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Sample records for binding profile study

  1. Comparative study of heparin-binding proteins profile of Murrah buffalo (Bubalus bubalis semen

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    S. S. Ramteke

    2014-09-01

    Full Text Available Aim: The experiment was conducted to study the total seminal plasma protein (TSPP and heparin-binding proteins (HBPs in relation to initial semen quality of buffalo bull. Materials and Methods: Semen from two Murrah buffalo bulls (bull no. 605 and 790 with mass motility of ≥3+ were used for the study and categorized into three groups (Group I- Mass motility 3+, Group II- Mass motility 4+ and Group III- Mass motility 5+. Seminal plasma from semen was separated by centrifugation. HBPs was isolated and purified from heparin-agarose affinity column by modified elution buffer. TSPP and isolated HBPs concentration was estimated by Lowry’s method. The purified HBPs were resolved on Sodium dodecyl sulfate polyacrylamide gel electrophoresis to check the protein profile of two bulls. Results: The mean values of TSPP concentrations in bull no. 605 and 790 in Group I, II and III were 30.64±0.12, 31.66±0.09, 32.53±0.19 and 28.51±0.09, 29.49±0.15, 30.45±0.17 mg/mL, respectively. The mean values of HBPs concentrations in bull no. 605 and 790 in Group I, II and III were 3.11±0.07, 3.32±0.06, 3.46±0.08 and 2.51±0.08, 2.91±0.05, 3.10±0.03 mg/mL, respectively. Both the values of TSPP and HBPs were significantly higher (p<0.01 in bull no. 605 when compared to 790 in all the three groups. 31 kDa HBP was more intensely present in bull no. 605, thus may indicate its superiority over bull no. 790 in relation to fertility potential. Conclusion: TSPP and HBPs shows variation in concentration with respect to initial semen quality. Furthermore, presence of fertility related 31 kDa HBPs in one of the bull may be an indication of high fertility of a bull. In future, in-vivo and in-vitro correlative study on larger basis is needed for the establishment of fertility-related HBPs in semen which might establish criteria for selection of buffalo bull with high fertility potential.

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

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    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

  3. Is there a link between selectivity and binding thermodynamics profiles?

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    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding.

  4. Fluorescence Correlation Spectroscopy in Drug Discovery: Study of Alexa532-Endothelin 1 Binding to the Endothelin ETA Receptor to Describe the Pharmacological Profile of Natural Products

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    Catherina Caballero-George

    2012-01-01

    Full Text Available Fluorescence correlation spectroscopy and the newly synthesized Alexa532-ET1 were used to study the dynamics of the endothelin ETA receptor-ligand complex alone and under the influence of a semisynthetic selective antagonist and a fungal extract on living A10 cells. Dose-dependent increase of inositol phosphate production was seen for Alexa532-ET1, and its binding was reduced to 8% by the selective endothelin ETA antagonist BQ-123, confirming the specific binding of Alexa532-ET1 to the endothelin ETA receptor. Two different lateral mobilities of the receptor-ligand complexes within the cell membrane were found allowing the discrimination of different states for this complex. BQ-123 showed a strong binding affinity to the “inactive” receptor state characterized by the slow diffusion time constant. A similar effect was observed for the fungal extract, which completely displaced Alexa532-ET1 from its binding to the “inactive” receptor state. These findings suggest that both BQ-123 and the fungal extract act as inverse agonists.

  5. Genome-wide promoter binding profiling of protein phosphatase-1 and its major nuclear targeting subunits.

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    Verheyen, Toon; Görnemann, Janina; Verbinnen, Iris; Boens, Shannah; Beullens, Monique; Van Eynde, Aleyde; Bollen, Mathieu

    2015-07-13

    Protein phosphatase-1 (PP1) is a key regulator of transcription and is targeted to promoter regions via associated proteins. However, the chromatin binding sites of PP1 have never been studied in a systematic and genome-wide manner. Methylation-based DamID profiling in HeLa cells has enabled us to map hundreds of promoter binding sites of PP1 and three of its major nuclear interactors, i.e. RepoMan, NIPP1 and PNUTS. Our data reveal that the α, β and γ isoforms of PP1 largely bind to distinct subsets of promoters and can also be differentiated by their promoter binding pattern. PP1β emerged as the major promoter-associated isoform and shows an overlapping binding profile with PNUTS at dozens of active promoters. Surprisingly, most promoter binding sites of PP1 are not shared with RepoMan, NIPP1 or PNUTS, hinting at the existence of additional, largely unidentified chromatin-targeting subunits. We also found that PP1 is not required for the global chromatin targeting of RepoMan, NIPP1 and PNUTS, but alters the promoter binding specificity of NIPP1. Our data disclose an unexpected specificity and complexity in the promoter binding of PP1 isoforms and their chromatin-targeting subunits. PMID:25990731

  6. Concentration profiles of actin-binding molecules in lamellipodia

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    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.

  7. Structural studies of sugar binding proteins

    OpenAIRE

    Sooriyaarachchi, Sanjeewani

    2010-01-01

    Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose bindin...

  8. Transcriptome Profiling of Pediatric Core Binding Factor AML.

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    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

  9. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles.

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    Brender, Jeffrey R; Zhang, Yang

    2015-10-01

    The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell. Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes. Since experimental determination of protein-protein binding affinity remains difficult when performed on a large scale, computational methods for predicting the consequences of mutations on binding affinity are highly desirable. We show that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation. As a standalone feature, the differences between the interface profile score of the mutant and wild-type proteins has an accuracy equivalent to the best all-atom potentials, despite being two orders of magnitude faster once the profile has been constructed. Due to its unique sensitivity in collecting the evolutionary profiles of analogous binding interactions and the high speed of calculation, the interface profile score has additional advantages as a complementary feature to combine with physics-based potentials for improving the accuracy of composite scoring approaches. By incorporating the sequence-derived and residue-level coarse-grained potentials with the interface structure profile score, a composite model was constructed through the random forest training, which generates a Pearson correlation coefficient >0.8 between the predicted and observed binding free-energy changes upon mutation. This accuracy is comparable to, or outperforms in most cases, the current best methods, but does not require high-resolution full-atomic models of the mutant structures. The binding interface profiling approach should find useful application in human-disease mutation recognition and protein interface design studies.

  10. 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...

  11. 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 ...

  12. 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

  13. 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.

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    Sara Hägg

    2009-12-01

    Full Text Available 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(-27 and-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 A-module 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

  14. 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

  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

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

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    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

  18. The mu1, mu2, delta, kappa opioid receptor binding profiles of methadone stereoisomers and morphine

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    Kristensen, K; Christensen, C B; Christrup, Lona Louring

    1995-01-01

    The binding affinities of racemic methadone and its optical isomers R-methadone and S-methadone were evaluated for the opioid receptors mu1, mu2, delta and kappa, in comparison with that of morphine. The analgesic R-methadone had a 10-fold higher affinity for mu1 receptors than S-methadone (IC50 3...... receptors. This result suggests that S-methadone does not essentially contribute to opioid effect of racemic methadone. R-methadone has a receptor binding profile which resembles that of morphine....

  19. Distinct expression profiles and different functions of odorant binding proteins in Nilaparvata lugens Stal.

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    Peng He

    Full Text Available BACKGROUND: Odorant binding proteins (OBPs play important roles in insect olfaction. The brown planthopper (BPH, Nilaparvata lugens Stål (Delphacidae, Auchenorrhyncha, Hemiptera is one of the most important rice pests. Its monophagy (only feeding on rice, wing form (long and short wing variation, and annual long distance migration (seeking for rice plants of high nutrition imply that the olfaction would play a central role in BPH behavior. However, the olfaction related proteins have not been characterized in this insect. METHODOLOGY/PRINCIPAL FINDINGS: Full length cDNA of three OBPs were obtained and distinct expression profiles were revealed regarding to tissue, developmental stage, wing form and gender for the first time for the species. The results provide important clues in functional differentiation of these genes. Binding assays with 41 compounds demonstrated that NlugOBP3 had markedly higher binding ability and wider binding spectrum than the other two OBPs. Terpenes and Ketones displayed higher binding while Alkanes showed no binding to the three OBPs. Focused on NlugOBP3, RNA interference experiments showed that NlugOBP3 not only involved in nymph olfaction on rice seedlings, but also had non-olfactory functions, as it was closely related to nymph survival. CONCLUSIONS: NlugOBP3 plays important roles in both olfaction and survival of BPH. It may serve as a potential target for developing behavioral disruptant and/or lethal agent in N. lugens.

  20. '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.

  1. 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…

  2. 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

    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...

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

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    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

  4. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

    KAUST Repository

    Wong, Ka-Chun

    2015-04-20

    With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene\\'s function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins\\' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website: http://www.cs.toronto.edu/∼wkc/FullSignalRanker/ © 2015 IEEE.

  5. 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.

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

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    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

  7. Neutralization and Binding Profile of Monoclonal Antibodies Generated Against Influenza A H1N1 Viruses.

    Science.gov (United States)

    Shembekar, Nachiket; Mallajosyula, Vamsee V Aditya; Malik, Ankita; Saini, Ashok; Varadarajan, Raghavan; Gupta, Satish Kumar

    2016-08-01

    Monoclonal antibodies (MAbs) provide scope for the development of better therapeutics and diagnostic tools. Herein, we describe the binding and neutralization profile(s) for a panel of murine MAbs generated against influenza A H1N1 viruses elicited by immunization with pandemic H1 recombinant hemagglutinin (rHA)/whole virus or seasonal H1 rHA. Neutralizing MAbs, MA-2070 and MA-M, were obtained after pandemic A/California/07/2009 (H1N1) virus/rHA immunization(s). Both MAbs reacted specifically with rHA from A/California/07/2009 and A/England/195/2009 in ELISA. MA-2070 bound rHA of A/California/07/2009 with high affinity (KD = 51.36 ± 9.20 nM) and exhibited potent in vitro neutralization (IC50 = 2.50 μg/mL). MA-2070 bound within the stem domain of HA. MA-M exhibited both hemagglutination inhibition (HI, 1.50 μg/mL) and in vitro neutralization (IC50 = 0.66 μg/mL) activity against the pandemic A/California/07/2009 virus and showed higher binding affinity (KD = 9.80 ± 0.67 nM) than MA-2070. MAb, MA-H generated against the seasonal A/Solomon Islands/03/2006 (H1N1) rHA binds within the head domain and bound the seasonal H1N1 (A/Solomon Islands/03/2006 and A/New Caledonia/20/1990) rHAs with high affinity (KD; 0.72-8.23 nM). MA-H showed high HI (2.50 μg/mL) and in vitro neutralization (IC50 = 2.61 μg/mL) activity against the A/Solomon Islands/03/2006 virus. All 3 MAbs failed to react in ELISA with rHA from various strains of H2N2, H3N2, H5N1, H7N9, and influenza virus B, suggesting their specificity for either pandemic or seasonal H1N1 influenza virus. The MAbs reported here may be useful in developing diagnostic assays.

  8. Neutralization and Binding Profile of Monoclonal Antibodies Generated Against Influenza A H1N1 Viruses.

    Science.gov (United States)

    Shembekar, Nachiket; Mallajosyula, Vamsee V Aditya; Malik, Ankita; Saini, Ashok; Varadarajan, Raghavan; Gupta, Satish Kumar

    2016-08-01

    Monoclonal antibodies (MAbs) provide scope for the development of better therapeutics and diagnostic tools. Herein, we describe the binding and neutralization profile(s) for a panel of murine MAbs generated against influenza A H1N1 viruses elicited by immunization with pandemic H1 recombinant hemagglutinin (rHA)/whole virus or seasonal H1 rHA. Neutralizing MAbs, MA-2070 and MA-M, were obtained after pandemic A/California/07/2009 (H1N1) virus/rHA immunization(s). Both MAbs reacted specifically with rHA from A/California/07/2009 and A/England/195/2009 in ELISA. MA-2070 bound rHA of A/California/07/2009 with high affinity (KD = 51.36 ± 9.20 nM) and exhibited potent in vitro neutralization (IC50 = 2.50 μg/mL). MA-2070 bound within the stem domain of HA. MA-M exhibited both hemagglutination inhibition (HI, 1.50 μg/mL) and in vitro neutralization (IC50 = 0.66 μg/mL) activity against the pandemic A/California/07/2009 virus and showed higher binding affinity (KD = 9.80 ± 0.67 nM) than MA-2070. MAb, MA-H generated against the seasonal A/Solomon Islands/03/2006 (H1N1) rHA binds within the head domain and bound the seasonal H1N1 (A/Solomon Islands/03/2006 and A/New Caledonia/20/1990) rHAs with high affinity (KD; 0.72-8.23 nM). MA-H showed high HI (2.50 μg/mL) and in vitro neutralization (IC50 = 2.61 μg/mL) activity against the A/Solomon Islands/03/2006 virus. All 3 MAbs failed to react in ELISA with rHA from various strains of H2N2, H3N2, H5N1, H7N9, and influenza virus B, suggesting their specificity for either pandemic or seasonal H1N1 influenza virus. The MAbs reported here may be useful in developing diagnostic assays. PMID:27463230

  9. 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

  10. 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.

  11. Profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39.

    Science.gov (United States)

    Kocaoglu, Ozden; Tsui, Ho-Ching T; Winkler, Malcolm E; Carlson, Erin E

    2015-01-01

    Selective fluorescent β-lactam chemical probes enable the visualization of the transpeptidase activity of penicillin-binding proteins (PBPs) at different stages of bacterial cell division. To facilitate the development of new fluorescent probes for PBP imaging, we evaluated 20 commercially available β-lactams for selective PBP inhibition in an unencapsulated derivative of the D39 strain of Streptococcus pneumoniae. Live cells were treated with β-lactam antibiotics at different concentrations and subsequently incubated with Bocillin FL (Boc-FL; fluorescent penicillin) to saturate uninhibited PBPs. Fluorophore-labeled PBPs were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and fluorescence scanning. Among 20 compounds tested, carbapenems (doripenem and meropenem) were coselective for PBP1a, PBP2x, and PBP3, while six of the nine penicillin compounds were coselective for PBP2x and PBP3. In contrast, the seven cephalosporin compounds tested display variability in their PBP-binding profiles. Three cephalosporin compounds (cefoxitin, cephalexin, and cefsulodin) and the monobactam aztreonam exhibited selectivity for PBP3, while only cefuroxime (a cephalosporin) was selective for PBP2x. Treatment of S. pneumoniae cultures with a sublethal concentration of cefuroxime that inhibited 60% of PBP2x activity and less than 20% of the activity of other PBPs resulted in formation of elongated cells. In contrast, treatment of S. pneumoniae cultures with concentrations of aztreonam and cefoxitin that inhibited up to 70% of PBP3 activity and less than 30% of other PBPs resulted in no discernible morphological changes. Additionally, correlation of the MIC and IC50s for each PBP, with the exception of faropenem, amdinocillin (mecillinam), and 6-APA, suggests that pneumococcal growth inhibition is primarily due to the inhibition of PBP2x. PMID:25845878

  12. 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.

  13. 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.

  14. A STUDY OF LIPID PROFILE IN PREDIABETES

    Directory of Open Access Journals (Sweden)

    Manoj

    2016-06-01

    Full Text Available BACKGROUND Lipid abnormalities are common in diabetes mellitus and play an important role in acceleration of atherosclerosis leading to increased cardiovascular diseases. Due to increasing burden of diabetes, it is becoming important to identify dyslipidaemia in high-risk state for diabetes especially prediabetes so that early intervention can reduce cardiovascular risk. AIM To study lipid profile in prediabetes individuals. METHODS This study was a cross-sectional case control study which included 107 prediabetes and 101 healthy controls. Lipid profile of prediabetes and controls were measured and statistically analysed. RESULT Total cholesterol, LDL, triglycerides, VLDL, TG/HDL ratio, and LDL/HDL ratio were significantly high whereas HDL was significantly low in prediabetes subjects as compared to controls. CONCLUSION This study showed significant lipid abnormalities in prediabetes subjects. Because of these they are at high risk of developing atherosclerotic cardiovascular diseases. Therefore, proper screening and appropriate therapy of these conditions becomes important.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 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

  17. Conformational stability and aggregation of therapeutic monoclonal antibodies studied with ANS and Thioflavin T binding.

    Science.gov (United States)

    Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Trout, Bernhardt L

    2011-01-01

    Characterization of aggregation profiles of monoclonal antibodies (mAb) is gaining importance because an increasing number of mAb-based therapeutics are entering clinical studies and gaining marketing approval. To develop a successful formulation, it is imperative to identify the critical biochemical properties of each potential mAb drug candidate. We investigated the conformational change and aggregation of a human IgG1 using external dye-binding experiments with fluorescence spectroscopy and compared the aggregation profiles obtained to the results of size-exclusion chromatography. We show that using an appropriate dye at selected mAb concentration, unfolding or aggregation can be studied. In addition, dye-binding experiments may be used as conventional assays to study therapeutic mAb stability. PMID:21540645

  18. 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.

  19. 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...

  20. In vitro DNA binding studies of Aspartame, an artificial sweetener.

    Science.gov (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh

    2013-03-01

    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1).

  1. 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

  2. Binding Equilibrium Studies Between Co2+ and HAS or BSA

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    @@ Introduction Up to now,the interactions of Cu2+,Ni2+ and Zn2+ with serum albumin have been extensively studied[1-3].However,the interaction of serum with Co2+ has rarely been studied.Our study of Co2+-HSA by means of charge transfer spectra indicated that the metal center took an octahedron configuration and the binding site was probably located at the tripeptide segment of the N-terminal of albumin[4].Sadler et al.[5]has reported that the binding site of Co2+ in HSA is located at the tripeptide segment of HSA involving the four nitrogen atoms and a carboxyl oxygen atom of Aspl.In this paper the interaction of HSA and BSA with Co2+ at physiological pH is further studied by equilibrium dialysis.The number of binding sites and the cooperation among the binding sites are reported.According to the equilibrium dialysis results and the study of competition between Co2+ and Cu2+,Ca2+ or Zn2+ to be bound to HSA or BSA,it is suggested that there are three strong binding sites in both HSA and BSA.The possible locations of the strong binding sites of Co2+ in HSA and BSA have also been determined.

  3. 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.

  4. Competing binding of metal ions with protein studied by microdialysis

    Institute of Scientific and Technical Information of China (English)

    郭明; 孔亮; 毛希琴; 历欣; 邹汉法

    2002-01-01

    A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.

  5. Expression Profile of Six RNA-Binding Proteins in Pulmonary Sarcoidosis

    Science.gov (United States)

    Novosadova, Eva; Hagemann-Jensen, Michael; Kullberg, Susanna; Kolek, Vitezslav; Grunewald, Johan; Petrek, Martin

    2016-01-01

    Background Sarcoidosis is characterised by up-regulation of cytokines and chemokine ligands/receptors and proteolytic enzymes. This pro-inflammatory profile is regulated post-transcriptionally by RNA-binding proteins (RBPs). We investigated in vivo expression of six RBPs (AUF1, HuR, NCL, TIA, TIAR, PCBP2) and two inhibitors of proteolytic enzymes (RECK, PTEN) in pulmonary sarcoidosis and compared it to the expression in four control groups of healthy individuals and patients with other respiratory diseases: chronic obstructive pulmonary disease (COPD), asthma and idiopathic interstitial pneumonias (IIPs). Methods RT-PCR was used to quantify the mRNAs in bronchoalveolar (BA) cells obtained from 50 sarcoidosis patients, 23 healthy controls, 30 COPD, 19 asthmatic and 19 IIPs patients. Flow cytometry was used to assess intracellular protein expression of AUF1 and HuR in peripheral blood T lymphocytes (PBTLs) obtained from 9 sarcoidosis patients and 6 healthy controls. Results Taking the stringent conditions for multiple comparisons into consideration, we consistently observed in the primary analysis including all patients regardless of smoking status as well as in the subsequent sub-analysis limited for never smokers that the BA mRNA expression of AUF1 (p<0.001), TIA (p<0.001), NCL (p<0.01) and RECK (p<0.05) was decreased in sarcoidosis compared to healthy controls. TIA mRNA was also decreased in sarcoidosis compared to both obstructive pulmonary diseases (COPD and asthma; p<0.001) but not compared to IIPs. There were several positive correlations between RECK mRNA and RBP mRNAs in BA cells. Also sarcoidosis CD3+, CD4+ and CD8+ PBTLs displayed lower mean fluorescence intensity of AUF1 (p≤0.02) and HuR (p≤0.03) proteins than control healthy PBTLs. Conclusion mRNA expressions of three RBPs (AUF1, TIA and NCL) and their potential target mRNA encoding RECK in BA cells and additionally protein expression of AUF1 and HuR in PBTLs were down-regulated in our sarcoidosis

  6. Study of binding glycyrrhetic acid to AT1 receptor

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Fengyun; (张凤云); YUE; Baozhen; (岳保珍); HE; Shipeng; (贺师鹏)

    2003-01-01

    To analyze the binding of glycyrrhetic acid (GA) to angiotensin II type I (AT1) receptor and to explore the mechanisms underlying the binding, primary cell culture of rat vascular smooth muscle cell (VSMC), radioactive ligand-receptor binding assay, lascer confocal scanning microscope (LCSM), Northern blot, 3H-TdR incorporation DNA assay were used in this study. The results suggest that specific binding of GA to AT1 receptor (IC50 value was 35.0 μmol/L) increases intracellular [Ca2+]i of VSMC, activates transcription factor c-myc and promotes the proliferation of VSMC, therefore GA was probably an agonist of AT1 receptor, providing a new target for GA's pharmaceutical effects.

  7. 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%.

  8. Electron profile stiffness and critical gradient studies

    Science.gov (United States)

    DeBoo, J. C.; Petty, C. C.; White, A. E.; Burrell, K. H.; Doyle, E. J.; Hillesheim, J. C.; Holland, C.; McKee, G. R.; Rhodes, T. L.; Schmitz, L.; Smith, S. P.; Wang, G.; Zeng, L.

    2012-08-01

    Electron profile stiffness was studied in DIII-D L-mode discharges by systematically varying the heat flux in a narrow region with electron cyclotron heating and measuring the local change produced in ∇Te. Electron stiffness was found to slowly increase with toroidal rotation velocity. A critical inverse temperature gradient scale length 1/LC ˜ 3 m-1 was identified at ρ =0.6 and found to be independent of rotation. Both the heat pulse diffusivity and the power balance diffusivity, the latter determined by integrating the measured dependence of the heat pulse diffusivity on -∇Te, were fit reasonably well by a model containing a critical inverse temperature gradient scale length and varying linearly with 1/LT above the threshold.

  9. 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

  10. Curcumin Binding to Beta Amyloid: A Computational Study.

    Science.gov (United States)

    Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary

    2015-10-01

    Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.

  11. 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

  12. Molecular Characterization and Expression Profiling of Odorant-Binding Proteins in Apolygus lucorum.

    Directory of Open Access Journals (Sweden)

    Hai-Bin Yuan

    Full Text Available Apolygus lucorum (Meyer-Dür (Hemiptera: Miridae is one of the most important agricultural pests, with broad host range and cryptic feeding habits in China. Chemosensory behavior plays an important role in many crucial stages in the life of A. lucorum, such as the detection of sex pheromone cues during mate pursuit and fragrant odorants during flowering host plant localization. Odorant-binding proteins (OBPs are involved in the initial biochemical recognition steps in semiochemical perception. In the present study, a transcriptomics-based approach was used to identify potential OBPs in A. lucorum. In total, 38 putative OBP genes were identified, corresponding to 26 'classic' OBPs and 12 'Plus-C' OBPs. Phylogenetic analysis revealed that A. lucorum OBP proteins are more closely related to the OBP proteins of other mirid bugs as the same family OBP clustering together. Quantitative real-time PCR analysis for the first reported 23 AlucOBPs revealed that the expression level of 11 AlucOBP genes were significantly higher in antennae of both sexes than in other tissues. Three of them were male antennae-biased and six were female antennae-biased, suggesting their putative roles in the detection of female sex pheromones and host plant volatiles. In addition, three, four, two and one AlucOBPs had the highest degree of enrichment in the stylet, head, leg, and in abdomen tissues, respectively. Two other OBPs were ubiquitously expressed in the main tissues, including antennae, stylets, heads, legs and wings. Most orthologs had similar expression patterns, strongly indicating that these genes have the same function in olfaction and gustation.

  13. 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.

  14. Cloning and expression profiling of odorant-binding proteins in the tarnished plant bug, Lygus lineolaris

    Science.gov (United States)

    In insects, the perception and discrimination of odorants requires the involvement of odorant binding proteins (OBPs). To gain a better molecular understanding of olfaction in the agronomic pest, Lygus lineolaris (tarnished plant bug), we used a transcriptomics-based approach to identify potential ...

  15. 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

  16. 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-...

  17. Determination of solvation and binding site profile within electropolymerised poly(pyrrole-N-propionic acid)

    DEFF Research Database (Denmark)

    Glidle, A.; Swann, M.J.; Gadegaard, Nikolaj;

    2000-01-01

    Specular neutron reflectivity measurements were performed on electropolymerised films of poly(pyrrole-N-propionic acid) to determine the degree to which the solvents are capable of supporting biological macromolecules can penetrate the polymer film. The permeation profile of Ni2+ ions which chelate...

  18. Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome.

    Science.gov (United States)

    Yue, Hongjun; Fang, He; Wei, Sijie; Hayes, Jeffrey J; Lee, Tae-Hee

    2016-04-12

    Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.

  19. Binding equilibrium study between Mn( Ⅱ ) and HSA or BSA

    Institute of Scientific and Technical Information of China (English)

    LIANG, Hong; TU, Chu-Qiao; ZHANG, Hong-Zhi; SHEN, Xing-Can; ZHOU, Yong-Qia; SHEN, Pan-Wen

    2000-01-01

    The binding of Mn( Ⅱ ) to human serum allbumin (HSA) or bovine serum albumin (BSA) has been studied by equilibrium dialysis at physiological pH (7.43). The Scatchard analysis indicates that there are 1.8 and 1.9 strong binding sites of Mn( Ⅱ ) in HSA and BSA, respectively. The successive stobility constants which are reported for the first time are obtained by non-linear least-squares methods fitting Bjerrum formula.For both Mn( Ⅱ )-HSA and Mn( Ⅱ )-BSA systems, the order of magnitude of K1 was found to be 104. The analyses of Hill plots and free energy coupling show that the positive cooperative effect was found in both Mn( Ⅱ )-HSA and Mn(Ⅱ)-BSA systems. The results of Mn ( Ⅱ ) competing with Cu ( Ⅱ )、Zn( Ⅱ )、Cd( Ⅱ ) or Ca( Ⅱ ) to bind to HSA or BSA further support the conjecture that there are two strong binding sites of Mn( Ⅱ ) in both HSA and BSA. One is most probably located at the tripeptide segment of N-terminal sequence of HSA and BSA molecules involving four groups composed of nitrogen atoms, and the fifth coordination atom is the carboxyl oxygen of Asp1. The coordinated atoms of the other are most probably almost all oxygen atoms.

  20. 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.

  1. 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.

  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. 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 d...

  4. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Davydova, Olga I.; Lebedeva, Nataliya Sh.; Parfenyuk, Elena V

    2004-11-01

    Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of {beta}-lactose, {alpha},{alpha}-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 {beta}-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between {alpha},{alpha}-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)

  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. 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].

  8. 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.

  9. 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.

  10. 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....

  11. 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

  12. 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

  13. 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.

  14. Two ScFv antibody libraries derived from identical VL-VH framework with different binding site designs display distinct binding profiles.

    Science.gov (United States)

    Huovinen, Tuomas; Syrjänpää, Markku; Sanmark, Hanna; Brockmann, Eeva-Christine; Azhayev, Alex; Wang, Qi; Vehniäinen, Markus; Lamminmäki, Urpo

    2013-10-01

    In directed evolution experiments, a single randomization scheme of an antibody gene does not provide optimal diversity for recognition of all sizes of antigens. In this study, we have expanded the recognition potential of our universal library, termed ScFvP, with a second distinct diversification scheme. In the second library, termed ScFvM, diversity was designed closer to the center of the antigen binding site in the same antibody framework as earlier. Also, the CDR-H3 loop structures were redesigned to be shorter, 5-12 aa and mostly without the canonical salt bridge between Arg106H and Asp116H to increase the flexibility of the loop and to allow more space in the center of the paratope for binding smaller targets. Antibodies were selected from the two libraries against various antigens separately and as a mixture. The origin and characteristics of the retrieved antibodies indicate that complementary diversity results in complementary functionality widening the spectrum of targets amenable for selection.

  15. 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

  16. 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)

  17. 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)

  18. 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.

  19. Synthesis, Characterization, and DNA Binding Studies of Nanoplumbagin

    Directory of Open Access Journals (Sweden)

    Sheik Dawood Shahida Parveen

    2014-01-01

    Full Text Available The traditional anticancer medicine plumbagin (PLN was prepared as nanostructured material (nanoplumbagin, NPn1 from its commercial counterparts, simultaneously coencapsulating with cetyltrimethylammonium bromide or cyclodextrin as stabilizers using ultrasonication technique. Surface morphology of NPn analysed from atomic force microscopy (AFM indicates that NPn has tunable size between 75 nm and 100 nm with narrow particle size distribution. Its binding efficiency with herring sperm DNA was studied using spectral and electrochemical techniques and its efficiency was found to be more compared to the commercial microcrystalline plumbagin (PLN. DNA cleavage was also studied by gel electrophoresis. The observed results indicate that NPn1 has better solubility in aqueous medium and hence showed better bioavailability compared to its commercial counterparts.

  20. 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...

  1. 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

  2. Study of CNC Grinding Machining Method About Isometric Polygon Profile

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The formed principle and CNC grinding machining method of isometric polygonal profile are studied deeply and systematically. Equation about section curve of isometric polygon profile is set up by means of geometric principle. With the use of differential geometry theory, the curve is proved to be with geometric feature of convex curve. It is referred to as Isometric Polygonal Curve (IPC), because that is a kind of convex curve on which the distance between any parallel tangent lines is equal. Isometric Poly...

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Matching profiles of masked perpetrators: a pilot study

    DEFF Research Database (Denmark)

    Lynnerup, Niels; Bojesen, Sophie; Kuhlman, Michael Bilde

    2010-01-01

    indicate the possible matches, and perhaps even the best match, which may be helpful in police investigations, but it would not carry enough weight to be used as evidence per se. This study only focused on the profile. Future studies will use surface laser scans to analyse congruence between masked...

  9. 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

  10. Host response transcriptional profiling reveals extracellular components and ABC (ATP-binding cassette transporters gene enrichment in typhoid fever-infected Nigerian children

    Directory of Open Access Journals (Sweden)

    Resau James H

    2011-09-01

    Full Text Available Abstract Background Salmonella enterica serovar Typhi (S. Typhi is a human-specific pathogen that causes typhoid fever, and remains a global health problem especially in developing countries. Its pathogenesis is complex and host response is poorly understood. In Africa, typhoid fever can be a major cause of morbidity in young infected children. The onset of the illness is insidious and clinical diagnosis is often unreliable. Gold standard blood culture diagnostic services are limited, thus rapid, sensitive, and affordable diagnostic test is essential in poor-resourced clinical settings. Routine typhoid fever vaccination is highly recommended but currently licensed vaccines provide only 55-75% protection. Recent epidemiological studies also show the rapid emergence of multi-drug resistant S. Typhi strains. High-throughput molecular technologies, such as microarrays, can dissect the molecular mechanisms of host responses which are S. Typhi-specific to provide a comprehensive genomic component of immunological responses and suggest new insights for diagnosis and treatment. Methods Global transcriptional profiles of S. Typhi-infected young Nigerian children were obtained from their peripheral blood and compared with that of other bacteremic infections using Agilent gene expression microarrays. The host-response profiles of the same patients in acute vs. convalescent phases were also determined. The top 96-100 differentially-expressed genes were identified and four genes were validated by quantitative real-time PCR. Gene clusters were obtained and functional pathways were predicted by DAVID (Database for Annotation, Visualization and Integrated Discovery. Results Transcriptional profiles from S. Typhi-infected children could be distinguished from those of other bacteremic infections. Enriched gene clusters included genes associated with extracellular peptides/components such as lipocalin (LCN2 and systemic immune response which is atypical in

  11. 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

  12. 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.

  13. Analysis of the DNA-binding profile and function of TALE homeoproteins reveals their specialization and specific interactions with Hox genes/proteins.

    Science.gov (United States)

    Penkov, Dmitry; Mateos San Martín, Daniel; Fernandez-Díaz, Luis C; Rosselló, Catalina A; Torroja, Carlos; Sánchez-Cabo, Fátima; Warnatz, H J; Sultan, Marc; Yaspo, Marie L; Gabrieli, Arianna; Tkachuk, Vsevolod; Brendolan, Andrea; Blasi, Francesco; Torres, Miguel

    2013-04-25

    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.

  14. 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.

  15. 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.

  16. 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

  17. 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…

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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...

  6. 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

  7. 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.

  8. 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.)

  9. 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.

  10. 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)

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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...

  16. Electricity Profile Study for Domestic and Commercial Sectors

    OpenAIRE

    Asmarashid Ponniran; Nur Azura Mamat; Ariffudin Joret

    2012-01-01

    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 ...

  17. [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

  18. RUNX1/core binding factor A2 regulates platelet 12-lipoxygenase gene (ALOX12): studies in human RUNX1 haplodeficiency

    Science.gov (United States)

    Kaur, Gurpreet; Jalagadugula, Gauthami; Mao, Guangfen

    2010-01-01

    Haploinsufficiency of RUNX1 (also known as CBFA2/AML1) is associated with familial thrombocytopenia, platelet dysfunction, and predisposition to acute leukemia. We have reported on a patient with thrombocytopenia and impaired agonist-induced aggregation, secretion, and protein phosphorylation associated with a RUNX1 mutation. Expression profiling of platelets revealed approximately 5-fold decreased expression of 12-lipoxygenase (12-LO, gene ALOX12), which catalyzes 12-hydroxyeicosatetraenoic acid production from arachidonic acid. We hypothesized that ALOX12 is a direct transcriptional target gene of RUNX1. In present studies, agonist-induced platelet 12-HETE production was decreased in the patient. Four RUNX1 consensus sites were identified in the 2-kb promoter region of ALOX12 (at −1498, −1491, −708, −526 from ATG). In luciferase reporter studies in human erythroleukemia cells, mutation of each site decreased activity; overexpression of RUNX1 up-regulated promoter activity, which was abolished by mutation of RUNX1 sites. Gel shift studies, including with recombinant protein, revealed RUNX1 binding to each site. Chromatin immunoprecipitation revealed in vivo RUNX1 binding in the region of interest. siRNA knockdown of RUNX1 decreased RUNX1 and 12-LO proteins. ALOX12 is a direct transcriptional target of RUNX1. Our studies provide further proof of principle that platelet expression profiling can elucidate novel alterations in platelets with inherited dysfunction. PMID:20181616

  19. 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

  20. A computational study of ligand binding affinities in iron(III) porphine and protoporphyrin IX complexes.

    Science.gov (United States)

    Durrant, Marcus C

    2014-07-01

    The search for novel anti-malarial drugs that can disrupt biomineralization of ferriprotoporphyrin IX to haemozoin requires an understanding of the fundamental chemistry of the porphyrin's iron(iii) centre at the water-lipid interface. Towards this end, the binding affinities for a diverse set of 31 small ligands with iron(iii) porphine have been calculated using density functional theory, in the gas phase and also with implicit solvent corrections for both water and n-octanol. In addition, the binding of hydroxide, chloride, acetate, methylamine and water to ferriprotoporphyrin IX has been studied, and very similar trends are observed for the smaller and larger models. Anionic ligands generally give stronger binding than neutral ones; the strongest binding is observed for RO(-) and OH(-) ligands, whilst acetate binds relatively weakly among the anions studied. Electron-rich nitrogen donors tend to bind more strongly than electron-deficient ones, and the weakest binding is found for neutral O and S donors such as oxazole and thiophene. In all cases, ligand binding is stronger in n-octanol than in water, and the differences in binding energies for the two solvents are greater for ionic ligands than for neutrals. Finally, dimerization of ferriprotoporphyrin IX by means of iron(iii)-carboxylate bond formation has been modelled. The results are discussed in terms of haemozoin crystal growth and its disruption by known anti-malarial drugs.

  1. Approving job profiles for curriculum profiles in health care programs : a study on process and product quality

    NARCIS (Netherlands)

    Mulder, Martin; Engels, Otto

    1992-01-01

    A study evaluated the approach used for validation of job profiles for curriculum development in three health care programs in the Netherlands: dietetics, podotherapy, and activity therapy. It also evaluated the quality of these job profiles and the relation between process and product quality. The

  2. 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.

  3. Phenotype-associated lectin-binding profiles of normal and transformed blood cells: a comparative analysis of mannose- and galactose-binding lectins from plants and human serum/placenta.

    Science.gov (United States)

    Mann, K K; André, S; Gabius, H J; Sharp, J G

    1994-10-01

    Surface glycoconjugates of normal and transformed blood cells are commonly characterized by plant lectins. To infer physiological significance of protein-carbohydrate interactions, mammalian lectins are obviously preferable as research tools. So far, human serum lectins have not been used to assess their binding to immunophenotyped human normal or transformed blood cells. Thus, our study combines two groups of lectins with different specificity from plant and human sources. Besides concanavalin A (ConA) we have isolated the mannose-binding protein and serum amyloid P component from human serum. Especially the mannose-binding protein is believed to play a role in host defence against bacteria and yeast cells with unknown impact on normal and tumor cells. These three lectins establish the first group. In addition to the immunomodulatory mistletoe lectin, whose binding can elicit enhanced cytokine secretion from mononuclear blood cells, we included the beta-galactoside-binding lectin (14 kDa) from human placenta in the second group. The initial series of measurements was undertaken using two-color flow cytometry to determine the phenotype-associated binding (based on cluster designation; CD) of the lectins to blood and bone marrow cells from normal donors and the cell line CEM (T-lymphoblastoid), KG1-A (primitive myeloid leukemia) and Croco II (B-lymphoblastoid). Heterogeneity was apparent for each lectin in the CD-defined cell populations. Significant differences in binding were noted between Viscum album agglutinin (VAA) and other lectins for CD4+ cells from blood and between mannose-binding protein (MBP) and VAA versus 14 kDa, ConA and serum amyloid P component (SAP) for CD19+ cells from bone marrow.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. 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

    within a species makes immune escape almost impossible for any intruding pathogen. Characterization of the SLA class I and class II gene products and their peptide binding capacity defines the T cell epitopes of any given pathogen proteome. To date the analysis of MHC peptide interactions, strength...... class I peptide binding characteristics in relation to immune responses to vaccination or infection. Applying proven technologies to newly produced, recombinant swine leukocyte antigen (SLA) class I proteins yielded a body of data for peptide:SLA:β2m (pSLA) complex affinity and stability. Mapping...... the SLA proteins for their peptide binding requirements along with the identification of their cognate virally derived peptides, made it possible to explore the nature of the SLA proteins and the roles they play in establishing adaptive immunity. The development of SLA tetramers, enabled investigation...

  5. 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.

  6. 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.;

    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...

  7. 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.

  8. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.

    Science.gov (United States)

    Enlow, Mark A

    2012-03-01

    Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.

  9. 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.

  10. 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.

  11. 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...

  12. 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).

  13. 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.)

  14. Cloud profiling radar design study for EarthCARE

    Science.gov (United States)

    Kumagai, Hiroshi; Orikasa, Teruaki; Ohno, Yuichi; Horie, Hiroaki; Kimura, Toshiyoshi

    2005-10-01

    EarthCARE Phase-A study was successfully conducted in collaboration between ESA and Japan (JAXA and NICT). In this study, high sensitivity Cloud Profiling Radar (CPR) design with Doppler capability was studied and demonstrated that the CPR satisfies mission requirements, system resource and launcher constraint. As a result of the study, a nadir looking CPR at 94 GHz with a 2.5 m diameter antenna reflector is designed with sensitivity exceeding -36 dBZ of requirement at TOA with 10 km horizontal integration. The Doppler measurement is a new challenge to attain velocity accuracy less than 1 m/s in vertical direction. In parallel to the CPR system design, algorithm development efforts have been conducted through field campaign. A suite of measured quantities that are very similar combination to the EarthCARE data was collected and applied to the retrieval algorithm test.

  15. The complexity of condensed tannin binding to bovine serum albumin--An isothermal titration calorimetry study.

    Science.gov (United States)

    Kilmister, Rachel L; Faulkner, Peta; Downey, Mark O; Darby, Samuel J; Falconer, Robert J

    2016-01-01

    Isothermal titration calorimetry was applied to study the binding of purified proanthocyanidin oligomers to bovine serum albumin (BSA). The molecular weight of the proanthocyanidin oligomer had a major impact on its binding to BSA. The calculated change in enthalpy (ΔH) and association constant (Ka) became greater as the oligomer size increased then plateaued at the heptameric oligomer. These results support a model for precipitation of proteins by proanthocyanidin where increased oligomer size enhanced the opportunity for cross linkages between proteins ultimately forming sediment-able complexes. The authors suggest tannin binding to proteins is opportunistic and involves multiple sites, each with a different Ka and ΔH of binding. The ΔH of binding comprises both an endothermic hydrophobic interaction and exothermic hydrogen bond component. This suggests the calculated entropy value (ΔS) for tannin-protein interactions is subject to a systematic error and should be interpreted with caution.

  16. 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.

  17. 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

  18. 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.

  19. Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

    Institute of Scientific and Technical Information of China (English)

    汪海林; 邹汉法; 张玉奎

    1997-01-01

    A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i

  20. 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).

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. Determination of paralytic shellfish toxins in shellfish by receptor binding assay: collaborative study.

    Science.gov (United States)

    Van Dolah, Frances M; Fire, Spencer E; Leighfield, Tod A; Mikulski, Christina M; Doucette, Gregory J

    2012-01-01

    A collaborative study was conducted on a microplate format receptor binding assay (RBA) for paralytic e shellfish toxins (PST). The assay quantifies the composite PST toxicity in shellfish samples based on the ability of sample extracts to compete with (3)H saxitoxin (STX) diHCl for binding to voltage-gated sodium channels in a rat brain membrane preparation. Quantification of binding can be carried out using either a microplate or traditional scintillation counter; both end points were included in this study. Nine laboratories from six countries completed the study. One laboratory analyzed the samples using the precolumn oxidation HPLC method (AOAC Method 2005.06) to determine the STX congener composition. Three laboratories performed the mouse bioassay (AOAC Method 959.08). The study focused on the ability of the assay to measure the PST toxicity of samples below, near, or slightly above the regulatory limit of 800 (microg STX diHCl equiv./kg). A total of 21 shellfish homogenates were extracted in 0.1 M HCl, and the extracts were analyzed by RBA in three assays on separate days. Samples included naturally contaminated shellfish samples of different species collected from several geographic regions, which contained varying STX congener profiles due to their exposure to different PST-producing dinoflagellate species or differences in toxin metabolism: blue mussel (Mytilus edulis) from the U.S. east and west coasts, California mussel (Mytilus californianus) from the U.S. west coast, chorito mussel (Mytilus chiliensis) from Chile, green mussel (Perna canaliculus) from New Zealand, Atlantic surf clam (Spisula solidissima) from the U.S. east coast, butter clam (Saxidomus gigantea) from the west coast of the United States, almeja clam (Venus antiqua) from Chile, and Atlantic sea scallop (Plactopecten magellanicus) from the U.S. east coast. All samples were provided as whole animal homogenates, except Atlantic sea scallop and green mussel, from which only the

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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...

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. [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

  6. 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

  7. 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

  8. Correlation study between sperm concentration, hyaluronic acid-binding capacity and sperm aneuploidy in Hungarian patients.

    Science.gov (United States)

    Mokánszki, Attila; Molnár, Zsuzsanna; Ujfalusi, Anikó; Balogh, Erzsébet; Bazsáné, Zsuzsa Kassai; Varga, Attila; Jakab, Attila; Oláh, Éva

    2012-12-01

    Infertile men with low sperm concentration and/or less motile spermatozoa have an increased risk of producing aneuploid spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding may reduce genetic risks such as chromosomal rearrangements and numerical aberrations. Fluorescence in-situ hybridization (FISH) has been used to evaluate the presence of aneuploidies. This study examined spermatozoa of 10 oligozoospermic, 9 asthenozoospermic, 9 oligoasthenozoospermic and 17 normozoospermic men by HA binding and FISH. Mean percentage of HA-bound spermatozoa in the normozoospermic group was 81%, which was significantly higher than in the oligozoospermic (Psex chromosomes (P=0.014) and chromosome 17 (P=0.0019), diploidy (P=0.03) and estimated numerical chromosome aberrations (P=0.004) were significantly higher in the oligoasthenozoospermic group compared with the other groups. There were statistically significant relationships (Pchromosome aberrations (r=-0.668) and between HA binding and estimated numerical chromosome aberrations (r=-0.682). HA binding and aneuploidy studies of spermatozoa in individual cases allow prediction of reproductive prognosis and provision of appropriate genetic counselling. Infertile men with normal karyotypes and low sperm concentrations and/or less motile spermatozoa have significantly increased risks of producing aneuploid (diminished mature) spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding, based on a binding between sperm receptors for zona pellucida and HA, may reduce the potential genetic risks such as chromosomal rearrangements and numerical aberrations. In the present study we examined sperm samples of 45 men with different sperm parameters by HA-binding assay and fluorescence in-situ hybridization (FISH). Mean percentage of HA-bound spermatozoa in the normozoospermic group was significantly higher than the oligozoospermic, the asthenozoospermic and the oligoasthenozoospermic groups. Using FISH, disomy of sex

  9. Characterization of the genome-wide TLX1 binding profile in T-cell acute lymphoblastic leukemia.

    Science.gov (United States)

    Durinck, K; Van Loocke, W; Van der Meulen, J; Van de Walle, I; Ongenaert, M; Rondou, P; Wallaert, A; de Bock, C E; Van Roy, N; Poppe, B; Cools, J; Soulier, J; Taghon, T; Speleman, F; Van Vlierberghe, P

    2015-12-01

    The TLX1 transcription factor is critically involved in the multi-step pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) and often cooperates with NOTCH1 activation during malignant T-cell transformation. However, the exact molecular mechanism by which these T-cell specific oncogenes cooperate during transformation remains to be established. Here, we used chromatin immunoprecipitation followed by sequencing to establish the genome-wide binding pattern of TLX1 in human T-ALL. This integrative genomics approach showed that ectopic TLX1 expression drives repression of T cell-specific enhancers and mediates an unexpected transcriptional antagonism with NOTCH1 at critical target genes, including IL7R and NOTCH3. These phenomena coordinately trigger a TLX1-driven pre-leukemic phenotype in human thymic precursor cells, reminiscent of the thymus regression observed in murine TLX1 tumor models, and create a strong genetic pressure for acquiring activating NOTCH1 mutations as a prerequisite for full leukemic transformation. In conclusion, our results uncover a functional antagonism between cooperative oncogenes during the earliest phases of tumor development and provide novel insights in the multi-step pathogenesis of TLX1-driven human leukemia. PMID:26108691

  10. Profiling of β-lactam selectivity for penicillin-binding proteins in Escherichia coli strain DC2.

    Science.gov (United States)

    Kocaoglu, Ozden; Carlson, Erin E

    2015-05-01

    Penicillin-binding proteins (PBPs) are integral players in bacterial cell division, and their catalytic activities can be monitored with β-lactam-containing chemical probes. Compounds that target a single PBP could provide important information about the specific role(s) of each enzyme, making identification of such molecules important. We evaluated 22 commercially available β-lactams for inhibition of the PBPs in live Escherichia coli strain DC2. Whole cells were titrated with β-lactam antibiotics and subsequently incubated with a fluorescent penicillin derivative, Bocillin-FL (Boc-FL), to label uninhibited PBPs. Protein visualization was accomplished by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) separation and fluorescent scanning. The examined β-lactams exhibited diverse PBP selectivities, with amdinocillin (mecillinam) showing selectivity for PBP2, aztreonam, piperacillin, cefuroxime, cefotaxime, and ceftriaxone for PBP3, and amoxicillin and cephalexin for PBP4. The remaining β-lactams did not block any PBPs in the DC2 strain of E. coli or inhibited more than one PBP at all examined concentrations in this Gram-negative organism. PMID:25733506

  11. 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.

  12. 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.

  13. 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.

  14. 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.)

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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)

  20. 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)

  1. 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.

  2. Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA.

    Science.gov (United States)

    Xue, Liang; Ranjan, Nihar; Arya, Dev P

    2011-04-12

    Synthesis of a novel perylene-neomycin conjugate (3) and the properties of its binding to human telomeric G-quadruplex DNA, 5'-d[AG3(T2AG3)3] (4), are reported. Various spectroscopic techniques were employed to characterize the binding of conjugate 3 to 4. A competition dialysis assay revealed that 3 preferentially binds to 4, in the presence of other nucleic acids, including DNA, RNA, DNA-RNA hybrids, and other higher-order structures (single strands, duplexes, triplexes, other G-quadruplexes, and the i-motif). UV thermal denaturation studies showed that thermal stabilization of 4 increases as a function of the increasing concentration of 3. The fluorescence intercalator displacement (FID) assay displayed a significantly tighter binding of 3 with 4 as compared to its parent constituents [220-fold stronger than neomycin (1) and 4.5-fold stronger than perylene diamine (2), respectively]. The binding of 3 with 4 resulted in pronounced changes in the molar ellipticity of the DNA absorption region as confirmed by circular dichroism. The UV-vis absorption studies of the binding of 3 to 4 resulted in a red shift in the spectrum of 3 as well as a marked hypochromic change in the perylene absorption region, suggesting that the ligand-quadruplex interaction involves stacking of the perylene moiety. Docking studies suggest that the perylene moiety serves as a bridge that end stacks on 4, making contacts with two thymine bases in the loop, while the two neomycin moieties branch into the grooves of 4.

  3. 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

  4. 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

  5. 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.

  6. Proton and iodine-127 nuclear magnetic resonance studies on the binding of iodide by lactoperoxidase

    Energy Technology Data Exchange (ETDEWEB)

    Sakurada, J.; Takahashi, S.; Shimizu, T.; Hatano, M.; Nakamura, S.; Hosoya, T.

    1987-10-06

    Interaction of an iodide ion with lactoperoxidase was studied by the use of /sup 1/H NMR, /sup 127/I NMR, and optical difference spectrum techniques. /sup 1/H NMR spectra demonstrated that a major broad hyperfine-shifted signal at about 60 ppm, which is ascribed to the heme peripheral methyl protons, was shifted toward high field by adding KI, indicating the binding of iodide to the active site of the enzyme; the dissociation constant was estimated to be 38 mM at pH 6.1. The binding was further detected by /sup 127/I NMR, showing no competition with cyanide. Both /sup 1/H NMR and /sup 127/I NMR revealed that the binding of iodide to the enzyme is facilitated by the protonation of an ionizable group with a pK/sup a/ value of 6.0-6.8, which is presumably the distal histidyl residue. Optical difference spectra showed that the binding of an aromatic donor molecule to the enzyme is slightly but distinctly affected by adding KI. On the basis of these results, it was suggested that an iodide ion binds to lactoperoxidase outside the heme crevice but at the position close enough to interact with the distal histidyl residue which possibly mediates electron transport in the iodide oxidation reaction.

  7. 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.

  8. 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.

  9. 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.

  10. Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies.

    Science.gov (United States)

    Sarwar, Tarique; Rehman, Sayeed Ur; Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Tabish, Mohammad

    2015-02-01

    DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

  11. 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

  12. 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

  13. 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

  14. Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution.

    Science.gov (United States)

    Singh, Amit K; Kumar, Ramasamy P; Pandey, Nisha; Singh, Nagendra; Sinha, Mau; Bhushan, Asha; Kaur, Punit; Sharma, Sujata; Singh, Tej P

    2010-01-01

    Isoniazid (INH) is an anti-tuberculosis prodrug that is activated by mammalian lactoperoxidase and Mycobacterium tuberculosis catalase peroxidase (MtCP). We report here binding studies, an enzyme assay involving INH, and the crystal structure of the complex of bovine lactoperoxidase (LPO) with INH to illuminate binding properties and INH activation as well as the mode of diffusion and interactions together with a detailed structural and functional comparison with MtCP. The structure determination shows that isoniazid binds to LPO at the substrate binding site on the distal heme side. The substrate binding site is connected to the protein surface through a long hydrophobic channel. The acyl hydrazide moiety of isoniazid interacts with Phe(422) O, Gln(423) O(epsilon1), and Phe(254) O. In this arrangement, pyridinyl nitrogen forms a hydrogen bond with a water molecule, W-1, which in turn forms three hydrogen bonds with Fe(3+), His(109) N(epsilon2), and Gln(105) N(epsilon2). The remaining two sides of isoniazid form hydrophobic interactions with the atoms of heme pyrrole ring A, C(beta) and C(gamma) atoms of Glu(258), and C(gamma) and C(delta) atoms of Arg(255). The binding studies indicate that INH binds to LPO with a value of 0.9 x 10(-6) m for the dissociation constant. The nitro blue tetrazolium reduction assay shows that INH is activated by the reaction of LPO-H(2)O(2) with INH. This suggests that LPO can be used for INH activation. It also indicates that the conversion of INH into isonicotinoyl radical by LPO may be the cause of INH toxicity.

  15. 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

  16. 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

  17. 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.

  18. 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.

    2011-04-01

    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 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

  19. 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

  20. 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.

  1. 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...

  2. 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.

  3. 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.

  4. Thermodynamic Study of Interactions Between ZnO and ZnO Binding Peptides Using Isothermal Titration Calorimetry.

    Science.gov (United States)

    Limo, Marion J; Perry, Carole C

    2015-06-23

    While material-specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modeling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully realized. Understanding the thermodynamic changes that occur during peptide-inorganic interactions and correlating these to structural modifications of the inorganic materials could be the key to achieving and mastering control over material formation processes. This study is a detailed investigation applying isothermal titration calorimetry (ITC) to directly probe thermodynamic changes that occur during interaction of ZnO binding peptides (ZnO-BPs) and ZnO. The ZnO-BPs used are reported sequences G-12 (GLHVMHKVAPPR), GT-16 (GLHVMHKVAPPR-GGGC), and alanine mutants of G-12 (G-12A6, G-12A11, and G-12A12) whose interaction with ZnO during solution synthesis studies have been extensively investigated. The interactions of the ZnO-BPs with ZnO yielded biphasic isotherms comprising both an endothermic and an exothermic event. Qualitative differences were observed in the isothermal profiles of the different peptides and ZnO particles studied. Measured ΔG values were between -6 and -8.5 kcal/mol, and high adsorption affinity values indicated the occurrence of favorable ZnO-BP-ZnO interactions. ITC has great potential in its use to understand peptide-inorganic interactions, and with continued development, the knowledge gained may be instrumental for simplification of selection processes of organic molecules for the advancement of material synthesis and design.

  5. Human Islet Amyloid Polypeptide Fibril Binding to Catalase: A Transmission Electron Microscopy and Microplate Study

    Directory of Open Access Journals (Sweden)

    Nathaniel G. N. Milton

    2010-01-01

    Full Text Available The diabetes-associated human islet amyloid polypeptide (IAPP is a 37-amino-acid peptide that forms fibrils in vitro and in vivo. Human IAPP fibrils are toxic in a similar manner to Alzheimer's amyloid-β (Aβ and prion protein (PrP fibrils. Previous studies have shown that catalase binds to Aβ fibrils and appears to recognize a region containing the Gly-Ala-Ile-Ile sequence that is similar to the Gly-Ala-Ile-Leu sequence found in human IAPP residues 24-27. This study presents a transmission electron microscopy (TEM—based analysis of fibril formation and the binding of human erythrocyte catalase to IAPP fibrils. The results show that human IAPP 1-37, 8-37, and 20-29 peptides form fibrils with diverse and polymorphic structures. All three forms of IAPP bound catalase, and complexes of IAPP 1-37 or 8-37 with catalase were identified by immunoassay. The binding of biotinylated IAPP to catalase was high affinity with a KD of 0.77nM, and could be inhibited by either human or rat IAPP 1-37 and 8-37 forms. Fibrils formed by the PrP 118-135 peptide with a Gly-Ala-Val-Val sequence also bound catalase. These results suggest that catalase recognizes a Gly-Ala-Ile-Leu—like sequence in amyloid fibril-forming peptides. For IAPP 1-37 and 8-37, the catalase binding was primarily directed towards fibrillar rather than ribbon-like structures, suggesting differences in the accessibility of the human IAPP 24-27 Gly-Ala-Ile-Leu region. This suggests that catalase may be able to discriminate between different structural forms of IAPP fibrils. The ability of catalase to bind IAPP, Aβ, and PrP fibrils demonstrates the presence of similar accessible structural motifs that may be targets for antiamyloid therapeutic development.

  6. Analytical methods to determine the comparative DNA binding studies of curcumin-Cu(II) complexes

    Science.gov (United States)

    Rajesh, Jegathalaprathaban; Rajasekaran, Marichamy; Rajagopal, Gurusamy; Athappan, Periakaruppan

    2012-11-01

    DNA interaction studies of two mononuclear [1:1(1); 1:2(2)] copper(II) complexes of curcumin have been studied. The interaction of these complexes with CT-DNA has been explored by physical methods to propose modes of DNA binding of the complexes. Absorption spectral titrations of complex 1 with CT-DNA shows a red-shift of 3 nm with the DNA binding affinity of Kb, 5.21 × 104 M-1 that are higher than that obtained for 2 (red-shift, 2 nm; Kb, 1.73 × 104 M-1) reveal that the binding occurs in grooves as a result of the interaction is via exterior phosphates. The CD spectra of these Cu(II) complexes show a red shift of 3-10 nm in the positive band with increase in intensities. This spectral change of induced CD due to the hydrophobic interaction of copper complexes with DNA is the characteristic of B to A conformational change. The EB displacement assay also reveals the same trend as observed in UV-Vis spectral titration. The addition of complexes 1 and 2 to the DNA bound ethidium bromide (EB) solutions causes an obvious reduction in emission intensities indicating that these complexes competitively bind to DNA with EB. The positive shift of both the Epc and E0' accompanied by reduction of peak currents in differential pulse voltammogram (DPV), upon adding different concentrations of DNA to the metal complexes, are obviously in favor of strong binding to DNA. The super coiled plasmid pUC18 DNA cleavage ability of Cu(II) complexes in the presence of reducing agent reveals the single strand DNA cleavage (ssDNA) is observed. The hydroxyl radical (HOrad ) and the singlet oxygen are believed to be the reactive species responsible for the cleavage.

  7. 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.

  8. 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

  9. 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

  10. Use of computational modeling approaches in studying the binding interactions of compounds with human estrogen receptors.

    Science.gov (United States)

    Wang, Pan; Dang, Li; Zhu, Bao-Ting

    2016-01-01

    Estrogens have a whole host of physiological functions in many human organs and systems, including the reproductive, cardiovascular, and central nervous systems. Many naturally-occurring compounds with estrogenic or antiestrogenic activity are present in our environment and food sources. Synthetic estrogens and antiestrogens are also important therapeutic agents. At the molecular level, estrogen receptors (ERs) mediate most of the well-known actions of estrogens. Given recent advances in computational modeling tools, it is now highly practical to use these tools to study the interaction of human ERs with various types of ligands. There are two common categories of modeling techniques: one is the quantitative structure activity relationship (QSAR) analysis, which uses the structural information of the interacting ligands to predict the binding site properties of a macromolecule, and the other one is molecular docking-based computational analysis, which uses the 3-dimensional structural information of both the ligands and the receptor to predict the binding interaction. In this review, we discuss recent results that employed these and other related computational modeling approaches to characterize the binding interaction of various estrogens and antiestrogens with the human ERs. These examples clearly demonstrate that the computational modeling approaches, when used in combination with other experimental methods, are powerful tools that can precisely predict the binding interaction of various estrogenic ligands and their derivatives with the human ERs.

  11. Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

    Institute of Scientific and Technical Information of China (English)

    HU; JianPing; CHANG; Shan; CHEN; WeiZu; WANG; CunXin

    2007-01-01

    Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

  12. 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

  13. 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....

  14. 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...

  15. Understanding binding affinity : A combined isothermal titration calorimetry/molecular dynamics study of the binding of a series of hydrophobically modified benzamidinium chloride inhibitors to trypsin

    NARCIS (Netherlands)

    Talhout, Reinskje; Villa, Alessandra; Mark, AE; Engberts, JBFN

    2003-01-01

    The binding of a series of p-alkylbenzamidinium chloride inhibitors to the serine proteinase trypsin over a range of temperatures has been studied using isothermal titration (micro)calorimetry and molecular dynamics simulation techniques. The inhibitors have small structural variations at the para p

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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...

  1. 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)

  2. 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...

  3. 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

  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. A CORRELATIVE STUDY OF FNAC THYROID WITH THYROID HORMONE PROFILE

    Directory of Open Access Journals (Sweden)

    Ritica

    2014-02-01

    Full Text Available BACKGROUND: Study aims to determine correlation of the cytological pattern of t hyr oid lesions in ad di t ion to the ut i l it y a nd accu r ac y o f F N A C a s in i t ia l dia g nostic me thod a lo n g with t hy roid h o rmone p ro f i l e ( T 3, T4 a nd TSH whi c h p r ovides info r mation a t p hy sio log i ca l a nd p a tho l o g ic a l lev e ls a nd thus ca n e nh a n c e the l i k e l i hood o f ea r l y de te c t i on of a mb ig uous t hyr oid dy sfu nc t i on with m i ni ma l clin ica l findin gs. OBJECTIVES: To obtain role of thyroid hormone profile (T3, T4 and TSH aimed at defining prognostic parameters and correlating it with cytology r e sul t s, dia g nosis of dif f use n o n t o xi c g oi te r, dia g nos i s of sol i ta ry /do m inant t hy roid nodule, c onfi r mation of c l i nic a l l y obvious t hyr oid ma l ig n anc y . MATERIALS AND METHODS: 150 patients with thyroid sw ellings underwent FNAC along with c omp le te t hy roid ho r mone p r o f i l e in Central Diagnostic Lab o f A JI MS Man ga lor e . P r oce d u re w a s p e r f o r med without L .A with the he lp of a spir a t i ng t ec hnique usi n g 23G nee dle a t tache d to 10 ml di s posa b le sy ri nge . An avera ge of one a t te mpt p e r nodule w a s p e r fo rm e d usual l y re sul t ing in 4 dir ec t sme a rs. B oth a ir d r ied a nd w e t fi xe d sme a rs fi xe d in 95% a l c ohol for a bout 30 m i n ute s a nd stain e d with Le ish ma n ’ s stain a nd Pa p stain e x a m i n e d und e r l ig ht m icr osco pe . T hy roid p ro file is a lso p e r f o r med in a ll the a bo v e p a t ie nts. RESULTS: One hund re d a nd fi ft y a spir a t i ons of p a t ie nts (both f e m a les a nd mal e s w er e analyse d. T 3, T4 a nd TSH w a s analy z e d f o r a ll 150 p a t ie nts . The me a n ag e of p a t ie nts in t his stu d y w a s 39.66 year s a nd ag e rang e w a s 1 - 76 yea rs. The r e w er e 142 femal e s (94. 6 6% a nd 8 mal e s (5.3 3% . M ax i m um nu m b e r of

  6. 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 ...

  7. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer.

    Science.gov (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A

    2013-06-01

    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

  8. A comparative study on river hydrokinetic turbines blade profiles

    Directory of Open Access Journals (Sweden)

    Kamal A.R.Ismail

    2015-05-01

    Full Text Available Diesel based electricity supply is the common practice in rural and isolated areas in the North of Brazil. The diesel fuel is usually transported from a nearby city as Manaus by river to these isolated communities. During wet seasons and inundations this means of transport is very risky and not usually safe. The hydrokinetic technology is among the promising technologies for most of the Amazon areas because of the large hydraulic capacity and low density population settlements. In this paper the authors propose a cheap hydrokinetic turbine system whose blades are easy to design, manufacture, replace when necessary and its operation is independent of flow direction. In this work CFD, RANS (Reynolds Average Navier Stokes equations are used to characterize and develop a methodology of numerical simulation of a vertical axis hydrokinetic turbine. In the simulations, four blade profiles were investigated. The effects of the number of blades, blade profile and water flow velocity on the turbine torque and power coefficients were presented and discussed.

  9. 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.

  10. 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

  11. 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

  12. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates.

    Science.gov (United States)

    Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P

    2010-07-01

    Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin neomycin. The binding of compounds 1-4 with poly(dA).2poly(dT) was mostly enthalpy

  13. 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.

  14. 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.

  15. Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence.

    Science.gov (United States)

    Wilson, Tom; Costa, Paulo J; Félix, Vítor; Williamson, Mike P; Thomas, Jim A

    2013-11-14

    We report DNA binding studies of the dinuclear ruthenium ligand [{Ru(phen)2}2tpphz](4+) in enantiomerically pure forms. As expected from previous studies of related complexes, both isomers bind with similar affinity to B-DNA and have enhanced luminescence. However, when tested against the G-quadruplex from human telomeres (which we show to form an antiparallel basket structure with a diagonal loop across one end), the ΛΛ isomer binds approximately 40 times more tightly than the ΔΔ, with a stronger luminescence. NMR studies show that the complex binds at both ends of the quadruplex. Modeling studies, based on experimentally derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz](4+), show that the ΛΛ isomer fits neatly under the diagonal loop, whereas the ΔΔ isomer is unable to bind here and binds at the lateral loop end. Molecular dynamics simulations show that the ΔΔ isomer is prevented from binding under the diagonal loop by the rigidity of the loop. We thus present a novel enantioselective binding substrate for antiparallel basket G-quadruplexes, with features that make it a useful tool for quadruplex studies.

  16. 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.

  17. 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.

  18. Spectroscopic Studies on the Binding of Bacteriophage Mequindox with Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)

    ZENG,Zhouhua; LIU,Yi; HU,Xianming; XU,Zhenqiang; ZENG,Kun

    2009-01-01

    Fluorescence spectra and UV-Vis absorption spectra have been used to study the binding of bacteriophage mequindox (MEQ) with bovine serum albumin (BSA),which performed a dynamic quenching process.The quenching constants and thermodynamic parameters at different temperatures were calculated.The binding was primarily driven by entropy,and hydrophobic forces also played a significant role.The distance between BSA and MEQ was estimated to be 4.5 nm based on the theory of F(o)rster's non-radioactive energy transfer.Furthermore,synchronous fluorescence spectra and 3-dimensional fluorescence spectra were used to figure out the configuration of BSA in the presence or absence of MEQ,which indicated that it was basically the same.

  19. The Binding of Roxarsone at the Silica/Water Interface Studied with Second Harmonic Generation

    Science.gov (United States)

    Konek, Christopher; Ostrowski, David; Geiger, Franz

    2005-03-01

    Arsenic is a carcinogen that can also cause chronic poisoning when ingested via drinking water in quantities as low as 10 micrograms/L. In the US, organic arsenicals such as Roxarsone are commonly used as feed additives in the poultry industry. The use of poultry litter as fertilizer results in environmental arsenic deposition rates of up to 50 metric tons per year; the subsequent environmental fate of Roxarsone is unknown. We use second harmonic generation (SHG) to study the thermodynamics and kinetics of Roxarsone binding to environmentally relevant mineral oxide/water interfaces. Roxarsone binding to water/SiO2 interfaces is fully reversible, consistent with high Roxarsone mobility. Results from Langmuir isotherm measurements and surface SHG spectra are presented as well.

  20. 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;

    2006-01-01

    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...... in HC during a 9-month period post-partum. No differences were observed between the vitamin B12-supplemented and the unsupplemented groups. Thus, supplementation with vitamin B12 has no impact on the circulating level of serum cobalamins or its binding proteins in a Danish population of lactating......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...

  1. 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

  2. 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.

  3. 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...

  4. 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

  5. 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)

  6. 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

  7. Synthesis and microarray-assisted binding studies of core xylose and fucose containing N-glycans.

    Science.gov (United States)

    Brzezicka, Katarzyna; Echeverria, Begoña; Serna, Sonia; van Diepen, Angela; Hokke, Cornelis H; Reichardt, Niels-Christian

    2015-05-15

    The synthesis of a collection of 33 xylosylated and core-fucosylated N-glycans found only in nonmammalian organisms such as plants and parasitic helminths has been achieved by employing a highly convergent chemo-enzymatic approach. The influence of these core modifications on the interaction with plant lectins, with the human lectin DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Nonintegrin), and with serum antibodies from schistosome-infected individuals was studied. Core xylosylation markedly reduced or completely abolished binding to several mannose-binding plant lectins and to DC-SIGN, a C-type lectin receptor present on antigen presenting cells. Employing the synthetic collection of core-fucosylated and core-xylosylated N-glycans in the context of a larger glycan array including structures lacking these core modifications, we were able to dissect core xylose and core fucose specific antiglycan antibody responses in S. mansoni infection sera, and we observed clear and immunologically relevant differences between children and adult groups infected with this parasite. The work presented here suggests that, quite similar to bisecting N-acetylglucosamine, core xylose distorts the conformation of the unsubstituted glycan, with important implications for the immunogenicity and protein binding properties of complex N-glycans.

  8. 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

  9. 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

  10. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

    Directory of Open Access Journals (Sweden)

    Keskin Ozlem

    2007-05-01

    Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

  11. 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.

  12. 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...

  13. 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.

  14. 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...

  15. Mucin profiles of the abomasum in bulls and rams: A comparative study.

    Science.gov (United States)

    Karakoç, Zelal; Sağsöz, Hakan; Ketani, Muzaffer Aydın

    2016-09-01

    Many pathogens require direct binding to mucosal cells to cause an infection. The mucosal epithelium of the digestive tract, which is covered by a mucin layer, fulfills several protective functions that are essential to maintaining the health of the digestive tract. Mucins are glycoproteins, which are found on membranes and in mucus gels and protect the underlying mucosal cells. Both membrane-associated mucins and secreted mucins are critical components of mucosal defense. The aim of this study was to determine the localization and expression of mucin profile of the abomasum via histochemistry and immunohistochemistry. The abomasums of 20 bulls and 20 rams were evaluated. Histochemical examination showed that neutral and acidic mucins were present in the mucosa and the glands of the pars cardiaca, fundus, and pars pylorica of the abomasums of both bulls and rams. However, the expression of acidic mucins was weak in the superficial glands and strong in the deep glands of the abomasum of rams. In both bulls and rams, MUC1, MUC5AC, and MUC6 were expressed in the glandular epithelial cells in all regions of the abomasum. Interestingly, while MUC2 was not expressed in the pars cardiaca and fundus, it was weakly expressed in the parietal cells of the pars pylorica in both species. In conclusion, the presence of neutral and acidic mucins and MUC1, MUC2, MUC5AC, and MUC6 proteins in luminal epithelial and glandular cells of abomasum in the bulls and rams support the hypothesis that mucins play a key role in the protection of the abomasal mucosa against infectious agents. PMID:27338724

  16. 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

  17. Comparative thermodynamic studies on substrate and product binding of O-Acetylserine Sulfhydrylase reveals two different ligand recognition modes†

    Directory of Open Access Journals (Sweden)

    Kumaran Sangaralingam

    2011-06-01

    Full Text Available Abstract Background The importance of understanding the detailed mechanism of cysteine biosynthesis in bacteria is underscored by the fact that cysteine is the only sulfur donor for all cellular components containing reduced sulfur. O-acetylserine sulfhydrylase (OASS catalyzes this crucial last step in the cysteine biosynthesis and has been recognized as an important gene for the survival and virulence of pathogenic bacteria. Structural and kinetic studies have contributed to the understanding of mechanistic aspects of OASS, but details of ligand recognition features of OASS are not available. In the absence of any detailed study on the energetics of ligand binding, we have studied the thermodynamics of OASS from Salmonella typhimurium (StOASS, Haemophilus influenzae (HiOASS, and Mycobacterium tuberculosis (MtOASS binding to their substrate O-acetylserine (OAS, substrate analogue (methionine, and product (cysteine. Results Ligand binding properties of three OASS enzymes are studied under defined solution conditions. Both substrate and product binding is an exothermic reaction, but their thermodynamic signatures are very different. Cysteine binding to OASS shows that both enthalpy and entropy contribute significantly to the binding free energy at all temperatures (10-30°C examined. The analyses of interaction between OASS with OAS (substrate or methionine (substrate analogue revealed a completely different mode of binding. Binding of both OAS and methionine to OASS is dominated by a favorable entropy change, with minor contribution from enthalpy change (ΔHSt-Met = -1.5 ± 0.1 kJ/mol; TΔSSt-Met = 8.2 kJ/mol at 20°C. Our salt dependent ligand binding studies indicate that methionine binding affinity is more sensitive to [NaCl] as compared to cysteine affinity. Conclusions We show that OASS from three different pathogenic bacteria bind substrate and product through two different mechanisms. Results indicate that predominantly entropy driven

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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...

  3. Study on the bindings of dichlorprop and diquat dibromide herbicides to human serum albumin by spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Tunç, Sibel, E-mail: stunc@akdeniz.edu.tr; Duman, Osman, E-mail: osmanduman@akdeniz.edu.tr; Soylu, İnanç; Kancı Bozoğlan, Bahar

    2014-05-01

    Highlights: • The affinity of DCP to HSA is higher than DQ. • DCP and DQ have quenched the fluorescence emission spectrum of HSA by static quenching mechanism. • Electrostatic interactions are very important in HSA-DCP and HSA-DQ complexes. • Binding constants, numbers of binding sites and thermodynamic parameters have been calculated. • The binding of DQ changes the conformation of protein, on the contrary to DCP. - Abstract: The interactions of dichlorprop (DCP) and diquat dibromide (DQ) herbicides with human serum albumin (HSA) protein were studied by UV absorption, fluorescence, synchronous fluorescence and circular dichroism (CD) spectroscopy. Both DCP and DQ quenched the fluorescence emission spectrum of HSA through the static quenching mechanism. The Stern–Volmer quenching constant, binding constant, the number of binding sites and thermodynamic parameters were determined at 288 K, 298 K, 310 K and 318 K. In HSA-DCP and HSA-DQ systems, an increase in temperature led to a decrease in the Stern–Volmer quenching constant and binding constant. One binding site was obtained for DCP and DQ on HSA. It was found that DCP can bind to HSA with higher affinity than DQ. Negative ΔH and positive ΔS values were obtained for the binding processes between protein and herbicide molecules. This result displayed that electrostatic interactions play a major role in the formation of HSA-DCP and HSA-DQ complexes. The binding processes were exothermic reactions and spontaneous. In addition, synchronous fluorescence and CD spectra of HSA revealed that the binding of DCP to HSA did not cause a significant conformational change in protein, but the interaction of DQ with HSA led to an alteration in the protein structure.

  4. The screening and functional study of proteins binding with the BmNPV polyhedrin promoter

    Directory of Open Access Journals (Sweden)

    Yu Wei

    2012-05-01

    Full Text Available Abstract Background The polyhedrin gene promoter has an essential role in regulating foreign gene expression in baculovirus expression vector systems (BEVS; however, the high-level transcription mechanism is still unknown. One-hybrid screening in yeast is a powerful way of identifying rapidly heterologous transcription factors that can interact with the polyhedrin promoter DNA sequence. In the current study, total RNA was extracted from the fat bodies of fifth-instar silkworm larvae that had been infected with Bombyx mori nuclear polyhedrosis virus (BmNPV for 5 days; complementary DNA (cDNA was then generated using reverse-transcription (RT-PCR to construct a silkworm gene expression library. Key polyhedrin promoter bait sequences were synthesized to generate a bait yeast strain, which was used to screen the one-hybrid cDNA library. Results In total, 12 positive yeast colonies were obtained from the SD/-Leu/AbA plates; sequencing analysis showed that they belong to two different protein cDNA colonies. Positive colonies underwent bioinformatics analysis, which revealed one colony to be ribosomal proteins [B. mori ribosomal protein SA (BmRPSA] and the other to be NPV DNA-binding proteins (DBP. To further verify the regulatory function of these two protein groups, transient expression vectors (pSK-IE-dbp and pSK-IE-BmRPSA were constructed. The recombinant plasmids were then transfected into cultured B. mori N (BmN cells, which had been infected with a recombinant bacmid containing the gene encoding luciferase (luc. The results showed that overexpression of either dbp or BmRPSA upregulated the polh promoter-driven transcription of luc in BmN cells. In addition, dbp or BmRPSA RNA interference (RNAi resulted in the downregulation of luciferase reporter expression in BmN cells, demonstrating that DBP and BmRPSA are important for luc transcription. EMSA results further confirmed that DBP could directly bind to the conserved single-stranded polh

  5. 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

  6. Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-Binding Domain Reveal How It Binds Copper Ions

    Energy Technology Data Exchange (ETDEWEB)

    Kong, G.K.-W.; Adams, J.J.; Harris, H.H.; Boas, J.F.; Curtain, C.C.; Galatis, D.; Master, C.L.; Barnham, K.J.; McKinstry, W.J.; Cappai, R.; Parker, M.W.; /Sydney U.

    2007-07-09

    Alzheimer's disease (AD) is the major cause of dementia. Amyloid {beta} peptide (A {beta}), generated by proteolytic cleavage of the amyloid precursor protein (APP), is central to AD pathogenesis. APP can function as a metalloprotein and modulate copper (Cu) transport, presumably via its extracellular Cu-binding domain (CuBD). Cu binding to the CuBD reduces A{beta} levels, suggesting that a Cu mimetic may have therapeutic potential. We describe here the atomic structures of apo CuBD from three crystal forms and found they have identical Cu-binding sites despite the different crystal lattices. The structure of Cu[2+]-bound CuBD reveals that the metal ligands are His147, His151, Tyrl68 and two water molecules, which are arranged in a square pyramidal geometry. The site resembles a Type 2 non-blue Cu center and is supported by electron paramagnetic resonance and extended X-ray absorption fine structure studies. A previous study suggested that Met170 might be a ligand but we suggest that this residue plays a critical role as an electron donor in CuBDs ability to reduce Cu ions. The structure of Cu[+]-bound CuBD is almost identical to the Cu[2+]-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavorable for Cu[+], thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.

  7. 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

  8. 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.

  9. Beach Profiles Characteristics Along Giao Thuy and Hai Hau Coasts,Vietnam: A Field Study

    Institute of Scientific and Technical Information of China (English)

    NGUYEN Viet Thanh; ZHENG Jin-hai; ZHANG Chi

    2012-01-01

    Giao Thuy and Hai Hau coasts are located in Nam Dinh province,Vietnam,with a total coastline of 54.42 km in length.The sea-dike system has been seriously damaged and there have been many dike breaches which caused floods and losses.This situation is considered of a general representative for coastal area in the northern part of Vietnam.A variety of studies have shown that the gradient in the longshore sediment transport rate and the offshore fine sediment lost are the main mechanisms causing the beach erosion.This study presents a field investigation of the beach profiles at Giao Thuy and Hai Hau beaches.Three types of empirical functions for the equilibrium beach profile are applied and compared with the observations.Results show that all observed beach profiles can be described by a single function.However,one specific equilibrium profile equation is not sufficient to assess all beach profiles.In Section 1 of Giao Thuy and Section 3 of Hai Thinh beaches,beach profiles are consistent with the logarithmic function,while the exponential function fits well in Section 2.This difference is explained with respect to coastal morphology,sediment characteristics and hydrodynamic conditions which vary in site.An analysis of the validity of the beach profile functions is recommended for the numerical modeling and engineering designs in this area.

  10. 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) ...

  11. 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

  12. 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.

  13. Mineralocorticoid specificity of renal type I receptors: in vivo binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Sheppard, K.; Funder, J.W.

    1987-02-01

    The authors have injected rats with (TH)aldosterone or (TH) corticosterone, plus 100-fold excess of the highly specific glucocorticoid RU 28362, with or without excess unlabeled aldosterone or corticosterone and compared type I receptor occupancy in kidney and hippocampus. Thirty minutes after subcutaneous injection (TH)aldosterone was well retained in renal papilla-inner medulla, renal cortex-outer medulla, and hippocampus; in contrast, (TH)corticosterone was well retained only in hippocampus. Competition studies for (TH)aldosterone binding sites showed corticosterone to be a poor competitor in the kidney compared with hippocampus. Time-course studies, with rats killed 10-180 min after tracer administration, showed very low uptake/retention of (TH)corticosterone by kidney; in hippocampus (TH)corticosterone retention was similar to that of (TH)aldosterone in kidney, and retention of (TH)aldosterone by hippocampus was much more prolonged than of either tracer in any other tissue. Studies in 10-day-old rats, with very low levels of corticosteroid binding globulin (CBG), showed a high degree of aldosterone selectivity in both zones of the kidney, whereas 9TH)aldosterone and (TH)corticosterone were equivalently bound in hippocampus. They interpret these data as evidenced for a mechanism unrelated to extravascular CBG conferring mineralocorticoid specificity on renal type I receptors and propose two models derived from their findings consistent with such differential selectivity.

  14. Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch

    Directory of Open Access Journals (Sweden)

    Herman O. Sintim

    2012-11-01

    Full Text Available C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues. We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering. Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.

  15. Endo-S-c-di-GMP analogues-polymorphism and binding studies with class I riboswitch.

    Science.gov (United States)

    Zhou, Jie; Sayre, David A; Wang, Jingxin; Pahadi, Nirmal; Sintim, Herman O

    2012-01-01

    C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues). We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering). Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch) revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch. PMID:23143150

  16. Multiple ligand simultaneous docking (MLSD): A novel approach to study the effect of inhibitors on substrate binding to PPO.

    Science.gov (United States)

    Raghavendra, S; Aditya Rao, S J; Kumar, Vadlapudi; Ramesh, C K

    2015-12-01

    Multiple ligand simultaneous docking, a computational approach is used to study the concurrent interactions between substrate and the macromolecule binding together in the presence of an inhibitor. The present investigation deals with the study of the effect of different inhibitors on binding of substrate to the protein Polyphenoloxidase (PPO). The protein was isolated from Mucuna pruriens and confirmed as tyrosinases involved in L-DOPA production. The activity was measured using different inhibitors at different concentrations taking catechol as substrate. A high-throughput binding study was conducted to compare the binding orientations of individual ligands and multiple ligands employing Autodock 4.2. The results of single substrate docking showed a better binding of urea with the binding energy of -3.48 kJ mol(-1) and inter molecular energy of -3.48 kJ mol(-1) while the results of MLSD revealed that ascorbic acid combined with the substrate showed better inhibition with a decreased binding energy of -2.37 kJ mol(-1). PMID:26414950

  17. 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...

  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. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    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...... around the phosphorylated residue are important for the binding affinity of ILKAP. We conclude that solid-phase affinity pull-down of proteins from complex mixtures can be applied in phosphoproteomics and systems biology.......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...

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

    OpenAIRE

    O'Loughlin, Jennifer; Brunet, Jennifer; Difranza, Joseph; Gervais, Andre; Gray-Donald, Katherine; Karp, Igor; Sabiston, Catherine; Sylvestre, Marie-Pierre; Dugas, Erika N.; Engert, James C.; Low, Nancy C.; Tyndale, Rachel F.

    2014-01-01

    International audience; 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...

  1. 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.

  2. Study on measurement of refractive index profile of GI-POF by light scattering

    Science.gov (United States)

    Huifen, Jiang; Xiang'e, Han

    2009-04-01

    This paper is devoted to the study on measurement of refractive index profile of graded-index polymer optical fiber (GI-POF) by light scattering. Using Generalized Airy theory and Debye series of an inhomogeneous cylinder, the scattering intensity distributions are obtained of Airy structure of rainbows for different refractive index profile. The results show that positions of Airy peaks depend closely on refractive index profile of GI-POF. Since each order of rainbow penetrates it to different depths, such methods could be used to provide information of the refractive index profile of GI-POF. For GI-POF with given diameter, positions of Airy peaks of rainbows are simulated as a function of refractive index profile, which can be used to inverse unknown parameters of refractive index profile. The least square method is used in inversion of refractive index profile with the given refractive index of the cladding. The results obtained agree with theoretical values with high precision. The method has the advantages of non-instructive and on-line measurement, and can be used for the measurement of other inhomogeneous droplets.

  3. 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...

  4. 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...

  5. 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...

  6. 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

  7. 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.

  8. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Jalali, Fahimeh, E-mail: fahimehjalali@yahoo.com [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Dorraji, Parisa S. [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Mahdiuni, Hamid [Department of Biology, Razi University, 67346 Kermanshah (Iran, Islamic Republic of)

    2014-04-15

    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 (K{sub a}) 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.

  10. 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.

  11. 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 ...

  12. 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…

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. 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.

  20. 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...

  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).

  2. Cohort profile: the Hawai'i Family Study of Cognition.

    Science.gov (United States)

    Onoye, Jane M M; Hishinuma, Earl S; McArdle, John J; Zonderman, Alan B; Bumanglag, R Janine; Takeshita, Junji

    2014-12-01

    Intergenerational longitudinal studies over the lifespan provide valuable information for understanding the contexts and dynamic relations among cognition, family and health in adults and the elderly. The Hawai'i Family Study of Cognition (HFSC), initiated in the early 1970s, included a cohort of over 6500 individuals representing over 1800 families of parents and their offspring. The HFSC gathered data on cognitive, personality, biological and other psychosocial variables, and provided novel information on the nature of cognitive abilities, especially on family issues. Some families were reassessed with short-term retesting in the 1970s. A select sample of offspring and their siblings and spouses were re-measured in the 1980s. Decades later, a 40-year follow-up of the original HFSC cohort was facilitated by the availability of contemporary tracking and tracing methods and internet-based testing. A subgroup of the original HFSC participants was re-contacted and retested on contemporary cognitive as well as socio-demographic and health measures. In this paper, we describe the original HFSC cohort and the design and methodology of the re-contact and retest studies of the HFSC, plans for expanding the re-contact and retesting, as well as directions for future research and collaborations. The Principal Investigator may be contacted for more information regarding the application, review and approval process for data access requests from qualified individuals outside the project.

  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. 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.

  5. Cadmium binding in mixtures of phytochelatins and their fragments: a voltammetric study assisted by multivariate curve resolution and mass spectrometry.

    Science.gov (United States)

    Gusmão, Rui; Ariño, Cristina; Díaz-Cruz, José Manuel; Esteban, Miquel

    2010-01-01

    Phytochelatins (PC(n), (gamma-Glu-Cys)(n)Gly) are cysteine-rich peptides synthesized by plants which are involved in metal bioregulation and phytoremediation. Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) is applied to voltammetric data obtained from the analysis of the competitive binding of Cys or Cys-Gly with PC(2) or PC(3) by Cd(2+). The displacements between ligands, the chain length dependence on the competitive binding to PC(n) and the possible existence of mixed ligand metal-complexes are investigated. The shape analysis of the resulting pure voltammograms and concentration profiles of the components resolved by MCR-ALS suggests that ligands containing more thiol groups are able to displace the shorter chain ligands from their metal complexes, whereas the opposite does not happen. Electrochemical results are compared with ESI-MS measurements.

  6. 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.

  7. 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

    2016-01-01

    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. PMID:27484975

  8. In vitro RNA-binding assay for studying trans-factors for RNA editing in chloroplasts.

    Science.gov (United States)

    Shikanai, Toshiharu; Okuda, Kenji

    2011-01-01

    In plant organelles, specific C residues are modified to U by RNA editing. Short RNA sequences surrounding the target site (i.e., cis-elements) are recognized by trans-factors, which were recently shown to be pentatricopeptide repeat (PPR) proteins. PPR proteins consist of tandem arrays of a highly degenerate unit of 35 (pentatrico) amino acids, and PPR motifs are believed to recognize specific RNA sequences. In Arabidopsis thaliana, more than 450 sites are edited in mitochondria and plastids, and a similar number of PPR proteins are encoded in the nuclear genome. To study how the tandem array of a PPR motif facilitates the recognition of RNA sequences, an efficient biochemical strategy is an in vitro binding assay of recombinant PPR proteins with target RNA. This analysis is especially powerful with a combination of in vivo analyses based on the phenotypes of mutants and transgenic plants. In this chapter, we describe methods for the expression of recombinant PPR proteins in Escherichia coli, preparation of probe RNAs, and RNA gel shift assays. These methods can also be utilized for other RNA-binding proteins.

  9. 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

  10. Interaction of Sodium Hyaluronate with a Biocompatible Cationic Surfactant from Lysine: A Binding Study.

    Science.gov (United States)

    Bračič, Matej; Hansson, Per; Pérez, Lourdes; Zemljič, Lidija F; Kogej, Ksenija

    2015-11-10

    Mixtures of natural and biodegradable surfactants and ionic polysaccharides have attracted considerable research interest in recent years because they prosper as antimicrobial materials for medical applications. In the present work, interactions between the lysine-derived biocompatible cationic surfactant N(ε)-myristoyl-lysine methyl ester, abbreviated as MKM, and the sodium salt of hyaluronic acid (NaHA) are investigated in aqueous media by potentiometric titrations using the surfactant-sensitive electrode and pyrene-based fluorescence spectroscopy. The critical micelle concentration in pure surfactant solutions and the critical association concentration in the presence of NaHA are determined based on their dependence on the added electrolyte (NaCl) concentration. The equilibrium between the protonated (charged) and deprotonated (neutral) forms of MKM is proposed to explain the anomalous binding isotherms observed in the presence of the polyelectrolyte. The explanation is supported by theoretical model calculations of the mixed-micelle equilibrium and the competitive binding of the two MKM forms to the surface of the electrode membrane. It is suggested that the presence of even small amounts of the deprotonated form can strongly influence the measured electrode response. Such ionic-nonionic surfactant mixtures are a special case of mixed surfactant systems where the amount of the nonionic component cannot be varied independently as was the case for some of the earlier studies.

  11. Methyltransferase and demethylase profiling studies during brown adipocyte differentiation.

    Science.gov (United States)

    Son, Min Jeong; Kim, Won Kon; Oh, Kyoung-Jin; Park, Anna; Lee, Da Som; Han, Baek Soo; Lee, Sang Chul; Bae, Kwang-Hee

    2016-07-01

    Although brown adipose tissue is important with regard to energy balance, the molecular mechanism of brown adipocyte differentiation has not been extensively studied. Specifically, regulation factors at the level of protein modification are largely unknown. In this study, we examine the changes in the expression level of enzymes which are involved in protein lysine methylation during brown adipocyte differentiation. Several enzymes, in this case SUV420H2, PRDM9, MLL3 and JHDM1D, were found to be up-regulated. On the other hand, Set7/9 was significantly down-regulated. In the case of SUV420H2, the expression level increased sharply during brown adipocyte differentiation, whereas the expression of SUV420H2 was marginally enhanced during the white adipocyte differentiation. The knock-down of SUV420H2 caused the suppression of brown adipocyte differentiation, as compared to a scrambled control. These results suggest that SUV420H2, a methyltransferase, is involved in brown adipocyte differentiation, and that the methylation of protein lysine is important in brown adipocyte differentiation. [BMB Reports 2016; 49(7): 388-393].

  12. 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

  13. Cohort Profile: Longitudinal Study of Adult Health (ELSA-Brasil)

    Science.gov (United States)

    Schmidt, Maria Inês; Duncan, Bruce B; Mill, José Geraldo; Lotufo, Paulo A; Chor, Dóra; Barreto, Sandhi Maria; Aquino, Estela ML; Passos, Valéria Maria Azeredo; Matos, Sheila MA; Molina, Maria del Carmen B; Carvalho, Marilia S; Bensenor, Isabela M

    2015-01-01

    Chronic diseases are a global problem, yet information on their determinants is generally scant in low- and middle-income countries. The Brazilian Longitudinal Study of Adult Health (ELSA-Brasil) aims to contribute relevant information regarding the development and progression of clinical and subclinical chronic diseases, particularly cardiovascular diseases and diabetes, in one such setting. At Visit 1, we enrolled 15 105 civil servants from predefined universities or research institutes. Baseline assessment (2008–10) included detailed interviews and measurements to assess social and biological determinants of health, as well as various clinical and subclinical conditions related to diabetes, cardiovascular diseases and mental health. A second visit of interviews and examinations is under way (2012–14) to enrich the assessment of cohort exposures and to detect initial incident events. Annual surveillance has been conducted since 2009 for the ascertainment of incident events. Biological samples (sera, plasma, urine and DNA) obtained at both visits have been placed in long-term storage. Baseline data are available for analyses, and collaboration via specific research proposals directed to study investigators is welcome. PMID:24585730

  14. Tight-binding study of hydrogen adsorption on palladium decorated graphene and carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Corral, I.; German, E.; Brizuela, G.P.; Juan, A. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Volpe, M.A. [Planta Piloto de Ingenieria Quimica, Universidad Nacional del Sur-CONICET, camino de La Carrindanga Km. 7, 8000 Bahia Blanca (Argentina)

    2010-03-15

    In this work we report a theoretical study on the atomic and molecular hydrogen adsorption onto Pd-decorated graphene monolayer and carbon nanotubes by a semi-empirical tight-binding method. We first investigated the preferential adsorption geometry, considering different adsorption sites on the carbon surface, and then studied the evolution of the chemical bonding by evaluation of the overlap population (OP) and crystal orbital overlap population (COOP). Our results show that strong C-Pd and H-Pd bonds are formed during atomic hydrogen adsorption, with an important role in the bonding of C 2p{sub z} and Pd 5s, 5p{sub z} and 4d{sub z}{sup 2} orbitals. The hydrogen storage mechanism in Pd-doped carbon-based materials seems to involve the dissociation of H{sub 2} molecule on the decoration points and the bonding between resultant atomic hydrogen and the carbon surface. (author)

  15. 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.

  16. Adverse effect profile of trichlormethiazide: a retrospective observational study

    Directory of Open Access Journals (Sweden)

    Nishida Yayoi

    2011-05-01

    Full Text Available Abstract Background Trichlormethiazide, a thiazide diuretic, was introduced in 1960 and remains one of the most frequently used diuretics for treating hypertension in Japan. While numerous clinical trials have indicated important side effects of thiazides, e.g., adverse effects on electrolytes and uric acid, very few data exist on serum electrolyte levels in patients with trichlormethiazide treatment. We performed a retrospective cohort study to assess the adverse effects of trichlormethiazide, focusing on serum electrolyte and uric acid levels. Methods We used data from the Clinical Data Warehouse of Nihon University School of Medicine obtained between Nov 1, 2004 and July 31, 2010, to identify cohorts of new trichlormethiazide users (n = 99 for 1 mg, n = 61 for 2 mg daily dosage and an equal number of non-users (control. We used propensity-score matching to adjust for differences between users and control for each dosage, and compared serum chemical data including serum sodium, potassium, uric acid, creatinine and urea nitrogen. The mean exposure of trichlormethiazide of 1 mg and 2 mg users was 58 days and 64 days, respectively. Results The mean age was 66 years, and 55% of trichlormethiazide users of the 1 mg dose were female. In trichlormethiazide users of the 2 mg dose, the mean age was 68 years, and 43% of users were female. There were no statistically significant differences in all covariates (age, sex, comorbid diseases, past drugs, and current antihypertensive drugs between trichlormethiazide users and controls for both doses. In trichlormethiazide users of the 2 mg dose, the reduction of serum potassium level and the elevation of serum uric acid level were significant compared with control, whereas changes of mean serum sodium, creatinine and urea nitrogen levels were not significant. In trichlormethiazide users of the 1 mg dose, all tests showed no statistically significant change from baseline to during the exposure period in

  17. 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.

  18. 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....

  19. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active...... related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein...

  20. 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.

  1. DNA-binding studies of the natural β-carboline eudistomin U.

    Science.gov (United States)

    Giulietti, Jennifer M; Tate, Patrick M; Cai, Ang; Cho, Bongsup; Mulcahy, Seann P

    2016-10-01

    Eudistomin U is a member of the β-carboline class of heterocyclic amine-containing molecules that are capable of binding to DNA. The structure of eudistomin U is unique since it contains an indole ring at the 1-position of the pyridine ring. While simple β-carbolines are reported to intercalate DNA, an examination of the mode of binding of eudistomin U has been lacking. We report preliminary spectroscopic (UV-Vis, thermal denaturation, CD) and calorimetric (DSC) data on the binding of eudistomin U to DNA, which suggest that eudistomin U binds weakly according to a mechanism that is more complicated than other members of its class. PMID:27567367

  2. 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.

  3. 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

  4. Elevated serotonin transporter binding in depressed patients with Parkinson's disease: a preliminary PET study with [11C]DASB.

    Science.gov (United States)

    Boileau, Isabelle; Warsh, Jerry J; Guttman, Mark; Saint-Cyr, Jean A; McCluskey, Tina; Rusjan, Pablo; Houle, Sylvain; Wilson, Alan A; Meyer, Jeffrey H; Kish, Stephen J

    2008-09-15

    This study investigated whether abnormalities in serotonin transporter binding occur in Parkinson's disease (PD) patients with concurrent depression. We estimated serotonin transporter levels in seven clinically depressed early-stage PD patients and in seven healthy matched-control subjects during a single positron emission tomography (PET) scan with the serotonin transporter radioligand, [(11)C]DASB. Depressed PD patients displayed a wide-spread increase (8-68%) in [(11)C]DASB specific binding outside of the striatum, which was significant in dorsolateral (37%) and prefrontal (68%) cortices. Elevated [(11)C]DASB binding was positively correlated with depressive symptoms but not with disease severity or duration. Compatible with recent PET/[(11)C]DASB findings in major depression, the present preliminary data suggest that increased [(11)C]DASB binding, possibly reflecting greater serotonin transporter density (up-regulation), might be a pathological feature of depression in Parkinson's disease-and possibly a characteristic of depressive illness in general.

  5. 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.

  6. 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.

  7. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1982-01-01

    ., & Garrett, R. A. (1981) Biochemistry 20, 7301--7307], reveal an extensive interaction site for protein L18 and a more localized one for L25. Generally comparable results, with a few important differences, were obtained in a study of the binding sites of the two E. coli proteins on Bacillus...... experiments were performed for both RNAs. The effects of the bound proteins on the ribonuclease digestion of the RNAs could generally be correlated with the results obtained with the E. coli proteins L18 and L25, although there was evidence for an additional protein-induced conformational change in the B...... stearothermophilus 5S RNA. Several protein-induced changes in the RNA structures were identified; some are possibly allosteric in nature. The two prokaryotic 5S RNAs were also incubated with total 50S subunit proteins from E. coli and B. stearothermophilus ribosomes. Homologous and heterologous reconstitution...

  8. Binding of chrysoidine to catalase: spectroscopy, isothermal titration calorimetry and molecular docking studies.

    Science.gov (United States)

    Yang, Bingjun; Hao, Fang; Li, Jiarong; Chen, Dongliang; Liu, Rutao

    2013-11-01

    Chrysoidine is an industrial azo dye and the presence of chrysoidine in water and food has become an environmental concern due to its negative effects on human beings. In this work, the interactions between chrysoidine and bovine liver catalase (BLC) were explored. Obvious loss in catalytic activity was observed after incubation of BLC with chrysoidine, and the inhibition effect of BLC was found to be of the non-competitive type. No profound conformational change of BLC occurs in the presence of chrysoidine as revealed by UV-vis absorption, circular dichroism and fluorescence spectroscopy studies. Isothermal titration calorimetry results indicate that catalase has two sets of binding sites for chrysoidine. Further, molecular docking simulations show that chrysoidine is located within the bottleneck in the main channel of the substrate to the active site of BLC, which explain the activity inhibition of BLC by chrysoidine.

  9. 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…

  10. MEASURING QUALITY-OF-LIFE WITH THE SICKNESS IMPACT PROFILE - A PILOT-STUDY

    NARCIS (Netherlands)

    HULSEBOS, RG; BELTMAN, FW; MIRANDA, DD; SPANGENBERG, JFA

    1991-01-01

    A pilot-study was done to investigate the applicability of the sickness impact profile (SIP) in ex-ICU patients. For this study 221 consecutively admitted patients were reviewed retrospectively after excluding children, deceased patients and readmissions. SIP was assessed in these patients by either

  11. 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…

  12. Genome-Wide Profiling of Liver X Receptor, Retinoid X Receptor, and Peroxisome Proliferator-Activated Receptor α in Mouse Liver Reveals Extensive Sharing of Binding Sites

    DEFF Research Database (Denmark)

    Boergesen, Michael; Pedersen, Thomas Åskov; Gross, Barbara;

    2012-01-01

    The liver X receptors (LXRs) are nuclear receptors that form permissive heterodimers with retinoid X receptor (RXR) and are important regulators of lipid metabolism in the liver. We have recently shown that RXR agonist-induced hypertriglyceridemia and hepatic steatosis in mice are dependent on LXRs...... increases the genomic binding of RXR, whereas the LXR agonist T0901317 greatly increases both LXR and RXR binding. Functional annotation of putative direct LXR target genes revealed a significant association with classical LXR-regulated pathways as well as peroxisome proliferator-activated receptor (PPAR...

  13. Biochemical studies of olfaction: binding specificity of odorants to a cilia preparation from rainbow trout olfactory rosettes

    Energy Technology Data Exchange (ETDEWEB)

    Rhein, L.D.; Cagan, R.H.

    1983-08-01

    Cilia isolated from the olfactory epithelium (olfactory rosettes) of rainbow trout (Salmo gairdneri) bind amino acids, which are odor stimuli to this species. We demonstrate that L-threonine, L-serine, and L-alanine bind to a common site, TSA, in the cilia preparation. All possible mixtures of two of the amino acids as competitors, with the third as the /sup 3/H-labeled ligand, were studied. The effect of two combined (unlabeled) competitors was always substantially less than additive compared with their actions singly. Along with additional inhibition studies using mixtures of inhibitors, the data show that the three odorants must interact with at least one common binding site, TSA. Binding of L-(/sup 3/H)lysine to site L was unaffected by addition of L-threonine, L-serine, or L-alanine, establishing its independence from site TSA. L-Arginine inhibited binding of L-(/sup 3/H)lysine, showing that both of these basic amino acids interact with site L. The data establish the presence, in trout olfactory cilia, of at least two separate and noninteracting populations of odorant binding sites, TSA and L.

  14. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila.

    Science.gov (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego

    2014-04-01

    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  2. 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.

  3. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray.

    Science.gov (United States)

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San

    2016-01-01

    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 = 8∼10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA 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 if choosing 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.

  4. 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.

  5. NMr studies of the AMP binding site and mechanism of adenylate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Kuby, S.A.; Fry, D.C.; Mildvan, A.S.

    1986-05-01

    The authors recently located by NMR the MgATP binding site on adenylate kinase correcting the proposed location for this site based on X-ray studies of the binding of salicylate. To determine the conformation and location of the other substrate, they have determined distances from Cr/sup 3 +/ AMPPCP to 6 protons and to the phosphorus atom of AMP on adenylate kinase using the paramagnetic-probe-T/sub 1/ method. They have also used time-dependent NOEs to measure five interproton distances on AMP, permitting evaluation of the conformation of enzyme-bound AMP and its position with respect to metal-ATP. Enzyme-bound AMP exhibits a high-anti glycosyl torsional angle (X = 110/sup 0/), a 3'-endo sugar pucker (delta = 105/sup 0/), and a gauche-trans orientation about the C/sub 4/'-C/sub 5/' bond (..gamma.. = 180/sup 0/). The distance from Cr/sup 3 +/ to the phosphorus of AMP is 6.4 +/- 0.3 A, indicating a reaction coordinate distance of greater than or equal to A which is consistent with an associative SN2 mechanism for the phosphoryl transfer. Ten intermolecular NOEs, from protons of the enzyme to those of AMP were detected. These constraints, together with the conformation of AMP and the X-ray structure of the enzyme, suggest proximity (less than or equal to A) of AMP to leu 116, arg 171, val 173, gln 185, thr 188, and asp 191.

  6. Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA).

    Science.gov (United States)

    Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua

    2015-12-01

    The binding interactions of three kinds of tyrosine kinase inhibitors (TKIs), such as gefitinib, lapatinib and sunitinib, with bovine serum albumin (BSA) were studied using ultraviolet spectrophotometry, fluorescence spectroscopy, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and molecular docking methods. The experimental results showed that the intrinsic fluorescence quenching of BSA induced by the three TKIs resulted from the formation of stable TKIs-BSA complexes through the binding interaction of TKIs with BSA. The stoichiometry of three stable TKIs-BSA complexes was 1:1 and the binding constants (Kb) of the three TKIs-BSA complexes were in the order of 10(4)M(-1) at 310 K, indicating that there was a strong binding interaction of the three TKIs with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be deduced that the binding process of the three TKIs with BSA was spontaneous and enthalpy-driven process, and the main interaction forces between the three TKIs and BSA were van der Waals force and hydrogen bonding interaction. Moreover, from the results of CD, FT-IR and molecular docking, it can be concluded that there was a significant difference between the three TKIs in the binding site on BSA, lapatinib was located on site II (m) of BSA while gefitinib and sunitinib were bound on site I of BSA, and there were some changes in the BSA conformation when binding three TKIs to BSA but BSA still retains its secondary structure α-helicity.

  7. A Comparative Study of Lipid Profile and Oestradiol in Pre- and Post-Menopausal Women

    Science.gov (United States)

    Reddy Kilim, Srinivas; Chandala, Srinivasa Rao

    2013-01-01

    Objectives: To investigate the relationship between the menopausal status and related hormonal variation of oestradiol with plasma lipid concentrations. Material and Methods: Fifty premenopausal women and fifty postmenopausal women subjects were selected. Data was collected through clinical evaluation from questionnaires and laboratory investigations. Plasma oestradiol and lipid profile determinations were done by using competitive binding immunoassay methods and enzymatic methods respectively. Student’s T test and Pearson’s test of correlation were used for the statistical analysis. P-values of < 0.05 were considered to be statistically significant. Results: There was a significant increase in serum Total Cholesterol (TC), Triglycerides (TG), LDL-cholesterol and VLDL-cholesterol levels in post-menopausal women. HDL-cholesterol level was significantly decreased in post-menopausal women. The calculated atherogenic index (Total Cholesterol/HDL ratio) was significantly increased in post-menopausal women as compared to that in premenopausal women. Oestradiol concentration was significantly lower (p<0.001) in post-menopausal women. Discussion: Oestrogen changes the vascular permeability by increasing nitrous oxide production. It maintains a healthy lipoprotein profile. It stabilizes the endothelial cells, enhances antioxidant effect and alters fibrinolysis protein. All these cardioprotective mechanisms are lost in menopause. Postmenopausal women develop an increased risk for cardiovascular disease. Conclusion: Menopause leads to changes in lipid profile by reducing HDL, and elevating Total Cholesterol (TC), triglycerides (TG), LDL-cholesterol and VLDL-cholesterol, thus increasing the risk for cardiovascular disease. These changes are caused by reduced oestrogen concentrations which are seen in menopause. PMID:24086849

  8. 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.

  9. Metabolomic Profiles of Body Mass Index in the Framingham Heart Study Reveal Distinct Cardiometabolic Phenotypes.

    Directory of Open Access Journals (Sweden)

    Jennifer E Ho

    Full Text Available Although obesity and cardiometabolic traits commonly overlap, underlying pathways remain incompletely defined. The association of metabolite profiles across multiple cardiometabolic traits may lend insights into the interaction of obesity and metabolic health. We sought to investigate metabolic signatures of obesity and related cardiometabolic traits in the community using broad-based metabolomic profiling.We evaluated the association of 217 assayed metabolites and cross-sectional as well as longitudinal changes in cardiometabolic traits among 2,383 Framingham Offspring cohort participants. Body mass index (BMI was associated with 69 of 217 metabolites (P<0.00023 for all, including aromatic (tyrosine, phenylalanine and branched chain amino acids (valine, isoleucine, leucine. Additional metabolic pathways associated with BMI included the citric acid cycle (isocitrate, alpha-ketoglutarate, aconitate, the tryptophan pathway (kynurenine, kynurenic acid, and the urea cycle. There was considerable overlap in metabolite profiles between BMI, abdominal adiposity, insulin resistance [IR] and dyslipidemia, modest overlap of metabolite profiles between BMI and hyperglycemia, and little overlap with fasting glucose or elevated blood pressure. Metabolite profiles were associated with longitudinal changes in fasting glucose, but the involved metabolites (ornithine, 5-HIAA, aminoadipic acid, isoleucine, cotinine were distinct from those associated with baseline glucose or other traits. Obesity status appeared to "modify" the association of 9 metabolites with IR. For example, bile acid metabolites were strongly associated with IR among obese but not lean individuals, whereas isoleucine had a stronger association with IR in lean individuals.In this large-scale metabolite profiling study, body mass index was associated with a broad range of metabolic alterations. Metabolite profiling highlighted considerable overlap with abdominal adiposity, insulin resistance

  10. Multispectroscopic studies of paeoniflorin binding to calf thymus DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guowen, E-mail: gwzhang@ncu.edu.cn [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China); Fu, Peng; Pan, Junhui [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China)

    2013-02-15

    The mechanism of paeoniflorin binding to calf thymus DNA in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and DNA melting techniques. The results suggested that paeoniflorin molecules could bind to DNA via groove binding mode as evidenced by no significant change in iodide quenching effect, increase in single-stranded DNA (ssDNA) quenching effect, and almost unchanged relative viscosity and melting temperature of DNA. The observed changes in CD signals revealed that DNA remains in the B-conformation. Further, the displacement experiments with Hoechst 33258 probe and the results of FT-IR spectra indicated that paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. The thermodynamic parameters, enthalpy change ({Delta}H Degree-Sign ) and entropy change ({Delta}S Degree-Sign ) were calculated to be -30.09{+-}0.18 kJ mol{sup -1} and -14.07{+-}0.61 J mol{sup -1} K{sup -1} by the van't Hoff equation, suggesting that hydrogen bond and van der Waals forces play a predominant role in the binding of paeoniflorin to DNA. - Highlights: Black-Right-Pointing-Pointer The binding mode of paeoniflorin to calf thymus DNA is the minor groove binding. Black-Right-Pointing-Pointer Paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. Black-Right-Pointing-Pointer The binding does not alter the native B-conformation of DNA. Black-Right-Pointing-Pointer The binding is driven mainly by hydrogen bonds and van der Waals forces.

  11. Effect of dactyloscopic powders on DNA profiling from enhanced fingerprints: results from an experimental study.

    Science.gov (United States)

    Tozzo, Pamela; Giuliodori, Alice; Rodriguez, Daniele; Caenazzo, Luciana

    2014-03-01

    We conducted a study on the effect of fingerprint enhancement methods on subsequent short tandem repeat profiling. First, we performed a study typing blood traces deposited on 5 different surfaces, treated with 8 types of dactyloscopic powders. Three different DNA extraction methods were used. Subsequently, we analyzed latent fingerprints on the same 5 surfaces enhanced with the 8 different powders used in the first part of the study. This study has demonstrated that DNA profiling can be performed on fingerprints left on different substrates, and the substrate will affect the amount of DNA that can be recovered for DNA typing. In the first phase of the study, a profile was obtained in 92% of the 120 samples analyzed; in the second part, in 55% of the 80 samples analyzed, we obtained a profile complete in 32.5% of the cases. From the results obtained, it seems that the powders used in latent fingerprints enhancement, rather than having a direct inhibitory effect on extraction and amplification of DNA, may cause partial degradation of DNA, reducing the efficiency of amplification reaction. It should not be forgotten that these results were obtained under laboratory conditions, and in real caseworks, there may still be different problems involved.

  12. Electrostatic interactions in the binding pathway of a transient protein complex studied by NMR and isothermal titration calorimetry.

    Science.gov (United States)

    Meneses, Erick; Mittermaier, Anthony

    2014-10-01

    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr-Purcell-Meiboom-Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes.

  13. 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

  14. Genome-wide annotation, expression profiling, and protein interaction studies of the core cell-cycle genes in Phalaenopsis aphrodite.

    Science.gov (United States)

    Lin, Hsiang-Yin; Chen, Jhun-Chen; Wei, Miao-Ju; Lien, Yi-Chen; Li, Huang-Hsien; Ko, Swee-Suak; Liu, Zin-Huang; Fang, Su-Chiung

    2014-01-01

    Orchidaceae is one of the most abundant and diverse families in the plant kingdom and its unique developmental patterns have drawn the attention of many evolutionary biologists. Particular areas of interest have included the co-evolution of pollinators and distinct floral structures, and symbiotic relationships with mycorrhizal flora. However, comprehensive studies to decipher the molecular basis of growth and development in orchids remain scarce. Cell proliferation governed by cell-cycle regulation is fundamental to growth and development of the plant body. We took advantage of recently released transcriptome information to systematically isolate and annotate the core cell-cycle regulators in the moth orchid Phalaenopsis aphrodite. Our data verified that Phalaenopsis cyclin-dependent kinase A (CDKA) is an evolutionarily conserved CDK. Expression profiling studies suggested that core cell-cycle genes functioning during the G1/S, S, and G2/M stages were preferentially enriched in the meristematic tissues that have high proliferation activity. In addition, subcellular localization and pairwise interaction analyses of various combinations of CDKs and cyclins, and of E2 promoter-binding factors and dimerization partners confirmed interactions of the functional units. Furthermore, our data showed that expression of the core cell-cycle genes was coordinately regulated during pollination-induced reproductive development. The data obtained establish a fundamental framework for study of the cell-cycle machinery in Phalaenopsis orchids.

  15. 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

  16. Studies of beam heating of proton beam profile monitor SEM's

    Energy Technology Data Exchange (ETDEWEB)

    Pavlovich, Zarko; Osiecki, Thomas H.; Kopp, Sacha E.; /Texas U.

    2005-05-01

    The authors present calculations of the expected temperature rise of proton beam profile monitors due to beam heating. The profile monitors are secondary emission monitors (SEM's) to be made of Titanium foils. The heating is studied to understand whether there is any loss of tension or alignment of such devices. Additionally, calculations of thermally-induced dynamic stress are presented. Ti foil is compared to other materials and also to wire SEM's. The calculations were initially performed for the NuMI beam, where the per-pulse intensity is quite high; for completeness the calculations are also performed for other beam energies and intensities.

  17. Molecular docking study investigating the possible mode of binding of C.I. Acid Red 73 with DNA.

    Science.gov (United States)

    Guo, Yumei; Yue, Qinyan; Gao, Baoyu

    2011-07-01

    C.I. Acid Red 73 is a reactive azo dye with a variable potential carcinogenicity. The mechanism mediating interactions that occur between the dye and DNA have not been completely understood thus far. In this study, molecular docking techniques were applied to describe the most probable mode of DNA binding as well as the sequence selectivity of the C.I. Acid Red 73 dye. These docking experiments revealed that the dye is capable of interacting with the minor groove of the DNA on the basis of its curved shape, which fits well with the topology of double-stranded DNA. In addition, the dye can bind selectively to the minor groove of the DNA by applying CGT sequence selectivity. Further, the minor groove can be recognized although DNA targets present intercalation gaps. However, intercalative binding can also occur when the DNA target possesses an appropriate intercalation gap. Compared with the other eight DNA sequences that were studied, the DNA dodecamer d(CGCGATATCGCG)(2) (PDB ID: 1DNE) presents a very favorable target for the binding of C.I. Acid Red 73 to the minor groove, with the lowest binding free energy -9.19 kcal/mol. Results reported from this study are expected to provide useful information for research involving further simulations of molecular dynamics and toxicology investigations of the dye.

  18. Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Hanna E. [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands); Koning, Peter E. de; Wouter Drijfhout, Jan [Leiden University Medical Centre, Department of Immunohematology and Blood Transfusion (Netherlands); Venezia, Brigida; Ubbink, Marcellus [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands)], E-mail: m.ubbink@chem.leidenuniv.nl

    2008-07-15

    Paramagnetic relaxation enhancement provides a tool for studying the dynamics as well as the structure of macromolecular complexes. The application of side-chain coupled spin-labels is limited by the mobility of the free radical. The cyclic, rigid amino acid spin-label TOAC (2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), which can be incorporated straightforwardly by peptide synthesis, provides an attractive alternative. In this study, TOAC was incorporated into a peptide derived from focal adhesion kinase (FAK), and the interaction of the peptide with the Src homology 3 (SH3) domain of Src kinase was studied, using paramagnetic NMR. Placing TOAC within the binding motif of the peptide has a considerable effect on the peptide-protein binding, lowering the affinity substantially. When the TOAC is positioned just outside the binding motif, the binding constant remains nearly unaffected. Although the SH3 domain binds weakly and transiently to proline-rich peptides from FAK, the interaction is not very dynamic and the relative position of the spin-label to the protein is well-defined. It is concluded that TOAC can be used to generate reliable paramagnetic NMR restraints.

  19. 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,…

  20. Protein Profile study of clinical samples using Laser Induced Fluorescence as the detection method

    DEFF Research Database (Denmark)

    Karemore, Gopal Raghunath; Raja, Sujatha N.; Rai, Lavanya;

    2009-01-01

    by using hard and Fuzzy clustering methods. The study was performed to test the utility of the HPLC-LIF protein profiling method for classification of tissue samples as well as to establish a complementary method for histopathology for clinical diagnosis of the tissue as normal or malignant.  ...

  1. Radiolabelling of phoneutria nigriventer spider toxin (Tx1): a tool to study its binding site

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Raquel Gouvea dos [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Diniz, Carlos Roberto; Nascimento, Marta Cordeiro [FUNED, Belo Horizonte, MG (Brazil); Lima, Maria Elena de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Bioquimica e Imunologia

    1996-07-01

    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 ({sup 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 Na{sup 125} I by the lactoperoxidase method. {sup 125} I-Tx1 specifically binds to a single class of noninteracting binding sites of high affinity (Kd= 3.5 x 10{sup -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 {sup 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)

  2. 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.

  3. 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...

  4. 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.

  5. 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

  6. 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...

  7. STUDY OF LIPID PROFILE IN CHRONIC RENAL FAILURE PATIENTS UNDERGOING HAEMODIALYSIS: A HOSPITAL BASED STUDY

    Directory of Open Access Journals (Sweden)

    Sreenivasulu

    2015-11-01

    Full Text Available INTRODUCTION: Chronic renal failure (CRF is decrease in glomerular filtration rate (GFR to 3 consecut ive months with multiple etiologies. CRF results in profound lipid disorder which stems largely from dysregulation of high density lipoproteins (HDL & triglyceride - rich lipoprotein metabolism. Many a time CRF patients live on hemodialysis on regular basis . Present study was done to know whether hemodialysis has any impact on the lipid profile of the CRF patients. MATERIALS AND METHODS: Study were divided into 7 groups, Group - 1: healthy controls (40, Group - 2: CRF patients who never undergone hemodialysis (40, Group - 3: CRF patients on hemodialysis (40, Group - 4: Healthy males (28, Group - 5: Healthy females (12, Group - 6: males with chronic renal failure (28, Group - 7: females with chronic renal failure (12. Sample analysed for high density lipoproteins (H DL, low density lipoproteins (LDL & very low density lipoproteins (VLDL. RESULTS: Among the various parameters tested triglyceride and VLDL levels were significantly higher in group - 2 and3 as compared to controls (p<0.0001. HDL levels were significant ly lower in group - 2 compared to Group - 1(p <0.0001. HDL level was found reduced in group - 3 as compare to Group - 2(p=0.0035. There was no significant change (p=0.132 observed in total cholesterol between healthy controls and CRF patients with hemodialysis. There is a significant change (p=0.0309 observed in LDL - c between CRF patients and controls and no significant change observed (P=0.6070 between Group - 2 and Group - 3. CONCLUSION: CRF patients are at risk of cardiovascular diseases due to the elevation of various forms of lipids. Prescribing lipid lowering treatment in CRF patients with dyslipidemias for preventing future episode of cardiovascular events and will a lso preserve renal function.

  8. 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;

    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......, and data analysis. About 47% of the peaks reported to be associated to ovarian cancer were also represented in our experimental study, and 34% of these redetected peaks also showed a significant difference between cases and controls in our study. Thus, despite known problems related to reproducibility...... an overlap in peaks between clinical studies was demonstrated, which indicate convergence toward a set of common discriminating, reproducible peaks for ovarian cancer. The potential of the discriminating protein peaks for clinical use as ovarian cancer biomarkers will be discussed and evaluated. This article...

  9. A comparative study of density functional and density functional tight binding calculations of defects in graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

    2012-02-15

    The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  10. 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].

  11. 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.

  12. 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.

  13. 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.

  14. 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)

  15. 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

  16. 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

  17. 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.

  18. 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...

  19. 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...

  20. 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...

  1. Crystallization and preliminary structural studies of champedak galactose-binding lectin.

    Science.gov (United States)

    Gabrielsen, Mads; Riboldi-Tunnicliffe, Alan; Abdul-Rahman, Puteri Shafinaz; Mohamed, Emida; Ibrahim, Wan Izlina Wan; Hashim, Onn Haji; Isaacs, Neil W; Cogdell, Richard J

    2009-09-01

    Galactose-binding lectin from champedak (Artocarpus integer) consists of two chains: alpha and beta (133 and 21 amino acids, respectively). It has been shown to recognize and bind to carbohydrates involved in IgA and C1 inhibitor molecules. The protein was purified and crystallized at 293 K. Crystals were observed in two space groups, P2(1) and P2(1)2(1)2, and diffracted to 1.65 and 2.6 A, respectively.

  2. 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

  3. 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

  4. Binding of thiocyanate to lactoperoxidase: 1H and 15N nuclear magnetic resonance studies

    Energy Technology Data Exchange (ETDEWEB)

    Modi, S.; Behere, D.V.; Mitra, S. (Tata Institute of Fundamental Research, Bombay (India))

    1989-05-30

    The binding of thiocyanate to lactoperoxidase (LPO) has been investigated by 1H and 15N NMR spectroscopy. 1H NMR of LPO shows that the major broad heme methyl proton resonance at about 61 ppm is shifted upfield by addition of the thiocyanate, indicating binding of the thiocyanate to the enzyme. The pH dependence of line width of 15N resonance of SC15N- in the presence of the enzyme has revealed that the binding of the thiocyanate to the enzyme is facilitated by protonation of an ionizable group (with pKa of 6.4), which is presumably distal histidine. Dissociation constants (KD) of SC15N-/LPO, SC15N-/LPO/I-, and SC15N-/LPO/CN- equilibria have been determined by 15N T1 measurements and found to be 90 +/- 5, 173 +/- 20, and 83 +/- 6 mM, respectively. On the basis of these values of KD, it is suggested that the iodide ion inhibits the binding of the thiocyanate but cyanide ion does not. The thiocyanate is shown to bind at the same site of LPO as iodide does, but the binding is considerably weaker and is away from the ferric ion. The distance of 15N of the bound thiocyanate ion from the iron is determined to be 7.2 +/- 0.2 A from the 15N T1 measurements.

  5. 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

  6. Dose profile measurements during respiratory-gated lung stereotactic radiotherapy: A phantom study

    Science.gov (United States)

    Jong, W. L.; Wong, J. H. D.; Ng, K. H.; Ung, N. M.

    2016-03-01

    During stereotactic body radiotherapy, high radiation dose (∼60 Gy) is delivered to the tumour in small fractionation regime. In this study, the dosimetric characteristics were studied using radiochromic film during respiratory-gated and non-gated lung stereotactic body radiotherapy (SBRT). Specifically, the effect of respiratory cycle and amplitude, as well as gating window on the dosimetry were studied. In this study, the dose profiles along the irradiated area were measured. The dose profiles for respiratory-gated radiation delivery with different respiratory or tumour motion amplitudes, gating windows and respiratory time per cycle were in agreement with static radiation delivery. The respiratory gating system was able to deliver the radiation dose accurately (±1.05 mm) in the longitudinal direction. Although the treatment time for respiratory-gated SBRT was prolonged, this approach can potentially reduce the margin for internal tumour volume without compromising the tumour coverage. In addition, the normal tissue sparing effect can be improved.

  7. 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

  8. 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...

  9. 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.

  10. Study of H-alpha Spicule Profiles with Line Inversion Techniques

    Science.gov (United States)

    Tziotziou, K.; Kontogiannis, I.; Tsiropoula, G.; Kotrc, P.

    2008-09-01

    High resolution optical spectra of chromospheric spicules obtained in the H? line are studied together with slit-jaw filtergrams. The spectra were recorded along a vertical slit parallel to the solar limb with the HSFA2 (Horizontal-Sonnen-Forschungs-Anlage) Solar Spectrograph at Ondrejov Observatory on August 19, 2007 and show H? line profiles taken in spicules - due to the limb curvature - at different heights from the solar limb. A multi-cloud model that considers two or more spicules along the line-of-sight (LOS), together with a statistical approach that takes into account a large set of initial conditions for solving the radiative transfer equation, is used for the fitting of the observed profiles and the derivation of several parameters such as the LOS velocity, the source function, the optical thickness and the Doppler width that describe the respective spicules. The height-dependence of the shape of the observed profiles, as well as their dependence on the values of the derived parameters are studied in detail. The derived results are compared with the statistical theoretical results of a multi-cloud model where the aforementioned physical parameters, as well as a random number of spicules along the LOS were taken into account, in order to define the dependence of several spicule profile characteristics on them. Specific steps of the used procedures, as well as crucial problems are discussed.

  11. 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

  12. 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

  13. 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....

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. Studies of (-)-pironetin binding to α-tubulin: conformation, docking, and molecular dynamics.

    Science.gov (United States)

    Bañuelos-Hernández, Angel E; Mendoza-Espinoza, José Alberto; Pereda-Miranda, Rogelio; Cerda-García-Rojas, Carlos M

    2014-05-01

    A comprehensive conformational analysis for the anticancer agent pironetin (1) was achieved by molecular modeling using density functional theory calculations at the B3PW91/DGTZVP level in combination with calculated and experimental (1)H-(1)H coupling constants comparison. Two solvent-dependent conformational families (L and M) were revealed for the optimum conformations. Docking studies of the pironetin-tubulin complex determined a quantitative model for the hydrogen-bond interactions of pironetin through the αAsn249, αAsn258, and αLys352 amino groups in α-tubulin, which supported the formation of a covalent adduct between the αLys352 and the β carbon atom of the α,β-unsaturated lactone. Saturation-transfer difference NMR spectroscopy confirmed that pironetin binds to tubulin, while molecular dynamics exposed a distortion of the tubulin secondary structure at the H8 and H10 α-helices as well as at the S9 β-sheet, where αLys352 is located. A large structural perturbation in the M-loop geometry between the αIle274 and αLeu285 residues, an essential region for molecular recognition between α-α and β-β units of protofilaments, was also identified and provided a rationale for the pironetin inhibitory activity. PMID:24761989

  19. 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)

  20. 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

    the 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...

  1. 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

  2. A structure-activity-relationship (SAR) study of somatostatin receptor-binding peptides radiolabeled with Tc-99m

    Energy Technology Data Exchange (ETDEWEB)

    Lister-James, J.; McBride, W.J.; Moyer, B.R. [Diatech, Inc, Londonderry, NH (United States)] [and others

    1994-05-01

    Somatostatin receptor (SSTR)-expressing tumors can be detected with high accuracy using In-111-[DTPA]octreotide. We sought a high-affinity SSTR-binding peptide labeled with the preferred radioisotope Tc-99m. We have prepared over 120 SSTR-binding peptides each containing a (N{sub 3}S or N{sub 2}S{sub 2}) chelator for Tc-99m in a SAR study in which peptide structure was systematically altered to optimize SSTR-binding affinity, in vivo rumor uptake and favorable biodistribution and pharmacokinetics. The HPLC-purified (>90% purity), chelator-containing peptides were characterized by FAB/ESMS and assayed in vitro for SSTR binding affinity by a competition assay (I-125 somatostatin-14 tracer and AR42J rat pancreatic tumor cell membranes). The oxo-rhenium complexes of the peptides were prepared by ligand exchange, characterized by FAB or ESMS and assayed for SSTR binding affinity as surrogates for the Tc-99m complexes. The Tc-99m complexes of peptides giving high-affinity oxo-rhenium complexes were also prepared by ligand exchange with specific activities of approx 300 mCi/mmol and examined in vivo for biodistribution and tumor uptake characteristics in CA20948 tumor-bearing rats.

  3. 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.

  4. 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.

  5. 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

  6. Application of a simple calorimetric data analysis on the binding study of cyanide ions by Jack bean urease

    Institute of Scientific and Technical Information of China (English)

    G.Rezaei; Behbehani; A.A.Saboury; M.Mohebbian; S.Ghammamy

    2010-01-01

    Cyanide ion was studied as an effector of Jack bean urease(JBU) at 300 K in 30 mmol/LTris buffer,pH 7 by isothermal titration calorimetry(ITC).The simple novel model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the simple novel model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a noncooperative inhibitor of JBU,and there is a set of 12 identical and independent binding sites for CN~- ions.The...

  7. Structural and thermodynamic analysis of the binding of tRNA(phe) by the putative anticancer alkaloid chelerythrine: Spectroscopy, calorimetry and molecular docking studies.

    Science.gov (United States)

    Basu, Pritha; Payghan, Pavan V; Ghoshal, Nanda; Suresh Kumar, Gopinatha

    2016-08-01

    The interaction of the putative anticancer alkaloid chelerythrine with tRNA(phe) was characterized by spectroscopy, calorimetry and molecular docking studies. The charged iminium form of chelerythrine binds with tRNA(phe) in a cooperative mode with a binding affinity value of (4.06±0.01)×10(5)M(-1). The neutral alkanolamine form does not bind to tRNA(phe) but in the presence of high concentration of tRNA(phe) this form gets converted to the iminium form and then binds with tRNA(phe). The partial intercalative mode of binding of chelerythrine to the tRNA(phe) was characterized from the steady state anisotropy, iodide ion-induced fluorescence quenching and viscosity measurements. Chelerythrine binding induced conformational perturbations in tRNA(phe) as observed from the circular dichroism spectroscopy. The strong binding was also supported by the ethidium bromide displacement assay. The binding was favoured by both enthalpy and entropy contributions. Although the binding was dependent on the [Na(+)], non-electrostatic forces contributed predominantly to the Gibbs energy change. The negative value of the heat capacity change proposed the involvement of hydrophobic forces in the binding. Molecular docking study was carried out to decipher the details of the recognition of tRNA(phe) by chelerythrine. The study provided insights about the chelerythrine binding pockets on tRNA(phe) and marked the necessary interactions for binding of chelerythrine molecule. Partially intercalative mode of the alkaloid binding was supported by docking studies. In total, docking studies corroborated well with our experiential observations. The structural and thermodynamic results of chelerythrine binding to tRNA(phe) may be helpful to develop new RNA therapeutic agents. PMID:27289446

  8. 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

  9. Growth hormone-binding protein: II. Studies in pygmies and normal statured subjects.

    Science.gov (United States)

    Merimee, T J; Baumann, G; Daughaday, W

    1990-11-01

    The serum concentrations of a specific GH-binding protein, derived from the GH receptor, were assayed in sera from 62 African pygmies and 101 normal statured controls. Samples were assayed in the absence and presence of excess GH using 2 separatory procedures. Interassay variability for samples was corrected by a standard reference pool of sera from adults assayed with all unknown samples. Results were expressed as specific binding relative to this standard. The mean percent relative specific binding for GH increased with age in normal-statured controls throughout childhood and adolescence. Relative specific binding for GH was 37.0 +/- 2.0% (mean +/- SEM) in control subjects between the ages of 1-5 yr (mean age, 2.9 yr) and increased progressively to 93.0 +/- 7.0% in young adults (mean age, 23 yr). The relative specific binding of GH by serum from pygmies did not exceed 30.1 +/- 3.4% of the control adult standard at any age period (P less than 0.001), and there was no progressive age-related increase in binding. The decrease from normal binding was minimal in pygmies during childhood (29%), but the decrease from normal was 60-70% in adolescents and adults. Thus, short stature in pygmies probably results not from an absolute deficiency of GH receptors per se, as in Laron dwarfism, but from a failure of cellular GH receptors to increase in a normal manner. This is most compatible with a change in regulating expression of the GH receptor gene, rather than a structural defect in the coding sequence of the GH receptor gene.

  10. 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.

  11. Metal-ligand binding affinity vs reactivity: qualitative studies in Rh(I)-catalyzed asymmetric ring-opening reactions.

    Science.gov (United States)

    Tsui, Gavin Chit; Dougan, Patrick; Lautens, Mark

    2013-06-01

    Rh(I)-catalyzed asymmetric ring opening (ARO) of oxabenzonorbornadiene is used as a model system to qualitatively study reactions involving multiple metal-ligand interactions. The key feature of this approach is the use of product ee as an indicator to quickly gain important information such as the relative ligand binding affinity and relative reactivity of catalysts.

  12. 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].

  13. A Study of Air/Space-borne Dual-Wavelength Radar for Estimation of Rain Profiles

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    In this study, a framework is given by which air/space-borne dual-wavelength radar data can be used to estimate the characteristic parameters of hydrometeors. The focus of the study is on the Global Precipitation Measurement (GPM) precipitation radar, a dual-wavelength radar that will operate in the Ku (13.6 GHz) and Ka (35 GHz) bands. A key aspect of the retrievals is the relationship between the differential frequency ratio (DFR) and the median volume diameter, Do, and its dependence on the phase state of the hydrometeors. It is shown that parametric plots of Do and particle concentration in the plane of the DFR and the radar reflectivity factor in the Ku band can be used to reduce the ambiguities in deriving Do from DFR. A self-consistent iterative algorithm, which does not require the use of an independent pathattenuation constraint, is examined by applying it to the apparent radar reflectivity profiles simulated from a drop size distribution (DSD) model. For light to moderate rain, the self-consistent rain profiling approach converges to the correct solution only if the same shape factor of the Gamma distributions is used both to generate and retrieve the rain profiles. On the other hand, if the shape factors differ, the iteration generally converges but not to the correct solution. To further examine the dual-wavelength techniques, the selfconsistent iterative algorithm, along with forward and backward rain profiling algorithms, are applied to measurements taken from the 2nd generation Precipitation Radar (PR-2) built by the Jet Propulsion Laboratory. Consistent with the model results, it is found that the estimated rain profiles are sensitive to the shape factor of the size distribution when the iterative, self-consistent approach is used but relatively insensitive to this parameter when the forward- and backward-constrained approaches are used.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. Theoretical studies on the binding energy of β-sheet models

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In this paper,B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N―H···O═C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring,the binding energy increases obviously when one large ring unit is added,whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models,the binding energy increases almost exactly linearly with the increase of the chain length.

  20. 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.

  1. Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9.

    Science.gov (United States)

    Kiani, Amir; Almasi, Khadijeh; Shokoohinia, Yalda; Sadrjavadi, Komail; Nowroozi, Amin; Shahlaei, Mohsen

    2015-11-01

    The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy. The results revealed that GBA, as a biologically active sesquiterpene coumarin derivative, has an ability to bind strongly to MMP9. Molecular docking results indicated that the main active binding site for GBA has been located in a hydrophobic cavity in the vicinity of Zn atom. Moreover, MD simulation results suggested that GBA as a coumarin derivative can interact with MMP9, without affecting the secondary structure of MMP9. MD simulations, molecular docking as computational methods from one hand and experimental data from other hand reciprocally supported each other.

  2. 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.

  3. 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).

  4. 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

  5. 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.

  6. EPSP synthase: binding studies using isothermal titration microcalorimetry and equilibrium dialysis and their implications for ligand recognition and kinetic mechanism.

    Science.gov (United States)

    Ream, J E; Yuen, H K; Frazier, R B; Sikorski, J A

    1992-06-23

    Isothermal titration calorimetry measurements are reported which give important new binding constant (Kd) information for various substrate and inhibitor complexes of Escherichia coli EPSP synthase (EPSPS). The validity of this technique was first verified by determining Kd's for the known binary complex with the substrate, shikimate 3-phosphate (S3P), as well as the herbicidal ternary complex with S3P and glyphosate (EPSPS.S3P.glyphosate). The observed Kd's agreed very well with those from previous independently determined kinetic and fluorescence binding measurements. Further applications unequivocally demonstrate for the first time a fairly tight interaction between phosphoenolpyruvate (PEP) and free enzyme (Kd = 390 microM) as well as a correspondingly weak affinity for glyphosate (Kd = 12 mM) alone with enzyme. The formation of the EPSPS.PEP binary complex was independently corroborated using equilibrium dialysis. These results strongly suggest that S3P synergizes glyphosate binding much more effectively than it does PEP binding. These observations add important new evidence to support the hypothesis that glyphosate acts as a transition-state analogue of PEP. However, the formation of a catalytically productive PEP binary complex is inconsistent with the previously reported compulsory binding order process required for catalysis and has led to new studies which completely revise the overall EPSPS kinetic mechanism. A previously postulated ternary complex between S3P and inorganic phosphate (EPSPS.S3P.Pi, Kd = 4 mM) was also detected for the first time. Quantitative binding enthalpies and entropies were also determined for each ligand complex from the microcalorimetry data. These values demonstrate a clear difference in thermodynamic parameters for recognition at the S3P site versus those observed for the PEP, Pi, and glyphosate sites.

  7. 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.

  8. 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 ...

  9. A study of the Lyman-$\\alpha$ line profile in DBA white dwarfs

    CERN Document Server

    Genest-Beaulieu, C

    2016-01-01

    The hydrogen abundances in DBA white dwarfs determined from optical or UV spectra have been reported to differ significantly in some studies. We revisit this problem using our own model atmospheres and synthetic spectra, and present a theoretical investigation of the Lyman-$\\alpha$ line profile as a function of effective temperature and hydrogen abundance. We identify one possible solution to this discrepancy and show considerable improvement from a detailed analysis of optical and UV spectra of DBA stars.

  10. 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...

  11. 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...

  12. 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 ...

  13. 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...

  14. 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.

  15. Kinetic study of coniferyl alcohol radical binding to the (+)-pinoresinol forming dirigent protein.

    Science.gov (United States)

    Halls, Steven C; Davin, Laurence B; Kramer, David M; Lewis, Norman G

    2004-03-01

    An essential step in lignan and lignin formation in planta is one electron oxidation of (E)-coniferyl alcohol (CA) to generate the radical intermediate (CA(*)), which can then undergo directed radical-radical couplings in vivo. For lignan formation in vitro and in vivo, stereoselective coupling of CA(*) only occurs to afford (+)-pinoresinol in the additional presence of (+)-pinoresinol forming dirigent protein (DP). Presented herein is a kinetic and thermodynamic study which reveals the central mechanistic details of the coupling process involved in DP-mediated coupling. DP activity was maximal between pH 4.25 and pH 6.0, with activity being maintained at temperatures below 33 degrees C. Equilibrium binding assays revealed that coniferyl alcohol was only weakly bound to the DP, with a K(D) of 370 +/- 65 microM. On the other hand, the enantiomeric excess of (+)-pinoresinol formed was dependent on both DP concentration and rate of CA oxidation and, thus, on apparent steady-state [CA(*)]. The data obtained could best be explained using a kinetic model where radical-radical coupling via DP competes with that occurring in open solution. Using this model, an apparent K(M) of about 10 nM was estimated from the saturation behavior of (+)-pinoresinol formation with respect to apparent steady-state [CA(*)]. These data strongly suggest that CA(*), rather than CA, is the substrate for DP, in agreement with earlier predictions. A mechanism of directed radical-radical coupling, where two coniferyl alcohol radical substrates are bound per protein dimer, is proposed.

  16. 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

  17. Theory of dielectric loss in Graphene-on-substrate: A tight- binding model study

    Science.gov (United States)

    Sahu, Sivabrata; Panda, S. K.; Rout, G. C.

    2016-09-01

    Graphene-on-substrate exhibits interesting dielectric behaviour due to screening of coulomb interaction induced by many body effects. In this communication we attempt to study the dielectric loss property of graphene within tight-binding model approach. The Hamiltonian consisting of electron hopping upto third-nearest-neighbour's with impurities in two in equivalent sub-lattices. The graphene-on-substrate raises the energy +Δ at one sub lattice and reduces energy -Δ at other sub lattice. Further we introduced coulomb interaction between π - electrons at the two sub lattices separately with the same effective coulomb interaction. We calculate polarization function Π(q, ω) which is a two particle Green's function arising due to charge-charge correlation by using Zubarev's Green's function technique. Finally we calculate dielectric function of graphene i.e. ε(q, ω) =1+Π(q,ω) at arbitrary wave vector q and frequency ra. The dielectric loss in graphene calculated from the imaginary part of dielectric function which is a measure of absorption spectrum. Only a few Fragmentary theoretical attempts have been made to utilize the full frequency and wave vector dependent dielectric function. We compute numerically the frequency dependent dielectric loss function for 100x100 momentum grid points. We observe a low energy Plasmon resonance peak and a high energy flat peak arising due to absorption of optical energy at substrate induced gap. With increase of small Plasmon wave vector, both low and high energy peaks approach each other. The dielectric loss at low energies exhibits a parabolic curve, but it exhibit a clear peak on introduction of higher order electron hopping's. The Coulomb interaction suppresses induced gap in graphene and decreases the optical energy absorption spectra. The increase of substrate induced gap shifts the high energy flat peak to higher energies and enhances the dielectric loss throughout the frequency range. Finally the effect of doping on

  18. Apoferritin-based nanomedicine platform for drug delivery: equilibrium binding study of daunomycin with DNA

    Energy Technology Data Exchange (ETDEWEB)

    Ma Ham, Aihui; Wu, Hong J.; Wang, Jun; Kang, Xinhuang; Zhang, Youyu; Lin, Yuehe

    2011-05-11

    Apoferritin is a nanostructured material with a uniform size and spherical structure, and it has excellent bio-compatibility. In this work, we report the use of apoferritin as a novel and biocompatible carrier for stabilizing enzymes and their activities. We used glucose oxidase (GOx) as a model enzyme. GOx was immobilized on the surface of the apoferritin through a green synthetic approach taking advantage of bioaffinity binding between streptavidin and biotin. As a result, a glucose oxidase-biotin/streptavidin/biotin-apoferritin conjugate (Apo-GOx) was prepared using streptavidin as a bridge. The synthesized Apo-GOx was characterized with transmission electron microscopy, ultraviolet, and fluorescence spectroscopy. The activity and stability of GOx on the surface of the apoferritin were studied in different environments, such as temperature, chemicals, and pH, in comparison with the biotinylated GOx (B-GOx). The results showed that the activity of GOx on the apoferritin surface was significantly enhanced. The thermal and chemical stability of the GOx on the apoferritin was also greatly improved compared to free B-GOx in a solution. It was found that the activity of the GOx on the apoferritin only lost 30% in comparison to a 70% loss of free B-GOx after a 2-hr incubation at 50oC. There was almost no decrease in activity for the GOx on the apoferritin as compared to an 80% activity decrease for free B-GOx after 30 minutes of incubation in a 5 M urea solution. The GOx immobilized apoferritin nanoparticles exhibited high sensitivity for glucose detection with a detection limit of 3 nM glucose. This work offers a novel approach for immobilizing enzymes with enhanced stability and activity, and this method may find a number of applications, such as in catalysis and bioassys/biosensors.

  19. Curcumin effects on blood lipid profile in a 6-month human study.

    Science.gov (United States)

    Baum, Larry; Cheung, Stanley K K; Mok, Vincent C T; Lam, Linda C W; Leung, Vivian P Y; Hui, Elsie; Ng, Chelsia C Y; Chow, Moses; Ho, Ping C; Lam, Sherry; Woo, Jean; Chiu, Helen F K; Goggins, William; Zee, Benny; Wong, Adrian; Mok, Hazel; Cheng, William K F; Fong, Carmen; Lee, Jenny S W; Chan, Ming-Houng; Szeto, Samuel S L; Lui, Victor W C; Tsoh, Joshua; Kwok, Timothy C Y; Chan, Iris H S; Lam, Christopher W K

    2007-12-01

    Studies in animals and a short-term human study have suggested that curcumin, a polyphenolic compound concentrated in the curry spice turmeric, decreases serum cholesterol concentration. However, no controlled human trials have examined the effect of curcumin on cholesterol. This study investigated the effects of consuming curcumin on the serum lipid profile in men and women. Elderly subjects (n=36) consumed 4 g/d curcumin, 1g/d curcumin, or placebo in a 6-month, randomized, double-blind trial. Plasma curcumin and its metabolites were measured at 1 month, and the serum lipid profile was measured at baseline, 1 month, and 6 months. The plasma curcumin concentration reached a mean of 490 nmol/L. The curcumin concentration was greater after capsule than powder administration. Consumption of either dose of curcumin did not significantly affect triacylglycerols, or total, LDL, and HDL cholesterol over 1 month or 6 months. However, the concentrations of plasma curcumin and serum cholesterol were positively and significantly correlated. Curcumin consumption does not appear to have a significant effect on the serum lipid profile, unless the absorbed concentration of curcumin is considered, in which case curcumin may modestly increase cholesterol.

  20. Multispectroscopic DNA-binding studies of a terbium(III) complex containing 2,2'-bipyridine ligand.

    Science.gov (United States)

    Aramesh-Boroujeni, Zahra; Khorasani-Motlagh, Mozhgan; Noroozifar, Meissam

    2016-01-01

    Agarose gel electrophoresis, absorption, fluorescence, viscosity, and circular dichroism (CD) have been used in exploring the interaction of terbium(III) complex, [Tb(bpy)2Cl3(OH2)] where bipy is 2,2'-bipyridine, with Fish salmon DNA. Agarose gel electrophoresis assay, along with absorption and fluorescence studies, reveal interaction between the corresponding complex and FS-DNA. Also, the binding constants (Kb) and the Stern-Volmer quenching constants (Ksv) of Tb(III) complex with FS-DNA were determined. The calculated thermodynamic parameters suggested that the binding of mentioned complex to FS-DNA was driven mainly by hydrophobic interactions. A comparative study of this complex with respect to the effect of iodide-induced quenching, ionic strength effect, and ethidium bromide exclusion assay reflects binding of explicit to the FS-DNA primarily in a groove fashion. CD and viscosity data also support the groove binding mode. Furthermore, Tb(III) complex have been simultaneously screened for their antibacterial and antifungal activities.

  1. Binding mode of inhibitors and Cryptosporidium parvum IMP dehydrogenase: A combined ligand- and receptor-based study.

    Science.gov (United States)

    Li, R-J; Wang, Y-L; Wang, Q-H; Huang, W-X; Wang, J; Cheng, M-S

    2015-01-01

    A combined ligand- and target-based approach was used to analyse the interaction models of Cryptosporidium parvum inosine 5'-monophosphate dehydrogenase (CpIMPDH) with selective inhibitors. First, a ligand-based pharmacophore model was generated from 20 NAD(+) competitive CpIMPDH inhibitors with the HipHop module. The characteristic of the NAD(+) binding site of CpIMPDH was then described, and the binding modes of the representative inhibitors were studied by molecular docking. The combination of the pharmacophore model and the docking results allowed us to evaluate the pharmacophore features and structural information of the NAD(+) binding site of CpIMPDH. This research supports the proposal of an interaction model inside the NAD(+) binding site of CpIMPDH, consisting of four key interaction points: two hydrophobic-aromatic groups, a hydrophobic-aliphatic group and a hydrogen bond donor. This study also provides guidance for the design of more potent CpIMPDH inhibitors for the treatment of Cryptosporidium infections. PMID:25978645

  2. 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.

  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. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  5. Probing the human estrogen receptor-α binding requirements for phenolic mono- and di-hydroxyl compounds: a combined synthesis, binding and docking study.

    Science.gov (United States)

    McCullough, Christopher; Neumann, Terrence S; Gone, Jayapal Reddy; He, Zhengjie; Herrild, Christian; Wondergem Nee Lukesh, Julie; Pandey, Rajesh K; Donaldson, William A; Sem, Daniel S

    2014-01-01

    Various estrogen analogs were synthesized and tested for binding to human ERα using a fluorescence polarization displacement assay. Binding affinity and orientation were also predicted using docking calculations. Docking was able to accurately predict relative binding affinity and orientation for estradiol, but only if a tightly bound water molecule bridging Arg394/Glu353 is present. Di-hydroxyl compounds sometimes bind in two orientations, which are flipped in terms of relative positioning of their hydroxyl groups. Di-hydroxyl compounds were predicted to bind with their aliphatic hydroxyl group interacting with His524 in ERα. One nonsteroid-based dihdroxyl compound was 1000-fold specific for ERβ over ERα, and was also 25-fold specific for agonist ERβ versus antagonist activity. Docking predictions suggest this specificity may be due to interaction of the aliphatic hydroxyl with His475 in the agonist form of ERβ, versus with Thr299 in the antagonist form. But, the presence of this aliphatic hydroxyl is not required in all compounds, since mono-hydroxyl (phenolic) compounds bind ERα with high affinity, via hydroxyl hydrogen bonding interactions with the ERα Arg394/Glu353/water triad, and van der Waals interactions with the rest of the molecule.

  6. 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)

  7. 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.

  8. 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)

  9. 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.

  10. 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.

  11. 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

  12. TIGHT-BINDING MOLECULAR DYNAMICS STUDY OF C60-GRAPHITE COLLISIONS

    Institute of Scientific and Technical Information of China (English)

    Fang Yun-tuan; Luo Cheng-lin

    2000-01-01

    We report the tight-binding molecular dynamics simulations of C60 impacting on a graphite (0001) surface with different incident energy. The simulations provide detailed characterizations of the microscopic processes occurring during the collisions and show insight into the deposition mechanisms of C60 on semiconductor substrate.

  13. NMR studies of the GTP/GDP binding domain of translation initiation factor IF2

    NARCIS (Netherlands)

    Tishchenko, Evgeny Vladimirovich

    2005-01-01

    Translation Initiation Factor 2 (IF2) plays an important role in the initiation stage of bacterial protein biosynthesis. This protein binds both fMet-tRNA and 30S ribosomal subunit in the presence of GTP, and it stimulates the formation of the 70S initiation complex. The NMR samples of the 15N-, 15N

  14. Shortwave radiative heating rate profiles in hazy and clear atmosphere: a sensitivity study

    Science.gov (United States)

    Doppler, Lionel; Fischer, Jürgen; Ravetta, François; Pelon, Jacques; Preusker, René

    2010-05-01

    Aerosols have an impact on shortwave heating rate profiles (additional heating or cooling). In this survey, we quantify the impact of several key-parameters on the heating rate profiles of the atmosphere with and without aerosols. These key-parameters are: (1) the atmospheric model (tropical, midlatitude summer or winter, US Standard), (2) the integrated water vapor amount (IWV ), (3) the ground surface (flat and rough ocean, isotropic surface albedo for land), (4) the aerosol composition (dusts, soots or maritimes mixtures with respect to the OPAC-database classification), (5) the aerosol optical depth and (6) vertical postion, and (7) the single-scattering albedo (?o) of the aerosol mixture. This study enables us to evaluate which parameters are most important to take into account in a radiative energy budget of the atmosphere and will be useful for a future study: the retrieval of heating rates profiles from satellite data (CALIPSO, MODIS, MERIS) over the Mediterranean Sea. All the heating rates are computed by using the vector irradiances computed at each pressure level in the spectral interval 0.2 - 3.6μm (shortwave) by the 1D radiative transfer model for atmosphere and ocean: MOMO (Matrix-Operator MOdel) of the Institute for Space Science, FU Berlin 1

  15. Serum metabolomic profiles from patients with acute kidney injury: a pilot study.

    Science.gov (United States)

    Sun, Jinchun; Shannon, Melissa; Ando, Yosuke; Schnackenberg, Laura K; Khan, Nasim A; Portilla, Didier; Beger, Richard D

    2012-04-15

    Low sensitivity of current clinical markers (serum creatinine and blood urea nitrogen (BUN)) in early stages of the development of acute kidney injury (AKI) limits their utility. Rapid LC/MS-based metabolic profiling of serum demonstrated in a pilot study that metabolomics could provide novel indicators of AKI. Metabolic profiles of serum samples from seventeen hospitalized patients with newly diagnosed AKI were compared with the profiles of serum from age-matched subjects with normal kidney function. Increases in acylcarnitines and amino acids (methionine, homocysteine, pyroglutamate, asymmetric dimethylarginine (ADMA), and phenylalanine) and a reduction in serum levels of arginine and several lysophosphatidyl cholines were observed in patients with AKI compared to healthy subjects. Increases in homocysteine, ADMA and pyroglutamate have been recognized as biomarkers of cardiovascular and renal disease, and acylcarnitines represent biomarkers of defective fatty acid oxidation. The results of this pilot study demonstrate the utility of metabolomics in the discovery of novel serum biomarkers that can facilitate the diagnosis and determine prognosis of AKI in hospitalized patients.

  16. 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

  17. Acetaminophen structure-toxicity studies: In vivo covalent binding of a nonhepatotoxic analog, 3-hydroxyacetanilide

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, S.A.; Price, V.F.; Jollow, D.J. (Medical Univ. of South Carolina, Charleston (USA))

    1990-09-01

    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.

  18. 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.

  19. Depth profile study of Ti implanted Si at very high doses

    Science.gov (United States)

    Olea, J.; Pastor, D.; Toledano-Luque, M.; Mártil, I.; González-Díaz, G.

    2011-09-01

    A detailed study on the resulting impurity profile in Si samples implanted with high doses of Ti and subsequently annealed by pulsed-laser melting (PLM) is reported. Two different effects are shown to rule the impurity profile redistribution during the annealing. During the melting stage, the thickness of the implanted layer increases while the maximum peak concentration decreases (box-shaped effect). On the contrary, during the solidifying stage, the thickness of the layer decreases and the maximum peak concentration increases (snow-plow effect). Both effects are more pronounced as the energy density of the annealing increases. Moreover, as a direct consequence of the snow-plow effect, part of the impurities is expelled from the sample through the surface.

  20. Studies on the antiplatelet and antithrombotic profile of anti-inflammatory coumarin derivatives.

    Science.gov (United States)

    Kontogiorgis, Christos; Nicolotti, Orazio; Mangiatordi, Giuseppe Felice; Tognolini, Massimiliano; Karalaki, Foteini; Giorgio, Carmine; Patsilinakos, Alexandros; Carotti, Angelo; Hadjipavlou-Litina, Dimitra; Barocelli, Elisabetta

    2015-12-01

    The interest towards coumarin-based structures stems from their polypharmacological profile. Herein, we present a series of Mannich bases and 7-azomethine-linked coumarin derivatives exhibiting antiplatelet and antithrombotic activities, in addition to the already known anti-inflammatory and antioxidant activities. Among others, compounds 15 and 16 were found to be the most potent and selective inhibitors of platelet aggregation whereas compound 3 also proved to be the most potent in the clot retraction assay. Structure-activity relationship studies were conducted to elucidate the molecular determinants responsible for the herein observed activities. The chance of inhibiting cyclooxygenase-1 was also investigated for evaluating the platelet aggregation induced by arachidonic acid. Taken together, these results suggest that the investigation of other targets connected to the antiplatelet activity, such as phosphodiesterase-3 (PDE3), could be a viable strategy to shed light on the polypharmacological profile of coumarin-based compounds. Docking simulations towards PDE3 were also carried out.

  1. 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...

  2. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa

    International Nuclear Information System (INIS)

    Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples. Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) was used to identify promoters enriched for histone H3 trimethylated on lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in paired normal colon mucosa and tumor samples from two CRC patients and for the CRC cell line HT29. By comparing histone modification patterns in normal mucosa and tumors, we found that alterations predicted to have major functional consequences were quite rare. Furthermore, when normal or tumor tissue samples were compared to HT29, high similarities were observed for H3K4me3. However, the differences found for H3K27me3, which is important in determining cellular identity, indicates that cell lines do not represent optimal tissue models. Finally, using public expression data, we uncovered previously unknown changes in CRC expression patterns. Genes positive for H3K4me3 in normal and/or tumor samples, which are typically already active in normal mucosa, became hyperactivated in tumors, while genes with H3K27me3 in normal and/or tumor samples and which are expressed at low levels in normal mucosa, became hypersilenced in tumors. Genome wide histone modification profiles can be used to find epigenetic aberrations in genes associated with cancer. This strategy gives further insights into the epigenetic contribution to the oncogenic process and may identify new biomarkers

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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

  9. A STUDY ON CLINICAL, LABORATORY PROFILE AND OUTCOME OF DENGUE FEVER

    Directory of Open Access Journals (Sweden)

    Vanamali

    2013-12-01

    Full Text Available 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. MATERIALS AND METHODS: A prospective study was conducted over one year at Mamata General Hospital, during which 190 cases were diagnosed as dengue fever which were taken into study and eval uated for clinical, laboratory profile and their outcome. RESULTS : Out of 190 patients taken into study, fever was the most common presentation followed by headache. Thrombocytopenia was seen in 75% of the patients. Bleeding manifestations were seen in pat ients with platelet counts less than 40000/mm 3 . 18 patients were diagnosed as DHF, 6 patients were diagnosed as DSS. During our study 10 patients expired. CONCLUSION: The clinical and hematological picture of dengue fever is like any other viral fevers and the bleeding manifestations are seen in patients whose platelet counts decreases less than 40000/mm 3 only

  10. Airborne DOAS limb measurements of tropospheric trace gas profiles: case study on the profile retrieval of O4 and BrO

    Directory of Open Access Journals (Sweden)

    M. Van Roozendael

    2010-08-01

    Full Text Available A novel limb scanning mini-DOAS spectrometer for the detection of UV/vis absorbing radicals (e.g., O3, BrO, IO, HONO was deployed on the DLR-Falcon (Deutsches Zentrum für Luft- und Raumfahrt aircraft and tested during the ASTAR 2007 campaign (Arctic Study of Tropospheric Aerosol, Clouds and Radiation that took place at Svalbard (78° N in spring 2007. Our main objectives during this campaign were to test the instrument, and to perform spectral and profile retrievals of tropospheric trace gases, with particular interest on investigating the distribution of halogen compounds (e.g., BrO during the so-called ozone depletion events (ODEs. In the present work, a new method for the retrieval of vertical profiles of tropospheric trace gases from tropospheric DOAS limb observations is presented. Major challenges arise from modeling the radiative transfer in an aerosol and cloud particle loaded atmosphere, and from overcoming the lack of a priori knowledge of the targeted trace gas vertical distribution (e.g., unknown tropospheric BrO vertical distribution. Here, those challenges are tackled by a mathematical inversion of tropospheric trace gas profiles using a regularization approach constrained by a retrieved vertical profile of the aerosols extinction coefficient εM. The validity and limitations of the algorithm are tested with in situ measured εM, and with an absorber of known vertical profile (O4. The method is then used for retrieving vertical profiles of tropospheric BrO. Results indicate that, for aircraft ascent/descent observations, the limit for the BrO detection is roughly 1.5 pptv (pmol/mol, and the BrO profiles inferred from the boundary layer up to the upper troposphere and lower stratosphere have around 10 degrees of freedom. For the ASTAR 2007 deployments during ODEs, the retrieved BrO vertical profiles consistently indicate high BrO mixing ratios (~15 pptv within the boundary layer, low BrO mixing ratios (≤1.5 pptv in the free

  11. Airborne DOAS limb measurements of tropospheric trace gas profiles: case studies on the profile retrieval of O4 and BrO

    Directory of Open Access Journals (Sweden)

    N. Theys

    2011-06-01

    Full Text Available A novel limb scanning mini-DOAS spectrometer for the detection of UV/vis absorbing radicals (e.g., O3, BrO, IO, HONO was deployed on the DLR-Falcon (Deutsches Zentrum für Luft- und Raumfahrt aircraft and tested during the ASTAR 2007 campaign (Arctic Study of Tropospheric Aerosol, Clouds and Radiation that took place at Svalbard (78° N in spring 2007. Our main objectives during this campaign were to test the instrument, and to perform spectral and profile retrievals of tropospheric trace gases, with particular interest on investigating the distribution of halogen compounds (e.g., BrO during the so-called ozone depletion events (ODEs. In the present work, a new method for the retrieval of vertical profiles of tropospheric trace gases from tropospheric DOAS limb observations is presented. Major challenges arise from modeling the radiative transfer in an aerosol and cloud particle loaded atmosphere, and from overcoming the lack of a priori knowledge of the targeted trace gas vertical distribution (e.g., unknown tropospheric BrO vertical distribution. Here, those challenges are tackled by a mathematical inversion of tropospheric trace gas profiles using a regularization approach constrained by a retrieved vertical profile of the aerosols extinction coefficient EM. The validity and limitations of the algorithm are tested with in situ measured EM, and with an absorber of known vertical profile (O4. The method is then used for retrieving vertical profiles of tropospheric BrO. Results indicate that, for aircraft ascent/descent observations, the limit for the BrO detection is roughly 1.5 pptv (pmol mol−1, and the BrO profiles inferred from the boundary layer up to the upper troposphere and lower stratosphere have around 10 degrees of freedom. For the ASTAR 2007 deployments during ODEs, the retrieved BrO vertical profiles consistently indicate high BrO mixing ratios (∼15 pptv within the boundary layer, low BrO mixing ratios (≤1.5 pptv in the free

  12. Ethanol intake and sup 3 H-serotonin uptake II: A study in alcoholic patients using platelets sup 3 H-paroxetine binding

    Energy Technology Data Exchange (ETDEWEB)

    Daoust, M.; Boucly, P. (U.F.R. de Medecine et Pharmacie, Saint Etienne du Rouvrary (France)); Ernouf, D. (Institut du Medicament, Tours (France)); Breton, P. (Centre National de Transfusion Sanguine de Rouen (France)); Lhuintre, J.P.

    1991-01-01

    The kinetic parameters of {sup 3}H-paroxetine binding and {sup 3}H-serotonin uptake were studied in platelets of alcoholic patients. There was no difference between alcoholic and non alcoholic subjects in {sup 3}H-paroxetine binding. When binding and {sup 3}H-serotonin uptake were studied, in the same plasma of the same subjects, the Vmax of serotonin uptake was increased in alcoholics. The data confirm the involvement of serotonin uptake system in alcohol dependance and suggest that serotonin uptake and paroxetine binding sites may be regulated independently in this pathology.

  13. Differences in activity profile of bacterial cultures studied by dynamic speckle patterns

    Science.gov (United States)

    Ramírez-Miquet, E. E.; Otero, I.; Rodríguez, D.; Darias, J. G.; Combarro, A. M.; Contreras, O. R.

    2013-02-01

    We outline the main differences in the activity profile of bacterial cultures studied by dynamic laser speckle (or biospeckle) patterns. The activity is detected in two sorts of culture mediums. The optical setup and the experimental procedure are presented. The experimentally obtained images are processed by the temporal difference method and a qualitative assessment is made with the time history of speckle patterns of the sample. The main differences are studied after changing the culture medium composition. We conclude that the EC medium is suitable to detect the E. coli bacterial presence in early hours and that Mueller Hinton agar delays some additional hours to make possible the assessment of bacteria in time.

  14. A study of the Ionospheric electron density profile with FORMOSAT-3/COSMIC observation data

    Science.gov (United States)

    Chou, Min-Yang; Tsai, Ho-Fang; Lin, Chi-Yen; Lee, I.-Te; Lin, Charles; Liu, Jann-Yenq

    2015-04-01

    The GPS Occultation Experiment payload onboard FORMOSAT-3/COSMIC microsatellite constellation is capable of scanning the ionospheric structure by the radio occultation (RO) technique to retrieve precise electron density profiles since 2006. Due to the success of FORMOSAT-3/COSMIC, the follow-on mission, FORMOSAT-7/COSMIC-2, is to launch 12 microsatellites in 2016 and 2018, respectively, with the Global Navigation Satellite Systems (GNSS) RO instrument onboard for tracking GPS, Galileo and/or GLONASS satellite signals and to provide more than 8,000 RO soundings per day globally. An overview of the validation of the FORMOSAT-3/COSMIC ionospheric profiling is given by means of the traditional Abel transform through bending angle and total electron content (TEC), while the ionospheric data assimilation is also applied, based on the Gauss-Markov Kalman filter with the International Reference Ionosphere model (IRI-2007) and global ionosphere map (GIM) as background model, to assimilate TEC observations from FORMOSAT-3/COSMIC. The results shows comparison of electron density profiles from Abel inversion and data assimilation. Furthermore, an observing system simulation experiment is also applied to determine the impact of FORMOSAT-7/COSMIC-2 on ionospheric weather monitoring, which reveals an opportunity on advanced study of small spatial and temporal variations in the ionosphere.

  15. Personality Profiles Identify Depressive Symptoms over Ten Years? A Population-Based Study

    Directory of Open Access Journals (Sweden)

    Kim Josefsson

    2011-01-01

    Full Text Available Little is known about the relationship between temperament and character inventory (TCI profiles and depressive symptoms. Personality profiles are useful, because personality traits may have different effects on depressive symptoms when combined with different combinations of other traits. Participants were from the population-based Young Finns study with repeated measurements in 1997, 2001, and 2007 (=1402 to 1902. TCI was administered in 1997 and mild depressive symptoms (modified Beck’s depression inventory, BDI were reported in 1997, 2001, and 2007. BDI-II was also administered in 2007. We found that high harm avoidance and low self-directedness related strongly to depressive symptoms. In addition, sensitive (NHR and fanatical people (ScT were especially vulnerable to depressive symptoms. high novelty seeking and reward dependence increased depressive symptoms when harm avoidance was high. These associations were very similar in cross-sectional and longitudinal analysis. Personality profiles help in understanding the complex associations between depressive symptoms and personality.

  16. Experimental study of vertical stress profiles of a confined granular bed under static and dynamic conditions.

    Science.gov (United States)

    Mandato, S; Cuq, B; Ruiz, T

    2012-07-01

    In a wet agglomeration process inside a low shear mixer, the blade function is to induce i) homogenization of the liquid sprayed on the powder surface and ii) a stress field able to transfer the mechanical energy at the particle scale. In this work we study the mechanical state of a confined powder bed through the analysis of stress distributions (by force measurements) in a rectangular cell in two cases: for a classical model powder (i.e. glass beads) and a complex powder (i.e. wheat semolina). Two types of vertical stress profiles are obtained according to the type of measurements carried out in the powder bed, either locally (at different positions in the cell) or globally (at the entire base). The global vertical stress profile follows Janssen's model and the local vertical stress profile highlights a critical length, identified as the percolation threshold of the force network, and a shielding length near the bottom, which is similar to an influence length of the side walls. In the context of wet agglomeration, the results allow to consider the role of the characteristic lengths in the mixing bowl under vertical mechanical solicitation. PMID:22772594

  17. Vertical Tracer Concentration Profiles Measured During the Joint Urban 2003 Dispersion Study

    Energy Technology Data Exchange (ETDEWEB)

    Flaherty, Julia E.; Lamb, Brian K.; Allwine, K Jerry; Allwine, Eugene J.

    2007-12-01

    An atmospheric tracer dispersion study known as Joint Urban 2003 was conducted in Oklahoma City, Oklahoma during the summer of 2003. As part of this field program, vertical concentration profiles were measured at approximately 1 km from downtown tracer gas release locations. These profiles indicated that the urban landscape was very effective in mixing the plume vertically. The height of the plume centerline (as determined by the maximum concentration over the depth of the measurements) for any specific 30 min period varied over the 65 m measurement range. Most of the variations in tracer concentration observed in the profile time series were related to changes in wind direction as opposed to changes in turbulence. As a simple analysis tool for emergency response, maximum normalized concentration curves were developed with 5-minute averaged measurements. These curves give the maximum concentration (normalized by the release rate) that would be observed as a function of downwind distance in an urban area. The 5-min data resulted in greater concentrations than predicted with a simple Gaussian plume model. However, the curve compared well with results from a computational fluid dynamics simulation. This dispersion dataset is a valuable asset not only for refining air quality models, but also for developing new tools for emergency response personnel in the event of a toxic release.

  18. Compton profile study of V3Ge and Cr3Ge

    Indian Academy of Sciences (India)

    Y C Sharma; V Vyas; V Purvia; K B Joshi; B K Sharma

    2008-02-01

    In this paper the results of a Compton profile study of two polycrystalline A15 compounds, namely, V3Ge and Cr3Ge, have been reported. The measurements have been performed using 59.54 keV -rays from an 241Am source. The theoretical Compton profiles have been computed for both the compounds using ab-initio linear combination of atomic orbitals (LCAO) method employing CRYSTAL98. For both the A15 compounds, the isotropic experimental profiles are found to be in good overall agreement with the calculations. The comparison points out residual differences in V3Ge whereas for Cr3Ge the differences are within experimental error. The behaviour of valence electrons in the two iso-structural compounds has been examined on the scale of Fermi momentum. The valence electron distribution seems to be dominated by the metallic constituents rather than Ge and two compounds show covalent nature of bonding which is larger in V3Ge compared to Cr3Ge.

  19. Development of an in vitro digestive model for studying the peptide profile of breast milk.

    Science.gov (United States)

    Dall'Asta, Chiara; Florio, Paola; Lammardo, Anna Maria; Prandi, Barbara; Mazzeo, Teresa; Budelli, Andrea; Pellegrini, Nicoletta

    2015-01-01

    Human milk is a highly valuable food for newborns and infants. Its protein fraction plays an important role for the development of the newborn. In the present study, an in vitro digestive model, developed for resembling closely the digestive system of an infant, was applied to human milk in order to identify and characterize the peptide profile. The peptide profile obtained after digestion was analyzed by μLC-LTQ-Orbitrap-MS. A total of 149 peptides from β-casein, 30 peptides from α-lactalbumin, 26 peptides from αs1-casein, 24 peptides from κ-casein, 28 peptides from osteopontin, and 29 from lactoferrin was recovered. The identified peptide profile of partially hydrolyzed proteins, such as caseins, α-lactalbumin, and osteopontin, was different from that previously reported demonstrating a different performance of the developed neonatal digestive system with respect to other previously applied. These results would be useful as a starting point to investigate the physiological function of breast milk peptides.

  20. Mechanical properties of phosphorene nanotubes: a density functional tight-binding study

    Science.gov (United States)

    Sorkin, V.; Zhang, Y. W.

    2016-09-01

    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 · nm2, 0.47 and 0.11 for AC PNTs, and 49.2 GPa, 0.071 eV · nm2, 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.

  1. Students of physical therapy. A comparative study of student profiles at a college and university in Israel

    OpenAIRE

    Nitza Davidovitch; Josepha Danziger

    2006-01-01

    This study focuses on the attributes of students of physical therapy in order to compare the profiles of students of physical therapy (PT) in two institutions of higher learning in Israel: Ben Gurion University (BGU) and the Academic College of Judea and Samaria (ACJS). This study focuses on a department where studies have an occupational/applicative/practical orientation and high status in the higher education system. Findings of this study indicate broad similarities in the profiles of stud...

  2. Sports injuries profile of a first division Brazilian soccer team: a descriptive cohort study

    Directory of Open Access Journals (Sweden)

    Guilherme F. Reis

    2015-10-01

    Full Text Available ABSTRACTObjective:To establish the injury profile of soccer players from a first division Brazilian soccer team. In addition, we investigated the association between the characteristics of the injuries and the player's age and position.Method: Forty-eight players from a Brazilian first division soccer team were followed during one season. Descriptive statistics were used to characterize the injury profile. Spearman's tests were used to verify the association between the number and severity of injuries and the player's age. Chi-square test was used to verify the association between type of injury and player's position. Fisher's exact test was used to verify the association between the severity of injuries and player's position.Results: The incidence of injuries was 42.84/1000 hours in matches and 2.40/1000 hours in training. The injury severity was 19.5±34.4 days off competition or training. Lower limb was the most common location of injury and most injuries were muscular/tendinous, overuse, non-recurrent, and non-contact injuries. Player's age correlated with the amount and severity of muscle and tendon injuries. Defenders had more minimal injuries (1-3 days lost, while forwards had more moderate (8-28 days lost and severe injuries (>28 days lost. Furthermore, wingbacks had more muscle and tendon injuries, while midfielders had more joint and ligament injuries.Conclusion: The injury profile of the Brazilian players investigated in this study reflected regional differences in soccer practices. Results confirm the influence of the player's age and position on the soccer injuries profile.

  3. Lectin binding studies on a glycopolymer brush flow-through biosensor by localized surface plasmon resonance.

    Science.gov (United States)

    Rosencrantz, Ruben R; Nguyen, Vu Hoa; Park, Hyunji; Schulte, Christine; Böker, Alexander; Schnakenberg, Uwe; Elling, Lothar

    2016-08-01

    A localized surface plasmon resonance biosensor in a flow-through configuration was applied for investigating kinetics of lectin binding to surface-grafted glycopolymer brushes. Polycarbonate filter membranes with pore sizes of 400 nm were coated with a 114-nm thick gold layer and used as substrate for surface-initiated atom-transfer radical polymerization of a glycomonomer. These grafted from glycopolymer brushes were further modified with two subsequent enzymatic reactions on the surface to yield an immobilized trisaccharide presenting brush. Specific binding of lectins including Clostridium difficile toxin A receptor domain to the glycopolymer brush surface could be investigated in a microfluidic setup with flow-through of the analytes and transmission surface plasmon resonance spectroscopy. Graphical abstract Glycopolymer brushes serve as high affinity ligands for lectin and toxin interactions in a sensitive, disposable flow-through LSPR biosensor. PMID:27277814

  4. Binding of Breviscapine Toward Serum Albumin Studied by Spectroscopic and Electrochemical Techniques.

    Science.gov (United States)

    Liu, Wei; Chen, Yaqing; Chen, Hui; Zhang, Ying

    2016-09-01

    Breviscapine, a cerebrovascular drugs extracted from the Chinese herb Erigeron breviscapinus, has been frequently used to clinically treat cerebrovascular diseases such as cerebral thrombosis, cerebral infarction, and cerebral circulation insufficiency. In order to understand its pharmacology or toxicity, the binding mechanism of breviscapine to a model protein, human serum albumin (HSA), was probed by fluorescence, circular dichroism, Fourier transform infrared spectroscopy (FTIR), and electrochemical impedance spectroscopy approaches. The binding affinities and number of the drug with HSA were about 1.73 × 10(4)  M(-1) and 0.99 at 293 K, respectively. The conformation of the protein was slightly altered after interacting with breviscapine. The drug-protein complex was mainly stabilized by electrostatic forces.

  5. Emotional valence, sense of agency and responsibility: A study using intentional binding.

    Science.gov (United States)

    Christensen, J F; Yoshie, M; Di Costa, S; Haggard, P

    2016-07-01

    We investigated how the emotional valence of an action outcome influences the experience of control, in an intentional binding experiment. Voluntary actions were followed by emotionally positive or negative human vocalisations, or by neutral tones. We used mental chronometry to measure a retrospective component of sense of agency (SoA), triggered by the occurrence of the action outcome, and a prospective component, driven by the expectation that the outcome will occur. Positive outcomes enhanced the retrospective component of SoA, but only when both occurrence and the valence of the outcome were unexpected. When the valence of outcomes was blocked - and therefore predictable - we found a prospective component of SoA when neutral tones were expected but did not actually occur. This prospective binding was absent, and reversed, for positive and negative expected outcomes. Emotional expectation counteracts the prospective component of SoA, suggesting a distancing effect. PMID:27174794

  6. Metal ion binding sites of bacteriorhodopsin. Laser-induced lanthanide luminescence study

    International Nuclear Information System (INIS)

    Laser-excited luminescence lifetimes of lanthanide ions bound to bacteriorhodopsin have been measured in deionized membranes. The luminescence titration curve, as well as the binding curve of apomembrane (retinal-free) with Eu3+, has shown that the removal of the retinal does not significantly affect the affinity of Eu3+ for the two high affinity sites of bacteriorhodopsin. The D2O effects on decay rate constants indicate that Eu3+ bound to the high affinity sites of native membrane or apomembrane is coordinated by about six ligands in the first coordination sphere. Tb3+ is shown to be coordinated by four ligands. The data indicate that metal ions bind to the protein with a specific geometry. From intermetal energy transfer experiments using Eu3+-Pr3+, Tb3+-Ho3+, and Tb3+-Er3+, the distance between the two high affinity sites is estimated to be 7-8 A

  7. A facile method for studying interaction of rhodamine B and bovine serum albumin:Towards physical-binding mediated fluorescence labeling of proteins

    Institute of Scientific and Technical Information of China (English)

    马宇星; 钟睿博; 郭俊; 刘雨双; 袁鸣; 白志军; 刘涛涛; 赵欣敏; 张峰

    2015-01-01

    Strategies for labeling proteins with fluorophores are always important for biotechnology. Here we take a model protein (bovine serum albumin) and a typical fluorophore (rhodamine B) to demonstrate a direct labeling method just by physical adsorption. In combination with size exclusion chromatography and the Scartchard equation, we have developed a facile analysis method for calculating the binding constant and binding sites. The molecular docking method has been used to study the binding site in amino acid level.

  8. Preliminary Crystallographic Study of Streptomyces coelicolor Single-stranded DNA-binding Protein

    OpenAIRE

    Štefanić, Zoran; Vujaklija, Dušica; Andrišić, Luka; Mikleušević, Goran; Andrejašič, Miha; Turk, Dušan; Luić, Marija

    2007-01-01

    Single-stranded DNA-binding proteins (SSBs) play a crucial role in DNA processing such as replication, repair and recombination in all organisms, from bacteria to human. Streptomyces coelicolor ssb gene was overexpressed in a heterologous host, Escherichia coli NM522. 15 mg of purified protein from 1 dm(3) of culture was obtained in one-step procedure applying Ni2+ chelating chromatography. Among bacterial SSBs with the solved crystal structure, the S. coelicolor SSB displayed significant seq...

  9. Minor Groove Binding between Norfloxacin and DNA Duplexes in Solution: A Molecular Dynamics Study

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Molecular dynamics were used to investigate the interaction between norfloxacin and DNA duplex. The results showed that norfloxacin was situated in the minor groove of DNA,binding to the TCGA region of d [ATATCGATAT] 2. Specific hydrogen bonds were formed between norfloxacin and guanine base of DNA during the 2 ns MD, which may be the reason for the preferentiality of quinolone antibacterial towards the guanine base of DNA duplex.

  10. A Study on Efficient Mobile IPv6 Fast Handover Scheme Using Reverse Binding Mechanism

    Science.gov (United States)

    Tolentino, Randy S.; Lee, Kijeong; Kim, Sung-Gyu; Kim, Miso; Park, Byungjoo

    This paper proposes a solution for solving the packet handover issues of MIPv6. We propose an efficient scheme that can support fast handover effectively in standard Mobile IPv6 (MIPv6) by optimizing the associated data and the flow of signal during handover. A new signaling message Reverse Packet Binding Mechanism is defined and utilized to hasten the handover procedure by adding a buffer in access point (AP) and home agent (HA).

  11. Interaction study on bovine serum albumin physically binding to silver nanoparticles: Evolution from discrete conjugates to protein coronas

    Science.gov (United States)

    Guo, Jun; Zhong, Ruibo; Li, Wanrong; Liu, Yushuang; Bai, Zhijun; Yin, Jun; Liu, Jingran; Gong, Pei; Zhao, Xinmin; Zhang, Feng

    2015-12-01

    The nanostructures formed by inorganic nanoparticles together with organic molecules especially biomolecules have attracted increasing attention from both industries and researching fields due to their unique hybrid properties. In this paper, we systemically studied the interactions between amphiphilic polymer coated silver nanoparticles and bovine serum albumins by employing the fluorescence quenching approach in combination with the Stern-Volmer and Hill equations. The binding affinity was determined to 1.30 × 107 M-1 and the interaction was spontaneously driven by mainly the van der Waals force and hydrogen-bond mediated interactions, and negatively cooperative from the point of view of thermodynamics. With the non-uniform coating of amphiphilic polymer, the silver nanoparticles can form protein coronas which can become discrete protein-nanoparticle conjugates when controlling their molar ratios of mixing. The protein's conformational changes upon binding nanoparticles was also studied by using the three-dimensional fluorescence spectroscopy.

  12. Pilot study on binding of bovine salivary proteins to grit silicates and plant phytoliths

    Institute of Scientific and Technical Information of China (English)

    Marcus MAU; Thomas M.KAISER; Karl-Heinz S(U)DEKUM

    2013-01-01

    Mostly fed with grass in fresh or conserved form,cattle and other livestock have to cope with silicate defence bodies from plants (phytoliths) and environmental silicates (grit),which abrade tooth enamel and could additionally interact with various salivary proteins.To detect potential candidates for silicate-binding proteins,bovine whole saliva was incubated with grass-derived phytoliths and silicates.Interactions of salivary proteins with pulverized bovine dental enamel and dentine were additionally analysed.After intense washing,the powder fractions were loaded onto 1D-polyacrylamide gels,most prominent adhesive protein bands were cut out and proteins were identified by mass spectrometry within three independent replicates.All materials were mainly bound by bovine odorant-binding protein,bovine salivary protein 30× 103 and carbonic anhydrase VI.The phytolith/silicate fraction showed additional stronger interaction with haemoglobin β and lactoperoxidase.Conceivably,the binding of these proteins to the surfaces may contribute to biological processes occurring on them.

  13. Binding Interaction of Captopril with Metal Ions: A Fluorescence Quenching Study

    Institute of Scientific and Technical Information of China (English)

    SIDDIQI K.S.; BANO Shaista; MOHD Ayaz; KHAN Aslam Aftab Parwaz

    2009-01-01

    The binding interaction of captopril(CPL)with biologically active metal ions Mg2+,Ca2+,Mn2+,Co2+,Ni2+,Cu2+ and Zn2+ was investigated in an aqueous acidic medium by fluorescence spectroscopy.The experimental results showed that the metal ions quenched the intrinsic fluorescence of CPL by forming CPL-metal complexes.It was found that static quenching was the main reason for the fluorescence quenching.The quenching constant in the case of Cu2+ was highest among all quenchers,perhaps due to its high nuclear charge and small size.Quenching of CPL by metal ions follows the order Cu2+> Ni2+> Co2+> Ca2+>Zn2+ > Mn2+ > Mg2+.The quenching constant Ksv,bimolecular quenching constant Kq,binding constant K and the binding sites "n" were determined together with their thermodynamic parameters at 27 and 37℃.The positive entropy change indicated the gain in configurational entropy as a result of chelation.The process of interaction was spontaneous and mainly △S-driven.

  14. Demographic and histopathologic profile of pediatric brain tumors: A hospital-based study

    Directory of Open Access Journals (Sweden)

    Harshil C Shah

    2015-01-01

    Full Text Available Background: Very few hospital-based or population-based studies are published in the context to the epidemiologic profile of pediatric brain tumors (PBTs in India and Indian subcontinent. Aim: To study the demographic and histopathologic profile of PBTs according to World Health Organization 2007 classification in a single tertiary health care center in India. Materials and Methods: Data regarding age, gender, topography, and histopathology of 76 pediatric patients (0–19 years with brain tumors operated over a period of 24 months (January-2012 to December-2013 was collected retrospectively and analyzed using EpiInfo 7. Chi-square test and test of proportions (Z-test were used wherever necessary. Results: PBTs were more common in males (55.3% as compared to females (44.7% with male to female ratio of 1.23:1. Mean age was 10.69 years. Frequency of tumors was higher in childhood age group (65.8% when compared to adolescent age group (34.2%. The most common anatomical site was cerebellum (39.5%, followed by hemispheres (22.4%. Supratentorial tumors (52.6% were predominant than infratentorial tumors (47.4%. Astrocytomas (40.8% and embryonal tumors (29.0% were the most common histological types almost contributing more than 2/3rd of all tumors. Craniopharyngiomas (11.8% and ependymomas (6.6% were the third and fourth most common tumors, respectively. Conclusion: Astrocytomas and medulloblastomas are the most common tumors among children and adolescents in our region, which needs special attention from the neurosurgical department of our institute. Demographic and histopathologic profile of cohort in the present study do not differ substantially from that found in other hospital-based and population-based studies except for slight higher frequency of craniopharyngiomas.

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

    OpenAIRE

    Pamella de Brito Ximenes; Eduardo Isidoro Carneiro Beltrão; Danielle Patrícia Cerqueira Macêdo; Maria Daniela Silva Buonafina; Reginaldo Gonçalves de Lima-Neto; Rejane Pereira Neves

    2015-01-01

    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 ...

  16. The Study of Stability of Compression-Loaded Multispan Composite Panel Upon Failure of Elements Binding it to Panel Supports

    Science.gov (United States)

    Zamula, G. N.; Ierusalimsky, K. M.; Fomin, V. P.; Grishin, V. I.; Kalmykova, G. S.

    1999-01-01

    The present document is a final technical report carried out within co-operation between United States'NASA Langley RC and Russia's Goskomoboronprom in aeronautics, and continues similar programs, accomplished in 1996, 1997, and 1998, respectively). The report provides results of "The study of stability of compression-loaded multispan composite panels upon failure of elements binding it to panel supports"; these comply with requirements established at TsAGI on 24 March 1998 and at NASA on 15 September 1998.

  17. Cyanide binding to human plasma heme-hemopexin: A comparative study

    Energy Technology Data Exchange (ETDEWEB)

    Ascenzi, Paolo, E-mail: ascenzi@uniroma3.it [Laboratorio Interdipartimentale di Microscopia Elettronica, Universita Roma Tre, Roma (Italy); Istituto Nazionale di Biostrutture e Biosistemi, Roma (Italy); Leboffe, Loris [Istituto Nazionale di Biostrutture e Biosistemi, Roma (Italy); Polticelli, Fabio [Dipartimento di Biologia, Universita Roma Tre, Roma (Italy)

    2012-11-16

    Highlights: Black-Right-Pointing-Pointer Cyanide binding to ferric HHPX-heme-Fe. Black-Right-Pointing-Pointer Cyanide binding to ferrous HHPX-heme-Fe. Black-Right-Pointing-Pointer Dithionite-mediated reduction of ferric HHPX-heme-Fe-cyanide. Black-Right-Pointing-Pointer Cyanide binding to HHPX-heme-Fe is limited by ligand deprotonation. Black-Right-Pointing-Pointer Cyanide dissociation from HHPX-heme-Fe-cyanide is limited by ligand protonation. -- Abstract: Hemopexin (HPX) displays a pivotal role in heme scavenging and delivery to the liver. In turn, heme-Fe-hemopexin (HPX-heme-Fe) displays heme-based spectroscopic and reactivity properties. Here, kinetics and thermodynamics of cyanide binding to ferric and ferrous hexa-coordinate human plasma HPX-heme-Fe (HHPX-heme-Fe(III) and HHPX-heme-Fe(II), respectively), and for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex, at pH 7.4 and 20.0 Degree-Sign C, are reported. Values of thermodynamic and kinetic parameters for cyanide binding to HHPX-heme-Fe(III) and HHPX-heme-Fe(II) are K = (4.1 {+-} 0.4) Multiplication-Sign 10{sup -6} M, k{sub on} = (6.9 {+-} 0.5) Multiplication-Sign 10{sup 1} M{sup -1} s{sup -1}, and k{sub off} = 2.8 Multiplication-Sign 10{sup -4} s{sup -1}; and H = (6 {+-} 1) Multiplication-Sign 10{sup -1} M, h{sub on} = 1.2 Multiplication-Sign 10{sup -1} M{sup -1} s{sup -1}, and h{sub off} = (7.1 {+-} 0.8) Multiplication-Sign 10{sup -2} s{sup -1}, respectively. The value of the rate constant for the dithionite-mediated reduction of the HHPX-heme-Fe(III)-cyanide complex is l = 8.9 {+-} 0.8 M{sup -1/2} s{sup -1}. HHPX-heme-Fe reactivity is modulated by proton acceptor/donor amino acid residue(s) (e.g., His236) assisting the deprotonation and protonation of the incoming and outgoing ligand, respectively.

  18. Comparative Study of Variations Cephalometrics of the Tooth-Skeleton Maxilar Profile and Soft Nasolabial Profile of Individuals of Different Ethnics

    Directory of Open Access Journals (Sweden)

    Karis Barbosa GUIMARÃES

    2006-04-01

    Full Text Available Objective: Starting from the presupposed idea that the cephalometric norms must be ethnic-specific, this research has made a comparative study between linear and angled cephalometrics dimensions of anatomical points related with the tooth-skeleton maxilar profile and nasolabial soft profile. Method: The samples compused this study were taked from teleradiographs, in lateral norm, and grouped according to the white and black ethnics of 20 individuals each. The radiographs were submitted to the Ricketts computerized cephalometric analyses, using the 2.0® Radiocef Program. The obtained numbers were submitted to statistics usage, using the parametric Anova test, considering p≤0,05. Results: The cephalometrics dimensions that express the distance point A to point subnasal, the higher lip length, the inclination of the foreteeth and the nasolabial angle are the most representative of the differences among the etnics studied. Conclusion: The obtained results allow us to conclude that there are statistically significant differences between linear and angled cephalometrics dimensions and between the white and black ethnics, indicating that the facial structure of black is larger than that of white subjects and consequently has maxilar, tooth and labial convex profile in these individuals. This study reinforces the hypothesis that the cephalometrics norms must be elaborated for each racial group individually.

  19. Stereoselective binding of chiral drugs to plasma proteins

    Institute of Scientific and Technical Information of China (English)

    Qi SHEN; Lu WANG; Hui ZHOU; Hui-di JIANG; Lu-shan YU; Su ZENG

    2013-01-01

    Chiral drugs show distinct biochemical and pharmacological behaviors in the human body.The binding of chiral drugs to plasma proteins usually exhibits stereoselectivity,which has a far-reaching influence on their pharmacological activities and pharmacokinetic profiles.In this review,the stereoselective binding of chiral drugs to human serum albumin (HSA),α1-acid glycoprotein (AGP)and lipoprotein,three most important proteins in human plasma,are detailed.Furthermore,the application of AGP variants and recombinant fragments of HSA for studying enantiomer binding properties is also discussed.Apart from the stereoselectivity of enantiomer-protein binding,enantiomer-enantiomer interactions that may induce allosteric effects are also described.Additionally,the techniques and methods used to determine drug-protein binding parameters are briefly reviewed.

  20. Synthesis, in vitro binding studies and docking of long-chain arylpiperazine nitroquipazine analogues, as potential serotonin transporter inhibitors.

    Science.gov (United States)

    Jarończyk, Małgorzata; Wołosewicz, Karol; Gabrielsen, Mari; Nowak, Gabriel; Kufareva, Irina; Mazurek, Aleksander P; Ravna, Aina W; Abagyan, Ruben; Bojarski, Andrzej J; Sylte, Ingebrigt; Chilmonczyk, Zdzisław

    2012-03-01

    It is well known that 6-nitroquipazine exhibits about 150-fold higher affinity for the serotonin transporter (SERT) than quipazine and recently we showed quipazine buspirone analogues with high to moderate SERT affinity. Now we have designed and synthesized several 6-nitroquipazine buspirone derivatives. Unexpectedly, their SERT binding affinities were moderate, and much lower than that of the previously studied quipazine buspirone analogues. To explain these findings, docking studies of both groups of compounds into two different homology models of human SERT was performed using a flexible target-ligand docking approach (4D docking). The crystal structures of leucine transporter from Aquifex aeolicus in complex with leucine and with tryptophan were used as templates for the SERT models in closed and outward-facing conformations, respectively. We found that the latter conformation represents the most reliable model for binding of buspirone analogues. Docking into that model showed that the nitrated compounds acquire a rod like shape in the binding pocket with polar groups (nitro- and imido-) at the ends of the rod. 6-Nitro substituents gave steric clashes with amino acids located at the extracellular loop 4, which may explain their lower affinity than corresponding quipazine buspirone analogues. The results from the present study may suggest chemical design strategies to improve the SERT modulators. PMID:22309909