMR analysis of ligand binding to the human plasminogen kringle 4 domain has been carried out at 300 MHz. The ligands that were investigated are Nα-acetyl-L-lysine, L-lysine methyl ester, Nα-acetyl-L-lysine methyl ester, L-lysine hydroxamic acid, trans-(aminomethyl)cyclohexanecarboxylic acid (AMCHA), and 4-(aminomethyl)bicyclo[2.2.2]octane-1-carboxylic acid (AMBOC). Specific ligand-binding effects were detected via two-dimensional COSY experiments. The side chains that are the most perturbed by ligand presence are those from Trp62, Phe64, and Trp72. Ligand-kringle saturation transfer (Overhauser) experiments show that the aromatic rings from these three residues are in direct contact with the ligand. These results add support to a previously reported model of the kringle 4 lysine-binding site by which these aromatic groups are assigned a key role in establishing hydrophobic interactions with the ligand molecule. Equilibrium association constants (Ka) and kinetic rate constants (kon, koff) were determined for the binding of the various linear and cyclic ligands to kringle 4. The numerical data are discussed in terms of optimal ligand structure and requirements for fibrin binding in vivo

  12. Evidence from opiate binding studies that heroin acts through its metabolites.

    Science.gov (United States)

    Inturrisi, C E; Schultz, M; Shin, S; Umans, J G; Angel, L; Simon, E J

    1983-01-01

    The relative affinity to opiate receptors of heroin, 6-acetylmorphine and morphine was estimated by determining their ability to displace specifically bound 3H-naltrexone from rat brain opiate binding sites. In vitro hydrolysis of heroin to 6-acetylmorphine was monitored in the binding assay filtrate by use of a quantitative HPLC procedure. The rate of heroin hydrolysis was significantly slower at 0 degrees C than at 37 degrees C. The displacement of 1 nM 3H-naltrexone by unlabeled ligand at concentrations ranging from 7 to 500 nM was measured at 0 degrees C for 120 minutes, yielding IC50 values of heroin = 483 nM, 6-acetylmorphine = 73 nM and morphine = 53 nM. When the binding data for heroin were recalculated to include the displacement that could be attributed to the 6-acetylmorphine derived from heroin degradation during the incubation, all of the apparent heroin binding was accounted for by the 6-acetylmorphine. These results are consistent with previous reports of the low binding affinity of morphine congeners (e.g., codeine) that lack a free phenolic 3-hydroxyl group and support the view that heroin is a prodrug which serves to determine the distribution of its intrinsically active metabolites, 6-acetylmorphine and morphine. PMID:6319928

  13. Binding studies of a large antiviral polyamide to a natural HPV sequence.

    Science.gov (United States)

    He, Gaofei; Vasilieva, Elena; Harris, George Davis; Koeller, Kevin J; Bashkin, James K; Dupureur, Cynthia M

    2014-07-01

    PA1 is a large hairpin polyamide (dImPyPy-β-PyPyPy-γ-PyPy-β-PyPyPyPy-β-Ta; Py = pyrrole, Im = imidazole, β = beta alanine) that targets the sequence 5'-WWGWWWWWWW-3' (W = A or T) and is effective in eliminating HPV16 in cell culture (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are its DNA binding properties toward a natural DNA, a 523 bp portion of HPV16 (2150-2672) containing three predicted perfect match sites. Strategies for obtaining binding data on large fragments using capillary electrophoresis are also described. Using an Fe EDTA conjugate of PA1, 19 affinity cleavage (AC) patterns were detected for this fragment. In many cases, there are multiple possible binding sequences (perfect, single and double mismatch sites) consistent with the AC data. Quantitative DNase I footprinting analysis indicates that perfect and most single mismatch sites bind PA1 with Kds between 0.7 and 4 nM, indicating excellent tolerance for the latter. Double mismatch sites exhibit Kds between 12 and 62 nM. A large fraction of the accessible sequence is susceptible to PA1 binding, much larger than predicted based on the literature of polyamide-DNA recognition rules. PMID:24582833

  14. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen; Gammeltoft, Steen

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... profile of the integrin-linked kinase associated phosphatase (ILKAP), a member of the protein phosphatase 2C (PP2C) family. Phosphatases can potentially dephosphorylate these phosphopeptide substrates but, interestingly, performing the binding studies at 4 °C allowed efficient binding to phosphopeptides......, without the need for phosphopeptide mimics or phosphatase inhibitors. As no proven ILKAP substrates were available, we selected phosphopeptide substrates among known PP2Cδ substrates including the protein kinases: p38, ATM, Chk1, Chk2 and RSK2 and synthesized directly on PEGA solid supports through a BAL...

  15. Leadership development study :success profile competencies and high-performing leaders at Sandia National Laboratories.

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Katherine M.; Mulligan, Deborah Rae; Szenasi, Gail L.; Crowder, Stephen Vernon

    2005-04-01

    Sandia is undergoing tremendous change. Sandia's executive management recognized the need for leadership development. About ten years ago the Business, Leadership, and Management Development department in partnership with executive management developed and implemented the organizational leadership Success Profile Competencies to help address some of the changes on the horizon such as workforce losses and lack of a skill set in the area of interpersonal skills. This study addresses the need for the Business, Leadership, and Management Development department to provide statistically sound data in two areas. One is to demonstrate that the organizational 360-degree success profile assessment tool has made a difference for leaders. A second area is to demonstrate the presence of high performing leaders at the Labs. The study utilized two tools to address these two areas. Study participants were made up of individuals who have solid data on Sandia's 360-degree success profile assessment tool. The second assessment tool was comprised of those leaders who participated in the Lockheed Martin Corporation Employee Preferences Survey. Statistical data supports the connection between leader indicators and the 360-degree assessment tool. The study also indicates the presence of high performing leaders at Sandia.

  16. SOLUBILITY AND DISSOLUTION PROFILE STUDIES OF GLICLAZIDE IN PHARMACEUTICAL FORMULATIONS BY RP-HPLC

    OpenAIRE

    Narasimha Swamy Lakka; Nishant Goswami

    2012-01-01

    This study describes the solubility and dissolution profile of Gliclazide. The solubility study was evaluated by using the shake flask method. The dissolution study has been carried out in different buffers for Gliclazide solid dosage form and estimated by using the RP-HPLC technique. In the present study a dissolution medium was developed and selected on the basis of solubility data of Gliclazide at 37 °C. The solubility data revealed that pH 7.4 phosphate buffer (0.6375 mg/ml) shall be sui...

  17. Comparative study of the binding of trypsin to caffeine and theophylline by spectrofluorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Kang, Xiaohui [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Wang, Ruiqiang [The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052 (China); Wang, Rui; Dou, Huanjing; Wu, Jing; Song, Chuanjun [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China)

    2013-06-15

    The interactions between trypsin and caffeine/theophylline were investigated by fluorescence spectroscopy, UV–visible absorption spectroscopy, resonance light scattering and synchronous fluorescence spectroscopy under mimic physiological conditions. The results revealed that the fluorescence quenching of trypsin by caffeine and theophylline was the result of the formed complex of caffeine–trypsin and theophylline–trypsin. The binding constants and thermodynamic parameters at three different temperatures were obtained. The hydrophobic interaction was the predominant intermolecular forces to stabilize the complex. Results showed that caffeine was the stronger quencher and bound to trypsin with higher affinity than theophylline. -- Highlights: ► The fluorescence of trypsin can be quenched by caffeine or theophylline via hydrophobic contacts. ► Caffeine binds to trypsin with higher affinity than theophylline. ► The influence of molecular structure on the binding aspects is reported.

  18. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  19. Comparative study of the binding of trypsin to caffeine and theophylline by spectrofluorimetry

    International Nuclear Information System (INIS)

    The interactions between trypsin and caffeine/theophylline were investigated by fluorescence spectroscopy, UV–visible absorption spectroscopy, resonance light scattering and synchronous fluorescence spectroscopy under mimic physiological conditions. The results revealed that the fluorescence quenching of trypsin by caffeine and theophylline was the result of the formed complex of caffeine–trypsin and theophylline–trypsin. The binding constants and thermodynamic parameters at three different temperatures were obtained. The hydrophobic interaction was the predominant intermolecular forces to stabilize the complex. Results showed that caffeine was the stronger quencher and bound to trypsin with higher affinity than theophylline. -- Highlights: ► The fluorescence of trypsin can be quenched by caffeine or theophylline via hydrophobic contacts. ► Caffeine binds to trypsin with higher affinity than theophylline. ► The influence of molecular structure on the binding aspects is reported

  20. Membrane orientation and binding determinants of G protein-coupled receptor kinase 5 as assessed by combined vibrational spectroscopic studies.

    Directory of Open Access Journals (Sweden)

    Pei Yang

    Full Text Available G-protein coupled receptors (GPCRs are integral membrane proteins involved in a wide variety of biological processes in eukaryotic cells, and are targeted by a large fraction of marketed drugs. GPCR kinases (GRKs play important roles in feedback regulation of GPCRs, such as of β-adrenergic receptors in the heart, where GRK2 and GRK5 are the major isoforms expressed. Membrane targeting is essential for GRK function in cells. Whereas GRK2 is recruited to the membrane by heterotrimeric Gβγ subunits, the mechanism of membrane binding by GRK5 is not fully understood. It has been proposed that GRK5 is constitutively associated with membranes through elements located at its N-terminus, its C-terminus, or both. The membrane orientation of GRK5 is also a matter of speculation. In this work, we combined sum frequency generation (SFG vibrational spectroscopy and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR to help determine the membrane orientation of GRK5 and a C-terminally truncated mutant (GRK51-531 on membrane lipid bilayers. It was found that GRK5 and GRK51-531 adopt a similar orientation on model cell membranes in the presence of PIP2 that is similar to that predicted for GRK2 in prior studies. Mutation of the N-terminal membrane binding site of GRK5 did not eliminate membrane binding, but prevented observation of this discrete orientation. The C-terminus of GRK5 does not have substantial impact on either membrane binding or orientation in this model system. Thus, the C-terminus of GRK5 may drive membrane binding in cells via interactions with other proteins at the plasma membrane or bind in an unstructured manner to negatively charged membranes.

  1. RNA and DNA binding properties of HIV-1 Vif protein: a fluorescence study.

    Science.gov (United States)

    Bernacchi, Serena; Henriet, Simon; Dumas, Philippe; Paillart, Jean-Christophe; Marquet, Roland

    2007-09-01

    The HIV-1 viral infectivity factor (Vif) is a small basic protein essential for viral fitness and pathogenicity. Some "non-permissive" cell lines cannot sustain replication of Vif(-) HIV-1 virions. In these cells, Vif counteracts the natural antiretroviral activity of the DNA-editing enzymes APOBEC3G/3F. Moreover, Vif is packaged into viral particles through a strong interaction with genomic RNA in viral nucleoprotein complexes. To gain insights into determinants of this binding process, we performed the first characterization of Vif/nucleic acid interactions using Vif intrinsic fluorescence. We determined the affinity of Vif for RNA fragments corresponding to various regions of the HIV-1 genome. Our results demonstrated preferential and moderately cooperative binding for RNAs corresponding to the 5'-untranslated region of HIV-1 (5'-untranslated region) and gag (cooperativity parameter omega approximately 65-80, and K(d) = 45-55 nM). In addition, fluorescence spectroscopy allowed us to point out the TAR apical loop and a short region in gag as primary strong affinity binding sites (K(d) = 9.5-14 nM). Interestingly, beside its RNA binding properties, the Vif protein can also bind the corresponding DNA oligonucleotides and their complementary counterparts with an affinity similar to the one observed for the RNA sequences, while other DNA sequences displayed reduced affinity. Taken together, our results suggest that Vif binding to RNA and DNA offers several non-exclusive ways to counteract APOBEC3G/3F factors, in addition to the well documented Vif-induced degradation by the proteasome and to the Vif-mediated repression of translation of these antiviral factors. PMID:17609216

  2. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Carson M Andorf

    Full Text Available BACKGROUND: Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are hub proteins that can interact with large numbers of partners and often play essential roles in cellular control. Depending on the number of binding sites, protein hubs can be classified at a structural level as singlish-interface hubs (SIH with one or two binding sites, or multiple-interface hubs (MIH with three or more binding sites. In terms of kinetics, hub proteins can be classified as date hubs (i.e., interact with different partners at different times or locations or party hubs (i.e., simultaneously interact with multiple partners. METHODOLOGY: Our approach works in 3 phases: Phase I classifies if a protein is likely to bind with another protein. Phase II determines if a protein-binding (PB protein is a hub. Phase III classifies PB proteins as singlish-interface versus multiple-interface hubs and date versus party hubs. At each stage, we use sequence-based predictors trained using several standard machine learning techniques. CONCLUSIONS: Our method is able to predict whether a protein is a protein-binding protein with an accuracy of 94% and a correlation coefficient of 0.87; identify hubs from non-hubs with 100% accuracy for 30% of the data; distinguish date hubs/party hubs with 69% accuracy and area under ROC curve of 0.68; and SIH/MIH with 89% accuracy and area under ROC curve of 0.84. Because our method is based on sequence information alone, it can be used even in settings where reliable protein-protein interaction data or structures of protein-protein complexes are unavailable to obtain useful insights into the functional and evolutionary characteristics of proteins and their interactions. AVAILABILITY: We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.

  3. THE STUDY OF PREVALENCE AND CLINICAL PROFILE OF VALVULAR HEART DISEASES IN A TEACHING HOSPITAL

    OpenAIRE

    Radha Krishnan; Srinivas

    2015-01-01

    Valvular heart disease is still a common causes of mortality and morbidity in India and rheumatic heart disease is still far more frequent. AIMS AND OBJECTIVES: To study the prevalence and clinical profile of rheumatic and non - rheumatic valvular heart dise ase in patients attending to Government General Hospital, Kakinada. MATERIALS AND METHODS: 100 Adult patients with valvular abnormalities attending to the Medicine and Cardiol...

  4. MYOCARDIAL BRIDGING - CLINICAL AND ANGIOGRAPHIC PROFILE IN LAST 5 YEARS; A STUDY OF 129 CASES

    OpenAIRE

    Abhilash S P; Krishna Kumar B; Praveen Velappan; PrabhaniniGupta; Sunita Viswanathan; A. George Koshy

    2010-01-01

    Aims of study : To assess the clinical and angiographical profile of myocardial bridging from consecutive coronary angiograms done over last 5 years at Medical college, Thiruvananthapuram. To assess the risk of cardiovascular events and the risk of accelerated atherosclerosis in isolated myocardial bridging. Methods : Consecutive coronary angiograms done at Medical college Thiruvananthapuram from 04/02/2005 to 31/03/2010 were reviewed for myocardial bridging. A total of 10492 coronary angiogr...

  5. Systematic enrichment analysis of gene expression profiling studies identifies consensus pathways implicated in colorectal cancer development

    OpenAIRE

    Jesús Lascorz; Kari Hemminki; Asta Försti

    2011-01-01

    Background: A large number of gene expression profiling (GEP) studies on colorectal carcinogenesis have been performed but no reliable gene signature has been identified so far due to the lack of reproducibility in the reported genes. There is growing evidence that functionally related genes, rather than individual genes, contribute to the etiology of complex traits. We used, as a novel approach, pathway enrichment tools to define functionally related genes that are consistently up- or down-r...

  6. The distinct clinical profile of chronically critically ill patients: a cohort study

    OpenAIRE

    Estenssoro, Elisa; Reina, Rosa; Canales, Héctor S; Saenz, María Gabriela; Gonzalez, Francisco E; Aprea, María M; Laffaire, Enrique; Gola, Victor; Dubin, Arnaldo

    2006-01-01

    Introduction Our goal was to describe the epidemiology, clinical profiles, outcomes, and factors that might predict progression of critically ill patients to chronically critically ill (CCI) patients, a still poorly characterized subgroup. Methods We prospectively studied all patients admitted to a university-affiliated hospital intensive care unit (ICU) between 1 July 2002 and 30 June 2005. On admission, we recorded epidemiological data, the presence of organ failure (multiorgan dysfunction ...

  7. Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

    OpenAIRE

    Gong, Binsheng; Wang, Charles; Su, Zhenqiang; Hong, Huixiao; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Shi, Leming; Auerbach, Scott S.; Tong, Weida; Xu, Joshua

    2014-01-01

    RNA-Seq provides the capability to characterize the entire transcriptome in multiple levels including gene expression, allele specific expression, alternative splicing, fusion gene detection, and etc. The US FDA-led SEQC (i.e., MAQC-III) project conducted a comprehensive study focused on the transcriptome profiling of rat liver samples treated with 27 chemicals to evaluate the utility of RNA-Seq in safety assessment and toxicity mechanism elucidation. The chemicals represented multiple chemog...

  8. PROFILE OF THE ELECTRONIC COMMERCE CONSUMER: A STUDY WITH BRAZILIAN UNIVERSITY STUDENTS

    OpenAIRE

    Dario de Oliveira Lima-Filho; Camila de Souza Alves; Filipe Quevedo-Silva; Luísa Brito Moreira; Vicente Rodrigues Garcez; Willian Ferreira Aratani

    2012-01-01

    This work aimed to analyze the profile of electronic commerce costumers, as well as identify characteristics that differentiate costumers from non-costumers of electronic commerce. For this purpose, a quantitative-descriptive study was carried out with university students of a federal public univer sity of the south-western region of Brazil, during the first half of 2011, using a structured questionnaire. Data were analyzed through descriptive statistics, logistic regre...

  9. How different an emotional competence profile can be, when we became slim? – longitudinal case study

    OpenAIRE

    Veiga-Branco, Augusta

    2011-01-01

    This case study focuses on Emotional Competence (Saarni, 2000; Veiga Branco, 2004, 2007), the concept redefined from the initial Emotional Intelligence (Mayer-Salovey, 1990, 1997, Goleman, 1995), here applied, to perceive the behavioral differences when someone lost 43Kg of body weight, without pathology associated. The longitudinal research compares, the behavior profile, before (obese) and after (non obese) a weight loss, through Self-conscience, Self-motivation, Emotions ...

  10. A study of clinico-demographic profile of patients with dissociative disorder

    OpenAIRE

    SK Shah

    2013-01-01

    Objectives To study the clinical and socio demographic profile of patients with dissociative disorder and their comorbid mental illness. Materials and methods Fifty-one patients of dissociative disorder presenting to emergency and outpatient department of Psychiatry at College of Medical Sciences Teaching Hospital during the period from Jan to March 2012 were included. International statistical classification of diseases and related health problems tenth edition, diagnostic criteria for res...

  11. A preliminary MTD-PLS study for androgen receptor binding of steroid compounds

    Science.gov (United States)

    Bora, Alina; Seclaman, E.; Kurunczi, L.; Funar-Timofei, Simona

    The relative binding affinities (RBA) of a series of 30 steroids for Human Androgen Receptor (AR) were used to initiate a MTD-PLS study. The 3D structures of all the compounds were obtained through geometry optimization in the framework of AM1 semiempirical quantum chemical method. The MTD hypermolecule (HM) was constructed, superposing these structures on the AR-bonded dihydrotestosterone (DHT) skeleton obtained from PDB (AR complex, ID 1I37). The parameters characterizing the HM vertices were collected using: AM1 charges, XlogP fragmental values, calculated fragmental polarizabilities (from refractivities), volumes, and H-bond parameters (Raevsky's thermodynamic originated scale). The resulted QSAR data matrix was submitted to PCA (Principal Component Analysis) and PLS (Projections in Latent Structures) procedure (SIMCA P 9.0); five compounds were selected as test set, and the remaining 25 molecules were used as training set. In the PLS procedure supplementary chemical information was introduced, i.e. the steric effect was always considered detrimental, and the hydrophobic and van der Waals interactions were imposed to be beneficial. The initial PLS model using the entire training set has the following characteristics: R2Y = 0.584, Q2 = 0.344. Based on distances to the model criterions (DMODX and DMODY), five compounds were eliminated and the obtained final model had the following characteristics: R2Y D 0.891, Q2 D 0.591. For this the external predictivity on the test set was unsatisfactory. A tentative explanation for these behaviors is the weak information content of the input QSAR matrix for the present series comparatively with other successful MTD-PLS modeling published elsewhere.

  12. Mechanical properties of phosphorene nanotubes: a density functional tight-binding study.

    Science.gov (United States)

    Sorkin, V; Zhang, Y W

    2016-09-30

    Using the density functional tight-binding method, we studied the elastic properties, deformation and failure of armchair (AC) and zigzag (ZZ) phosphorene nanotubes (PNTs) under uniaxial tensile strain. We found that the deformation and failure of PNTs are very much anisotropic. For ZZ PNTs, three deformation phases are recognized: the primary linear elastic phase-which is associated with interactions between neighboring puckers, succeeded by the bond rotation phase-where the puckered configuration of phosphorene is smoothed via bond rotation, and lastly the bond elongation phase-where the P-P bonds are directly stretched up to the maximally allowed limit and failure is initiated by the rupture of the most stretched bonds. For AC PNTs, the applied strain stretches the bonds up to the maximally allowed limit, causing their ultimate failure. For both AC and ZZ PNTs, their failure strain and failure stress are sensitive- while the Young's modulus, flexural rigidity, radial Poisson's ratio and thickness Poisson's ratio are relatively insensitive-to the tube diameter. More specifically, for AC PNTs, the failure strain decreases from 0.40 to 0.25 and the failure stress increases from 13 GPa to 21 GPa when the tube diameter increases from 13.3 Å to 32.8 Å; while for ZZ PNTs, the failure strain decreases from 0.66 to 0.55 and the failure stress increases from 4 GPa to 9 GPa when the tube diameter increases from 13.2 Å to 31.1 Å. The Young's modulus, flexural rigidity, radial and thickness Poisson ratios are 114.2 GPa, 0.019 eV · nm(2), 0.47 and 0.11 for AC PNTs, and 49.2 GPa, 0.071 eV · nm(2), 0.07 and 0.21 for ZZ PNTs, respectively. The present findings provide valuable references for the design and application of PNTs as device elements. PMID:27535543

  13. Study of the Binding Energies between Unnatural Amino Acids and Engineered Orthogonal Tyrosyl-tRNA Synthetases

    Science.gov (United States)

    Ren, Wei; Truong, Tan M.; Ai, Hui-Wang

    2015-07-01

    We utilized several computational approaches to evaluate the binding energies of tyrosine (Tyr) and several unnatural Tyr analogs, to several orthogonal aaRSes derived from Methanocaldococcus jannaschii and Escherichia coli tyrosyl-tRNA synthetases. The present study reveals the following: (1) AutoDock Vina and ROSETTA were able to distinguish binding energy differences for individual pairs of favorable and unfavorable aaRS-amino acid complexes, but were unable to cluster together all experimentally verified favorable complexes from unfavorable aaRS-Tyr complexes; (2) MD-MM/PBSA provided the best prediction accuracy in terms of clustering favorable and unfavorable enzyme-substrate complexes, but also required the highest computational cost; and (3) MM/PBSA based on single energy-minimized structures has a significantly lower computational cost compared to MD-MM/PBSA, but still produced sufficiently accurate predictions to cluster aaRS-amino acid interactions. Although amino acid-aaRS binding is just the first step in a complex series of processes to acylate a tRNA with its corresponding amino acid, the difference in binding energy, as shown by MD-MM/PBSA, is important for a mutant orthogonal aaRS to distinguish between a favorable unnatural amino acid (unAA) substrate from unfavorable natural amino acid substrates. Our computational study should assist further designing and engineering of orthogonal aaRSes for the genetic encoding of novel unAAs.

  14. Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Wei; Tan, Jia-Heng; Chen, Shuo-Bin; Hou, Jin-Qiang; Li, Ding [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Huang, Zhi-Shu, E-mail: ceshzs@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China); Gu, Lian-Quan, E-mail: cesglq@mail.sysu.edu.cn [School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006 (China)

    2011-03-18

    Research highlights: {yields} Hydrophobic interaction provided an important driving force for the interaction between ligand and G-quadruplex. {yields} Constrained water molecules were released from surface of G-tetrad upon the formation of the complex. {yields} The end-stacking mode for quindoline derivative was validated through UV-vis, ITC, steady-state, and time-resolved fluorescence experiment. {yields} The binding of compound 1 to quadruplex was found to be a temperature-dependent and enthalpy-entropy compensation process. -- Abstract: Quindoline derivatives as telomeric quadruplex ligands have shown good biological activity for telomerase inhibition. In the present study, we used spectroscopic and calorimetric methods to investigate the interactions between a quindoline derivative (5-methyl-11-(2-morpholinoethylamino)-10-H-indolo-[3,2-b]quinolin-5-ium iodide, compound 1) and human telomeric G-quadruplex. The thermodynamic studies using isothermal titration calorimetry (ITC) indicated that their binding process was temperature-dependent and enthalpy-entropy co-driven. The significant negative heat capacity was obtained experimentally from the temperature dependence of enthalpy changes, which was consistent with that from theoretical calculation, and all suggesting significant hydrophobic contribution to the molecular recognition process. Based on the results from UV-vis, ITC, steady-state and time-resolved fluorescence, their binding mode was determined as two ligand molecules stacking on the quartets on both ends of the quadruplex. These results shed light on rational design and development of quindoline derivatives as G-quadruplex binding ligands.

  15. One-pot solvent free synthesis and DNA binding studies of thieno[2,3-b]-1,8-naphthyridines.

    Science.gov (United States)

    Naik, Tangali R Ravikumar; Naik, Halehatty S Bhojya; Prabhakara, Mustur C

    2008-01-01

    With the aim of evaluating interaction between double-stranded calf thymus (ds)DNA and sulphur containing fused planar rings, the derivatives of 1,8-naphthyridine containing thiono groups were synthesized by the condensation of 2-mercapto-3-formyl[1,8]naphthyridines using 1-chloroacetone, 2-chloroacetamide, chloroaceticacid, and 2-chloro-1-phenylethanone in the presence of anhydrous potassium carbonate as s catalyst under solvent free microwave irradiation. The structures of the compounds were elucidated on the basis of elemental analysis, IR, (1)H NMR, and mass spectra. The interaction of thieno[2,3-b]-1,8-naphthyridine-2-carboxylic acid (TNC) (3a) with ct-DNA was studied by UV-Vis spectrophotometry, viscosity, thermal denaturation, as well as cyclic voltammetry experiments. On binding to DNA, the absorption spectrum underwent bathochromic and hypochromic shifts. Binding parameters, determined from spectrophotometric measurements indicated a binding constant of Kb=2.1 x 10(6) M(-1). The thieno[2,3-b]-1,8-naphthyridine-2-carboxylic acid (3a) increases the viscosity of sonicated rod-like DNA fragments. The binding of TNC to DNA increased the melting temperature by about 4 degrees C. The decrease in peak current heights and shifts of peak potential values are observed by the addition of calf thymus DNA in cyclic voltammetry studies. PMID:18080916

  16. In silico studies on structure-function of DNA GCC- box binding domain of brassica napus DREB1 protein

    International Nuclear Information System (INIS)

    DREB1 is a transcriptional factor, which selectively binds with the promoters of the genes involved in stress response in the plants. Homology of DREB protein and its binding element have been detected in the genome of many plants. However, only a few reports exist that discusses the binding properties of this protein with the gene (s) promoter. In the present study, we have undertaken studies exploring the structure-function relationship of Brassica napus DREB1. Multiple sequence alignment, protein homology modeling and intermolecular docking of GCC-box binding domain (GBD) of the said protein was carried out using atomic coordinates of GBD from Arabdiopsis thaliana and GCC-box containing DNA respectively. Similarities and/or identities in multiple, sequence alignment, particularly at the functionally important amino acids, strongly suggested the binding specificity of B. napus DREB1 to GCC-box. Similarly, despite 56% sequence homology, tertiary structures of both template and modeled protein were found to be extremely similar as indicated by root mean square deviation of 0.34 A. More similarities were established between GBD of both A. thaliana and B. napus DREB1 by conducting protein docking with the DNA containing GCC-box. It appears that both proteins interact through their beta-sheet with the major DNA groove including both nitrogen bases and phosphate and sugar moieties. Additionally, in most cases the interacting residues were also found to be identical. Briefly, this study attempts to elucidate the molecular basis of DREB1 interaction with its target sequence in the promoter. (author)

  17. Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study.

    Directory of Open Access Journals (Sweden)

    Gugan Kothandan

    Full Text Available Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy. Owing to the importance of these receptors, information regarding the binding site is of prime importance. Structural studies have been hampered due to the lack of X-ray crystal structures, and templates with close homologs for comparative modeling. Most of the previous models were based on the bovine rhodopsin and β2-adrenergic receptor. In this study, based on a closer homolog with higher resolution (CXCR4, PDB code: 3ODU 2.5 Å, we constructed three-dimensional models. The main aim of this study was to provide relevant information on binding sites of these receptors. Molecular dynamics simulation was done to refine the homology models and PROCHECK results indicated that the models were reasonable. Here, binding poses were checked with some established inhibitors of high pharmaceutical importance against the modeled receptors. Analysis of interaction modes gave an integrated interpretation with detailed structural information. The binding poses confirmed that the acidic residues Glu291 (CCR2 and Glu283 (CCR5 are important, and we also found some additional residues. Comparisons of binding sites of CCR2/CCR5 were done sequentially and also by docking a potent dual antagonist. Our results can be a starting point for further structure-based drug design.

  18. Studies on the Synthesis, Characterization, DNA Binding, Cytotoxicity and Antioxidant activity of 2-methyl-4-nitrophenylferrocene

    International Nuclear Information System (INIS)

    We report herein the synthesis, structural characterization, DNA binding, BamH1 digestion, cytotoxicity and antioxidant activity of 2-methyl-4-nitrophenylferrocene. Structural characterization is based on multinuclear (1H and 13C) NMR, FT-IR spectroscopy and elemental analysis. Interaction of 2-methyl-4-nitrophenylferrocene with pBR322 plasmid DNA shows noncovalent interactions however these noncovalent interactions reveal the prevention of BamH1 restriction site (g/ggtcc). In the voltammogram, a negative shift in peak potential has been observed on addition of increasing concentration of CT-DNA, which shows electrostatic interaction for 2-methyl-4-nitrophenylferro with negatively charged phosphate of DNA backbone. The binding ratio, binding constant, binding free energy and diffusion coefficient of free and bound drug were calculated to understand the mechanism. The high negative value of -delta G signifies the spontaneity and high conformational stability of 2-methyl-4-nitrophenylferro with CT-DNA. The compound has the ability to scavenge free radicals as have been revealed by DPPH findings. (author)

  19. Studies on ATP-diphosphohydrolase nucleotide-binding sites by intrinsic fluorescence

    Directory of Open Access Journals (Sweden)

    A.M. Kettlun

    2000-07-01

    Full Text Available Potato apyrase, a soluble ATP-diphosphohydrolase, was purified to homogeneity from several clonal varieties of Solanum tuberosum. Depending on the source of the enzyme, differences in kinetic and physicochemical properties have been described, which cannot be explained by the amino acid residues present in the active site. In order to understand the different kinetic behavior of the Pimpernel (ATPase/ADPase = 10 and Desirée (ATPase/ADPase = 1 isoenzymes, the nucleotide-binding site of these apyrases was explored using the intrinsic fluorescence of tryptophan. The intrinsic fluorescence of the two apyrases was slightly different. The maximum emission wavelengths of the Desirée and Pimpernel enzymes were 336 and 340 nm, respectively, suggesting small differences in the microenvironment of Trp residues. The Pimpernel enzyme emitted more fluorescence than the Desirée apyrase at the same concentration although both enzymes have the same number of Trp residues. The binding of the nonhydrolyzable substrate analogs decreased the fluorescence emission of both apyrases, indicating the presence of conformational changes in the neighborhood of Trp residues. Experiments with quenchers of different polarities, such as acrylamide, Cs+ and I- indicated the existence of differences in the nucleotide-binding site, as further shown by quenching experiments in the presence of nonhydrolyzable substrate analogs. Differences in the nucleotide-binding site may explain, at least in part, the kinetic differences of the Pimpernel and Desirée isoapyrases.

  20. Modulation of [3H]-glutamate binding by serotonin in the rat hippocampus: An autoradiographic study

    International Nuclear Information System (INIS)

    Serotonin (5-HT) added in vitro increased [3H]-glutamate specific binding in the rat hippocampus, reaching statistical significance in layers rich in N-Methyl-D-Aspartate sensitive glutamate receptors. This effect was explained by a significant increase in the apparent affinity of [3H]-glutamate when 5-HT is added in vitro. Two days after lesion of serotonergic afferents to the hippocampus with 5,7- Dihydroxytryptamine [3H]-glutamate binding was significantly decreased in the CA3 region and stratum lacunosum moleculare of the hippocampus, this reduction being reversed by in vitro addition of 10 μM 5-HT. The decrease observed is due to a significant reduction of quisqualate-insensitive (radiatum CA3) and kainate receptors (strata oriens, radiatum, pyramidal of CA3). Five days after lesion [3H]-glutamate binding increased significantly in the CA3 region of the hippocampus but was not different from sham animals in the other hippocampal layers. Two weeks after lesion [3H]-glutamate binding to quisqualate-insensitive receptors was increased in all the hippocampal layers, while kainate and quisqualate-sensitive receptors were not affected. These data are consistent with the possibility that 5-HT is a direct positive modulator of glutamate receptor subtypes

  1. Molecular modeling and spectroscopic studies on the binding of guaiacol to human immunoglobulin

    Institute of Scientific and Technical Information of China (English)

    HE Wenying; YAO Xiaojun; LIU Pengjun; GAO Zhenxia; HU Zhide

    2006-01-01

    The fluorogenic property of guaiacol was exploited for the first time to analyze the interaction with target protein as a probe by molecular modeling, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. Molecular docking was performed to reveal the possible binding mode or mechanism and suggested that guaiacol can strongly bind to human immunoglobulin (HIgG). It is considered that guaiacol binds to HIgG mainly by a hydrophobic interaction and there are two hydrogen bond interactions between the drug and the residues LEU 80 and ASP 65, which is in good agreement with the results from the experimental thermodynamic parameters (the enthalpy change -H0 and the entropy change △S0 were calculated to be 65.55 kJ·mol(1 and 132.95 J·mol(1·K(1 according to the Vant' Hoff equation). Data obtained by the fluorescence spectroscopy indicated that binding of guaiacol with HIgG leads to dramatic enhancement in the fluorescence emission intensity along with significant occurrence of efficient F-rster resonance energy transfer (FRET) from the residue of HIgG to the protein bound guaiacol. From the low value of fluorescence anisotropy (r = 0.06), it is argued that the probe molecule is located in the motionally unrestricted environment of the protein. The alterations of protein's secondary structure in the presence of guaiacol in aqueous solution were quantitatively calculated by the evidences from FT-IR and CD spectroscopes.

  2. Spectroscopic Studies on Binding of Porphyrin-Phenazine Conjugate to Four-Stranded Poly(G).

    Science.gov (United States)

    Ryazanova, Olga; Zozulya, Victor; Voloshin, Igor; Dubey, Larysa; Dubey, Igor; Karachevtsev, Victor

    2015-07-01

    Binding of a novel cationic porphyrin-imidazophenazine conjugate, TMPyP(3+)-ImPzn, to four-stranded poly(G) was investigated in aqueous solutions of neutral pH under near physiological ionic conditions using absorption, polarized fluorescent spectroscopy and fluorescence titration techniques. In absence of the polymer the conjugate folds into stable internal heterodimer with stacking between the porphyrin and phenazine chromophores. Binding of TMPyP(3+)-ImPzn to poly(G) is realized by two competing ways. At low polymer-to-dye ratio (P/D self-stacking is predominant. It is accompanied by heterodimer dissociation and distancing of phenazine moieties from the polymer. This binding mode is characterized by strong quenching of the conjugate fluorescence. Increase of P/D results in the disintegration of the porphyrin stacks and redistribution of the bound conjugate molecules along the polymer chain. At P/D > 10 another binding mode becomes dominant, embedding of TMPyP(3+)-ImPzn heterodimers into poly(G) groove as a whole is occurred. PMID:26076929

  3. Distinct microRNA expression profile and targeted biological pathways in functional myeloid-derived suppressor cells induced by Δ9-tetrahydrocannabinol in vivo: regulation of CCAAT/enhancer-binding protein α by microRNA-690.

    Science.gov (United States)

    Hegde, Venkatesh L; Tomar, Sunil; Jackson, Austin; Rao, Roshni; Yang, Xiaoming; Singh, Udai P; Singh, Narendra P; Nagarkatti, Prakash S; Nagarkatti, Mitzi

    2013-12-27

    Δ(9)-Tetrahydrocannabinol (THC), the major bioactive component of marijuana, has been shown to induce functional myeloid-derived suppressor cells (MDSCs) in vivo. Here, we studied the involvement of microRNA (miRNA) in this process. CD11b(+)Gr-1(+) MDSCs were purified from peritoneal exudates of mice administered with THC and used for genome-wide miRNA profiling. Expression of CD31 and Ki-67 confirmed that the THC-MDSCs were immature and proliferating. THC-induced MDSCs exhibited distinct miRNA expression signature relative to various myeloid cells and BM precursors. We identified 13 differentially expressed (>2-fold) miRNA in THC-MDSCs relative to control BM precursors. In silico target prediction for these miRNA and pathway analysis using multiple bioinformatics tools revealed significant overrepresentation of Gene Ontology clusters within hematopoiesis, myeloid cell differentiation, and regulation categories. Insulin-like growth factor 1 signaling involved in cell growth and proliferation, and myeloid differentiation pathways were among the most significantly enriched canonical pathways. Among the differentially expressed, miRNA-690 was highly overexpressed in THC-MDSCs (∼16-fold). Transcription factor CCAAT/enhancer-binding protein α (C/EBPα) was identified as a potential functional target of miR-690. Supporting this, C/EBPα expression was attenuated in THC-MDSCs as compared with BM precursors and exhibited an inverse relation with miR-690. miR-690 knockdown using peptide nucleic acid-antagomiR was able to unblock and significantly increase C/EBPα expression establishing the functional link. Further, CD11b(+)Ly6G(+)Ly6C(+) and CD11b(+)Ly6G(-)Ly6C(+) purified subtypes showed high levels of miR-690 with attenuated C/EBPα expression. Moreover, EL-4 tumor-elicited MDSCs showed increased miR-690 expression. In conclusion, miRNA are significantly altered during the generation of functional MDSC from BM. Select miRNA such as miR-690 targeting genes involved in

  4. Competitive binding of phenylbutazone and colchicine to serum albumin in multidrug therapy: A spectroscopic study

    Science.gov (United States)

    Sułkowska, A.; Maciążek-Jurczyk, M.; Bojko, B.; Równicka, J.; Zubik-Skupień, I.; Temba, E.; Pentak, D.; Sułkowski, W. W.

    2008-06-01

    The binding sites for phenylbutazone and colchicine were identified in tertiary structure of bovine and human serum albumin with the use of spectrofluorescence analysis. It was found that phenylbutazone has two binding sites in both sera albumins (HSA and BSA), while colchicine has one binding site in BSA as well as in HSA. The comparison of the quenching effect of BSA and HSA fluorescence by phenylbutazone and colchicine allows us to identify subdomain IIA in protein as the binding site for these two drugs. In this subdomain tryptophan 214 is located. The participation of tyrosyl and tryptophanyl residues of protein was also estimated in the drug-albumin complex. The comparison of quenching of fluorescence of HSA and BSA excited at 280 nm with that at 295 nm allowed us to state that the participation of tyrosyl residues of albumin in the phenylbutazone-serum albumin interaction is significant. The analysis of quenching of fluorescence of BSA in the binary and ternary systems showed that phenylbutazone does not affect the complex formed between colchicine and BSA. Similarly, colchicine has no effect on the Phe-BSA complex. However marked differences were observed for the complex with HSA. On the basis of Ka and KQ values it was concluded that colchicine may probably cause displacement of phenylbutazone from its complex with serum albumin (SA). Static and dynamic quenching for the binary and ternary systems is also discussed. The competition of phenylbutazone and colchicine in binding to serum albumin should be taken into account in the multi-drug therapy.

  5. Acetaminophen structure-toxicity studies: In vivo covalent binding of a nonhepatotoxic analog, 3-hydroxyacetanilide

    International Nuclear Information System (INIS)

    High doses of 3-hydroxyacetanilide (3HAA), a structural isomer of acetaminophen, do not produce hepatocellular necrosis in normal male hamsters or in those sensitized to acetaminophen-induced liver damage by pretreatment with a combination of 3-methylcholanthrene, borneol, and diethyl maleate. Although 3HAA was not hepatotoxic, the administration of acetyl-labeled [3H or 14C]3HAA (400 mg/kg, ip) produced levels of covalently bound radiolabel that were similar to those observed after an equimolar, hepatotoxic dose of [G-3H]acetaminophen. The covalent nature of 3HAA binding was demonstrated by retention of the binding after repetitive organic solvent extraction following protease digestion. Hepatic and renal covalent binding after 3HAA was approximately linear with both dose and time. In addition, 3HAA produced only a modest depletion of hepatic glutathione, suggesting the lack of a glutathione threshold. 3-Methylcholanthrene pretreatment increased and pretreatment with cobalt chloride and piperonyl butoxide decreased the hepatic covalent binding of 3HAA, indicating the involvement of cytochrome P450 in the formation of the 3HAA reactive metabolite. The administration of multiple doses or a single dose of [ring-3H]3HAA to hamsters pretreated with a combination of 3-methylcholanthrene, borneol, and diethyl maleate produced hepatic levels of 3HAA covalent binding that were in excess of those observed after a single, hepatotoxic acetaminophen dose. These data suggest that the nature and/or the intracellular processing of the reactive metabolites of acetaminophen and 3HAA are different. These data also demonstrate that absolute levels of covalently bound xenobiotic metabolites cannot be utilized as absolute predictors of cytotoxic potential

  6. Face in profile view reduces perceived facial expression intensity: an eye-tracking study.

    Science.gov (United States)

    Guo, Kun; Shaw, Heather

    2015-02-01

    Recent studies measuring the facial expressions of emotion have focused primarily on the perception of frontal face images. As we frequently encounter expressive faces from different viewing angles, having a mechanism which allows invariant expression perception would be advantageous to our social interactions. Although a couple of studies have indicated comparable expression categorization accuracy across viewpoints, it is unknown how perceived expression intensity and associated gaze behaviour change across viewing angles. Differences could arise because diagnostic cues from local facial features for decoding expressions could vary with viewpoints. Here we manipulated orientation of faces (frontal, mid-profile, and profile view) displaying six common facial expressions of emotion, and measured participants' expression categorization accuracy, perceived expression intensity and associated gaze patterns. In comparison with frontal faces, profile faces slightly reduced identification rates for disgust and sad expressions, but significantly decreased perceived intensity for all tested expressions. Although quantitatively viewpoint had expression-specific influence on the proportion of fixations directed at local facial features, the qualitative gaze distribution within facial features (e.g., the eyes tended to attract the highest proportion of fixations, followed by the nose and then the mouth region) was independent of viewpoint and expression type. Our results suggest that the viewpoint-invariant facial expression processing is categorical perception, which could be linked to a viewpoint-invariant holistic gaze strategy for extracting expressive facial cues. PMID:25531122

  7. Terverticillate Penicillia studied by direct electrospray mass spectrometric profiling of crude extracts: I. Chemosystematics

    DEFF Research Database (Denmark)

    Smedsgaard, Jørn; Frisvad, Jens Christian

    1997-01-01

    mass profile, but a noise level was applied. Cluster analysis using the correlation coefficient resulted in dendrograms where approximately 75% of the included taxa could be considered segregated in distinct clusters. Standard normalized data (mass spectra) resulted in clear clusters, but grouped taxa......A chemosystematic study of 339 isolates from all known terverticillate Penicillium taxa was performed using electrospray mass spectrometric analysis of extractable metabolites. The mass profiles were made by injecting crude plug extracts made from cultures grown on Czapek Yeast Autolysate agar (CYA......) and Yeast Extract Sucrose agar (YES) directly into the electrospray source of the mass spectrometer. A data matrix was made from each substrate by transferring the complete centroid mass spectrum from 200 to 700 amu as 501 variables to individual columns. No attempt was made to identify ions in the...

  8. A STUDY OF SYMPTOM SCORE AND LIPID PROFILE IN SUBCLINICAL HYPOTHYROIDISM BEFORE AND AFTER THYROXINE SUPPLEMENTATION

    Directory of Open Access Journals (Sweden)

    Polu Poina

    2015-04-01

    Full Text Available Hypothyroidism is the most common form of thyroid disorder with a broad range of clinical spectrum. Sub clinical hypothyroidism (SH is the mildest form of the disease in which a few if any non - specific symptoms and/or lipid abnormalities are present. The effect of SH on lipid profile is controversial . [1,2] Elevation of total and LDL cholesterol is observed. SH is associated with subtle abnormalties in myocardial contractility, depression, sub fertility and ovalutary dysfunction. Thyroid replacement in SH is associated with improvement in above mentioned symptoms. This study was carried out to analyse symptom score and lipid profile in patients with SH before and after treatment with L - thyroxine.

  9. A STUDY OF PERSONALITY PROFILE AND PSYCHIATRIC MORBIDITY IN PEOPLE LIVING WITH HIV/AIDS

    Directory of Open Access Journals (Sweden)

    Niranjana Devi

    2015-09-01

    Full Text Available HIV infection and psychiatric disorders have a complex relationship. Being HIV infected could result in psychiatric disorders as a psychological consequence of the infection (or because of the effect of HIV virus on the brain. AIM : To evaluate the personality profile and associated psychiatric co m orbidity of people living with HIV/AIDS and to analyze the correlation between the two in a tertiary care center. MATERIALS & METHODS : PL W HA on ART irrespective of WHO - clinical staging, CD4 count, and duration of medication were subjected for study . The so cio – demographic data, Kuppusamy’s revised socio economic status scale and Eysenck personality questionnaire . Revised were administered to study population. ICD 10 clinical and diagnostic criteria were used to diagnose current and past psychiatric disorders . Data were analyzed using appropriate statistical methods. RESULTS : In total 50 study subjects, 12(24% were diagnosed to have psychiatric morbidity. Further, 26% among males (5 out of 19 males and 24% among females (7 out of 29 females were found to ha ve psychiatric morbidity. Mood disorders were the common diagnosis in our study group which comprises about 58% (7 out of 12. Other diagnoses noted in the study were substance dependence ( A lcohol, nicotine 16.6%, non - organic insomnia (16.6% and delusion al disorder (8.3%.In personality profile assessment, 72% of study population exhibited psychotic traits, 42% showed high neurotic traits and 18% scored high in High Extravert traits . CONCLUSION : Prevalence of psychiatric disorder (24% is similar to other reported studies. Even though females demonstrated higher mood disorder there is no gender difference in psychiatric morbidity. Staging of HIV illness showed significance in psychiatric morbidity. No significant personality profile was found. Most of them expressed mixed personality traits

  10. Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine-DNA adduct formation.

    Science.gov (United States)

    Agarwal, Shweta; Chadha, Deepti; Mehrotra, Ranjana

    2015-01-01

    Chloroethyl nitrosoureas constitute an important family of cancer chemotherapeutic agents, used in the treatment of various types of cancer. They exert antitumor activity by inducing DNA interstrand cross-links. Semustine, a chloroethyl nitrosourea, is a 4-methyl derivative of lomustine. There exist some interesting reports dealing with DNA-binding properties of chloroethyl nitrosoureas; however, underlying mechanism of cytotoxicity caused by semustine has not been precisely and completely delineated. The present work focuses on understanding semustine-DNA interaction to comprehend its anti-proliferative action at molecular level using various spectroscopic techniques. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy is used to determine the binding site of semustine on DNA. Conformational transition in DNA after semustine complexation is investigated using circular dichroism (CD) spectroscopy. Stability of semustine-DNA complexes is determined using absorption spectroscopy. Results of the present study demonstrate that semustine performs major-groove-directed DNA alkylation at guanine residues in an incubation-time-drug-concentration-dependent manner. CD spectral outcomes suggest partial transition of DNA from native B-conformation to C-form. Calculated binding constants (Ka) for semustine and lomustine interactions with DNA are 1.53 × 10(3) M(-1) and 8.12 × 10(3) M(-1), respectively. Moreover, molecular modeling simulation is performed to predict preferential binding orientation of semustine with DNA that corroborates well with spectral outcomes. Results based on comparative study of DNA-binding properties of semustine and lomustine, presented here, may establish a correlation between molecular structure and cytotoxicity of chloroethyl nitrosoureas that may be instrumental in the designing and synthesis of new nitrosourea therapeutics possessing better efficacy and fewer side effects. PMID:25350567

  11. Biophysical characterization and functional studies on calbindin-D28K: A vitamin D-induced calcium-binding protein

    International Nuclear Information System (INIS)

    Vitamin D dependent calcium binding protein, or calbindin-D, is the principal protein induced in the intestine in response to the steroid hormone 1,25(OH)2-vitamin D3. A definitive role for calbindin-D in vitamin D3 mediated biological responses remains unclear. Biophysical and functional studies on chick intestinal calbindin-D28K (CaBP) were initiated so that some insight might be gained into its relevance to the process of intestinal calcium transport. Calbindin-D belongs to a class of high affinity calcium binding proteins which includes calmodulin, parvalbumin and troponin C. The Ca 2+ binding stoichiometry and binding constants for calbindin-D28K were quantitated by Quin 2 titration analysis. The protein was found to bind 5-6 Ca 2+ ions with a KD on the order of 10-8, in agreement with the 6 domains identified from the amino acid sequence. A slow Ca 2+ exchange rate (80 s-1) as assessed by 43Ca NMR and extensive calcium dependent conformational changes in 1H NMR spectra were also observed. Functional studies on chick intestinal CaBP were carried out by two different methods. Interactions between CaBP and intestinal cellular components were assessed via photoaffinity labeling techniques. Specific calcium dependent complexes for CaBP were identified with bovine intestinal alkaline phosphatase and brush border membrane proteins of 60 and 150 kD. CaBP was also found to co-migrate with the alkaline phosphatase activity of chick intestinal brush border membranes as evaluated by gel filtration chromatography. The second procedure for evaluating CaBP functionality has involved the quantitation of CaBP association with vesicular transport components as assessed by ELISA. CaBP, immunoreactivity was observed in purified lysosomes, microsomes and microtubules

  12. Vasoactive intestinal peptide binding sites and fibers in the brain of the pigeon Columba livia: An autoradiographic and immunohistochemical study

    International Nuclear Information System (INIS)

    The distribution of vasoactive intestinal peptide (VIP) binding sites in the pigeon brain was examined by in vitro autoradiography on slide-mounted sections. A fully characterized monoiodinated form of VIP, which maintains the biological activity of the native peptide, was used throughout this study. The highest densities of binding sites were observed in the hyperstriatum dorsale, archistriatum, auditory field L of neostriatum, area corticoidea dorsolateralis and temporo-parieto-occipitalis, area parahippocampalis, tectum opticum, nucleus dorsomedialis anterior thalami, and in the periventricular area of the hypothalamus. Lower densities of specific binding occurred in the neostriatum, hyperstriatum ventrale and nucleus septi lateralis, dorsolateral area of the thalamus, and lateral and posteromedial hypothalamus. Very low to background levels of VIP binding were detected in the ectostriatum, paleostriatum primitivum, paleostriatum augmentatum, lobus parolfactorius, nucleus accumbens, most of the brainstem, and the cerebellum. The distribution of VIP-containing fibers and terminals was examined by indirect immunofluorescence using a polyclonal antibody against porcine VIP. Fibers and terminals were observed in the area corticoidea dorsolateralis, area parahippocampalis, hippocampus, hyperstriatum accessorium, hyperstriatum dorsale, archistriatum, tuberculum olfactorium, nuclei dorsolateralis and dorsomedialis of the thalamus, and throughout the hypothalamus and the median eminence. Long projecting fibers were visualized in the tractus septohippocampalis. In the brainstem VIP immunoreactive fibers and terminals were observed mainly in the substantia grisea centralis, fasciculus longitudinalis medialis, lemniscus lateralis, and in the area surrounding the nuclei of the 7th, 9th, and 10th cranial nerves

  13. Kinetics of in vivo binding of antagonist to muscarinic cholinergic receptor in the human heart studied by Positron Emission Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Syrota, A.; Paillotin, G.; Davy, J.M.; Aumont, M.C.

    1984-08-27

    Positron Emission Tomography (PET) was used to analyze in vivo antagonist binding to human myocardial muscarinic cholinergic receptor. The methiodide salt of the muscarinic antagonist, quinuclidinyl benzilate (MQNB), was labeled with the positron emitter, Carbon-11, and injected intravenously to 8 normal subjects. /sup 11/C-MQNB concentration was determined in vivo in the ventricular septum from 40 cross-sectional images acquired at the same transverse level over a period of 70 minutes. In 4 subjects, various amounts of unlabeled atropine were rapidly injected at 20 minutes to study whether atropine competitively inhibited MQNB. The kinetics of binding of /sup 11/C-MQNB were not the same in vivo and in vitro. The apparent dissociation rate of /sup 11/C-MQNB in vivo was much slower (by 1 to 2 orders of magnitude) than that observed in vitro with /sup 3/H-QNB. After atropine injection, /sup 11/C-MQNB dissociated from its binding sites at a rate that apparently depended on the amount of atropine present. /sup 11/C-MQNB kinetics were analyzed with a mathematical model which assumes the existence of a boundary layer containing free ligand in the vicinity of the binding sites. The dissociation rate of the radioligand depends on the probability of its rebinding to a free receptor site. 11 references, 1 table.

  14. The spectral studies on the effect of Glu 101 to the metal binding characteristic of Euplotes octocarinatus centrin

    Science.gov (United States)

    Guoting, Li; Zhijun, Wang; Yaqin, Zhao; Liexiang, Ren; Aihua, Liang; Binsheng, Yang

    2007-08-01

    Glu is highly conserved as the first amino acid of E-helix of the EF-hand protein. In this paper, Glu 101, the first amino acid of E-helix of the third EF-hand motif in Euplotes octocarinatus centrin (EoCen) was mutated to be Lys by the method of site direct mutation. Tb 3+ and TNS were used as fluorescence probes in the study of the effect of this mutation to the metal binding characteristic of EoCen by fluorescence spectra. Results indicate that compared with EoCen, the mutation protein (E101K) displays a different Tb 3+ binding characteristic and an increased hydrophobic exposure surface. Polyacrylamide gels electrophoresis indicated that the electrophoretic mobilities of EoCen and E101K are distinctly different. It can be deduced that the conformation of EoCen has been altered by this mutation. The general conditional binding constant of Tb 3+ to the three loops of EF-hand sites I-III in E101K was calculated to be (5.64 ± 0.57) × 10 5 M -1 according to the modified equation of the single binding process.

  15. Theoretical Study of Molecular Determinants Involved in Signal Binding to the TraR Protein of Agrobacterium tumefaciens

    Directory of Open Access Journals (Sweden)

    N. Kumar

    2005-10-01

    Full Text Available N-acylated homoserine lactone (AHL mediated cell-cell communication in bacteria is dependent on the recognition of the cognate signal by its receptor. This interaction allows the receptor-ligand complex to act as a transcriptional activator, controlling the expression of a range of bacterial phenotypes, including virulence factor expression and biofilm formation. One approach to determine the key features of signal- binding is to model the intermolecular interactions between the receptor and ligand using computational-based modeling software (LigandFit. In this communication, we have modeled the crystal structure of the AHL receptor protein TraR and its AHL signal N-(3- oxooctanoyl-homoserine lactone from Agrobacterium tumefaciens and compared it to the previously reported antagonist behaviour of a number of AHL analogues, in an attempt to determine structural constraints for ligand binding. We conclude that (i a common conformation of the AHL in the hydrophobic and hydrophilic region exists for ligand-binding, (ii a tail chain length threshold of 8 carbons is most favourable for ligand-binding affinity, (iii the positive correlation in the docking studies could be used a virtual screening tool.

  16. A study on the binding interaction between the imidazole derivative and bovine serum albumin by fluorescence spectroscopy

    International Nuclear Information System (INIS)

    The interaction between the imidazole derivative 2-(2,4-difluorophenyl)-1-phenyl-1H-imidazo[4,5-f][1,10]phenanthroline (dfppip) and bovine serum albumin (BSA) was investigated by fluorescence and UV–vis absorbance spectroscopy. From the experimental results, it was found that the imidazole derivative has strong ability to quench the intrinsic fluorescence of BSA by forming complexes. Electrostatic interactions play an important role to stabilize the complex. The binding constants and the number of binding sites have been determined in detail. The distance (r) between the donor and the acceptor was obtained according to fluorescence resonance energy transfer (FRET). Conformational changes of BSA were observed from synchronous fluorescence spectroscopy. The effect of metal ions such as Cu2+, Zn2+, Ca2+, Mg2+, Ni2+, Co2+ and Fe2+ on the binding constants between the imidazole derivative and BSA were also studied. - Highlights: ► Interactions between dfppip and BSA were investigated by fluorescence quenching. ► Quenching mechanism mainly arise from the formation of BSA-imidazole complex. ► D→A distance is <8 nm indicates that the energy transfer from BSA to dfppip. ► Synchronous fluorescence spectra to exploit the structural change of BSA. ► Effect of other ions on the binding constants between dfppip and BSA.

  17. Vasoactive intestinal peptide binding sites and fibers in the brain of the pigeon Columba livia: An autoradiographic and immunohistochemical study

    Energy Technology Data Exchange (ETDEWEB)

    Hof, P.R.; Dietl, M.M.; Charnay, Y.; Martin, J.L.; Bouras, C.; Palacios, J.M.; Magistretti, P.J. (Fishberg Research Center for Neurobiology, Mount Sinai School of Medicine, New York, NY (USA))

    1991-03-15

    The distribution of vasoactive intestinal peptide (VIP) binding sites in the pigeon brain was examined by in vitro autoradiography on slide-mounted sections. A fully characterized monoiodinated form of VIP, which maintains the biological activity of the native peptide, was used throughout this study. The highest densities of binding sites were observed in the hyperstriatum dorsale, archistriatum, auditory field L of neostriatum, area corticoidea dorsolateralis and temporo-parieto-occipitalis, area parahippocampalis, tectum opticum, nucleus dorsomedialis anterior thalami, and in the periventricular area of the hypothalamus. Lower densities of specific binding occurred in the neostriatum, hyperstriatum ventrale and nucleus septi lateralis, dorsolateral area of the thalamus, and lateral and posteromedial hypothalamus. Very low to background levels of VIP binding were detected in the ectostriatum, paleostriatum primitivum, paleostriatum augmentatum, lobus parolfactorius, nucleus accumbens, most of the brainstem, and the cerebellum. The distribution of VIP-containing fibers and terminals was examined by indirect immunofluorescence using a polyclonal antibody against porcine VIP. Fibers and terminals were observed in the area corticoidea dorsolateralis, area parahippocampalis, hippocampus, hyperstriatum accessorium, hyperstriatum dorsale, archistriatum, tuberculum olfactorium, nuclei dorsolateralis and dorsomedialis of the thalamus, and throughout the hypothalamus and the median eminence. Long projecting fibers were visualized in the tractus septohippocampalis. In the brainstem VIP immunoreactive fibers and terminals were observed mainly in the substantia grisea centralis, fasciculus longitudinalis medialis, lemniscus lateralis, and in the area surrounding the nuclei of the 7th, 9th, and 10th cranial nerves.

  18. Lipid Profile in Thyroid Dysfunction: A Study on Patients of Bastar

    Directory of Open Access Journals (Sweden)

    Farah Khan

    2013-10-01

    Full Text Available Aim: Function of thyroid gland is regulating a wide array of metabolic activities which have direct impact on some parameters. The objective of this study was to see the effect of thyroid dysfunction on serum lipid profile parameters among the people of Bastar region. Material and Method: Blood samples were collected from 60 subjects. The blood was analyzed for the levels of thyroid stimulating hormone (TSH, tri-iodothyroinine (T3, tetra-iodothyronine (T4, free tri-iodothyronine (FT3, free tetra-iodothyronine (FT4 by microplate immune enzymetric assay. Patients with thyroid dysfunction were categorized into hypothyroid and hyperthyroid with increased and decreased levels of TSH respectively. Levels of total cholesterol (TC, triacylglycerol (Tg, low density lipoprotein-cholesterol (LDL-C and high density lipoprotein-cholesterol (HDL-C were measured, and compared between normal and patients with thyroid dysfunction. Results: Elevated levels of TC, Tg, LDL-C, VLDL-C, TC/HDL ratio, and significantly decreased HDL-C were observed in hypothyroid patients. Hyperthyroid patients revealed low HDL-C levels with no significant changes in TC, Tg, LDL-C, VLDL-C, and TC/HDL ratio. Analysis of variance (ANOVA showed the significant difference among all the groups and Tukey’s honest test revealed the significant difference in the mean values of the biochemical parameters in all groups at 0.05 level of significance. Discussion: As there is a controversy regarding effect of thyroid dysfunction on lipid profile, the present work was conducted on thyroid dysfunction tribal patients of Bastar, and compared with the normal subjects. The study concluded increased lipid profile in hypothyroid subjects and found no effect on the lipid profile of hyperthyroid subjects.

  19. Study of major factors to affect photoresist profile on developable bottom anti-reflective coating process

    Science.gov (United States)

    Roh, Hyo Jung; Ju, Dong Kyu; Kim, Hyun Jin; Kim, Jaehyun

    2011-04-01

    As critical dimensions continue to shrink in lithography, new materials will be needed to meet the new demands imposed by this shrinkage. Recently, there are needs for novel materials with various substrates and immersing process, including double patterning process, a high resolution implant process, and so on. Among such materials, Developable Bottom Anti-reflective Coating material (DBARC) is a good candidate for high resolution implant application as well as double patterning. DBARC should have reflectivity control function as an ordinary BARC, as well as an appropriate solubility in TMAH-based conventional developer after exposure and bake process. The most distinguished advantage of DBARC is to skip BARC etch process that is required in normal BARC process. In spite of this advantage, the photoresist profile on DBARC could be influenced by components and process conditions of DBARC. Several groups have tried to solve this issue to implement DBARC to new process. We have studied material-related factors affecting photoresist profiles, such as a polymer, photo-acid generators (PAGs), and additives. And we explored the effect of process condition for photoresist and DBARC. In case of polymer, we studied the effect of dissolution rate in developer and crosslinking functionality. For PAGs and additives, the effect of acid diffusivity and cross-linking degree according to their bulkiness were examined. We also evaluated coated film stability in a photoresist solvent after BARC bake process and compared lithographic performance of various DBARC formulations. In addition, the effect of photoresist profile with bake condition of photoresist and DBARC were investigated. In this paper, we will demonstrate the most influential factors of DBARC to photoresist profile and suggest the optimum formulation and process condition for DBARC application.

  20. Experimental study on temperature profile of fixed - bed gasification of oil-palm fronds

    Science.gov (United States)

    Atnaw, Samson M.; Sulaiman, Shaharin A.; Moni, M. Nazmi Z.

    2012-06-01

    Currently the world's second largest palm oil producer Malaysia produces large amount of oil palm biomass each year. The abundance of the biomass introduces a challenge to utilize them as main feedstock for heat and energy generation. Although some oil palm parts and derivatives like empty fruit bunch and fibre have been commercialized as fuel, less attention has been given to oil palm fronds (OPF). Initial feasibility and characterization studies of OPF showed that it is highly feasible as fuel for gasification to produce high value gaseous fuel or syngas. This paper discusses the experimental gasification attempt carried out on OPF using a 50 kW lab scale downdraft gasifier and its results. The conducted study focused on the temperature distributions within the reactor and the characteristics of the dynamic temperature profile for each temperature zones during operation. OPF feedstock of one cubic inch in individual size with 15% average moisture content was utilized. An average pyrolysis zone temperature of 324°Cand an average oxidation zone temperature of 796°Cwere obtained over a total gasification period of 74 minutes. A maximum oxidation zone temperature of 952°Cwas obtained at 486 lpm inlet air flow rate and 10 kg/hr feedstock consumption rate. Stable bluish flare was produced for more than 70% of the total gasification time. The recorded temperature profiles produced closely similar patterns with the temperature profiles recorded from the gasification of woody materials. Similar temperature profile was obtained comparing the results from OPF gasification with that of woody biomass. Furthermore, the successful ignition of the syngas produced from OPF gasification ascertained that OPF indeed has a higher potential as gasification feedstock. Hence, more detailed studies need to be done for better understanding in exploiting the biomass as a high prospect alternative energy solution. In addition, a study of the effect of initial moisture content of OPF