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Sample records for functionally important sites

  1. Quantum coupled mutation finder: predicting functionally or structurally important sites in proteins using quantum Jensen-Shannon divergence and CUDA programming.

    Science.gov (United States)

    Gültas, Mehmet; Düzgün, Güncel; Herzog, Sebastian; Jäger, Sven Joachim; Meckbach, Cornelia; Wingender, Edgar; Waack, Stephan

    2014-04-03

    The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein functions. Despite the rich literature on compensatory mutations as well as sequence conservation analysis for the detection of those important residues, previous methods often rely on classical information-theoretic measures. However, these measures usually do not take into account dis/similarities of amino acids which are likely to be crucial for those residues. In this study, we present a new method, the Quantum Coupled Mutation Finder (QCMF) that incorporates significant dis/similar amino acid pair signals in the prediction of functionally or structurally important sites. The result of this study is twofold. First, using the essential sites of two human proteins, namely epidermal growth factor receptor (EGFR) and glucokinase (GCK), we tested the QCMF-method. The QCMF includes two metrics based on quantum Jensen-Shannon divergence to measure both sequence conservation and compensatory mutations. We found that the QCMF reaches an improved performance in identifying essential sites from MSAs of both proteins with a significantly higher Matthews correlation coefficient (MCC) value in comparison to previous methods. Second, using a data set of 153 proteins, we made a pairwise comparison between QCMF and three conventional methods. This comparison study strongly suggests that QCMF complements the conventional methods for the identification of correlated mutations in MSAs. QCMF utilizes the notion of entanglement, which is a major resource of quantum information, to model significant dissimilar and similar amino acid pair signals in the detection of functionally or structurally important sites. Our results suggest that on the one hand QCMF significantly outperforms the previous method, which mainly focuses on dissimilar amino acid signals, to detect essential sites

  2. The importance of the non-active site and non-periodical structure located histidine residue respect to the structure and function of exo-inulinase.

    Science.gov (United States)

    Arjomand, Maryam Rezaei; Ahmadian, Gholamreza; Habibi-Rezaei, Mehran; Hassanzadeh, Malihe; Karkhane, Ali Asghar; Moosavi-Movahedi, Ali Akbar; Amanlou, Massoud

    2017-05-01

    Here, we have studied the role of a histidine residue with the lowest solvent accessibility among other histidine residues at the end of a short connecting structure ((189)AELH(192)) of the catalytic domain of the exo-inulinase through creation of H192A mutant. Site-directed mutagenesis method was applied to create the mutant enzyme. Molecular dynamics (MD) simulations, spectroscopic, calorimetric and kinetics analysis were used to study the structural and functional consequences of His192 substitution. Accordingly, the thermo-stabilities and catalytic performance were decreased upon H192A mutation. In silico and experimental approaches evidently confirm that His192 residue of exo-inulinase possesses structural and functional importance regardless of the lack of direct interaction with the substrate or involvement in the catalytic activity of exo-inulinase. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Importance Sampling for the Infinite Sites Model*

    OpenAIRE

    Hobolth, Asger; Uyenoyama, Marcy K; Wiuf, Carsten

    2008-01-01

    Importance sampling or Markov Chain Monte Carlo sampling is required for state-of-the-art statistical analysis of population genetics data. The applicability of these sampling-based inference techniques depends crucially on the proposal distribution. In this paper, we discuss importance sampling for the infinite sites model. The infinite sites assumption is attractive because it constraints the number of possible genealogies, thereby allowing for the analysis of larger data sets. We recall th...

  4. Mutation of putative N-linked glycosylation sites on the human nucleotide receptor P2X7 reveals a key residue important for receptor function.

    Science.gov (United States)

    Lenertz, Lisa Y; Wang, Ziyi; Guadarrama, Arturo; Hill, Lindsay M; Gavala, Monica L; Bertics, Paul J

    2010-06-08

    The nucleotide receptor P2X(7) is an immunomodulatory cation channel and a potential therapeutic target. P2X(7) is expressed in immune cells such as monocytes and macrophages and is activated by extracellular ATP following tissue injury or infection. Ligand binding to P2X(7) can stimulate ERK1/2, the transcription factor CREB, enzymes linked to the production of reactive oxygen species and interleukin-1 isoforms, and the formation of a nonspecific pore. However, little is known about the biochemistry of P2X(7), including whether the receptor is N-linked glycosylated and if this modification affects receptor function. Here we provide evidence that P2X(7) is sensitive to the glycosidases EndoH and PNGase F and that the human receptor appears glycosylated at N187, N202, N213, N241, and N284. Mutation of N187 results in weakened P2X(7) agonist-induced phosphorylation of ERK1/2, CREB, and p90 ribosomal S6 kinase, as well as a decreased level of pore formation. In further support of a role for glycosylation in receptor function, treatment of RAW 264.7 macrophages with the N-linked glycosylation synthesis inhibitor tunicamycin attenuates P2X(7) agonist-induced, but not phorbol ester-induced, ERK1/2 phosphorylation. Interestingly, residue N187 belongs to an N-linked glycosylation consensus sequence found in six of the seven P2X family members, suggesting this site is fundamentally important to P2X receptor function. To address the mechanism whereby N187 mutation attenuates receptor activity, we developed a live cell proteinase K digestion assay that demonstrated altered cell surface expression of P2X(7) N187A. This is the first report to map human P2X(7) glycosylation sites and reveal residue N187 is critical for receptor trafficking and function.

  5. Weak-acid sites catalyze the hydrolysis of crystalline cellulose to glucose in water: importance of post-synthetic functionalization of the carbon surface.

    Science.gov (United States)

    To, Anh The; Chung, Po-Wen; Katz, Alexander

    2015-09-14

    The direct hydrolysis of crystalline cellulose to glucose in water without prior pretreatment enables the transformation of biomass into fuels and chemicals. To understand which features of a solid catalyst are most important for this transformation, the nanoporous carbon material MSC-30 was post-synthetically functionalized by oxidation. The most active catalyst depolymerized crystalline cellulose without prior pretreatment in water, providing glucose in an unprecedented 70 % yield. In comparison, virtually no reaction was observed with MSC-30, even when the reaction was conducted in aqueous solution at pH 2. As no direct correlations between the activity of this solid-solid reaction and internal-site characteristics, such as the β-glu adsorption capacity and the rate of catalytic hydrolysis of adsorbed β-glu strands, were observed, contacts of the external surface with the cellulose crystal are thought to be key for the overall efficiency.

  6. Functional importance of PAI-1 glycosylation

    DEFF Research Database (Denmark)

    Christensen, Anni; Naessens, Dominik; Skottrup, Peter Durand

    Structure-function studies of plasminogen activator inhibitor-1 (PAI-1) have previously been performed mostly with non-glycosylated material expressed in E. coli. We have now studied the importance of PAI-1 glycosylation for its functional properties. PAI-1 has 3 potential sites for N-linked glyc...

  7. Sacrifical sites, types and function

    Directory of Open Access Journals (Sweden)

    Örnulv Vorren

    1987-01-01

    Full Text Available Much has been written and said about Saami mythology and pre-Christian religion. There is, however, considerably less documentation of concrete cultural elements in scholarly descriptions. These investigations are considered important not only because they aim to provide documentation that can be used for studies of Saami mythology and pre-Christian religion. They also provide material that can throw light on the function of the holy places in a social context through analysis of their origin, their connections with certain families and persons, their associations with the siidas, their location within the areas where the Saamis from these siidas gained their livelihood, etc. The materials collected about the sacrificial sites also play an important role in studying the course of events leading up to the differentiation of Saami hunting and gathering culture. A question that has frequently arisen in the course of this work is with what powers or deities the different sacrificial sites were associated. This is naturally connected with their origin and their form. This, in turn, is reflected in the traditions and legends recounted concerning them. It is also reflected in their location in the physical environment and in the kinds of offerings that have been found. In the materials so far collected it is possible to distinguish between about eight different types of sacrificial site and holy mountain or fell according to their form and location: holy fells, rock formations, stone boulders, holes, cracks in fells, springs, lakes, ring-shaped sacrificial sites. Missionaries were urged to destroy the offering sites.

  8. Functional importance of PAI-1 glycosylation

    DEFF Research Database (Denmark)

    Christensen, Anni; Naessens, Dominik; Skottrup, Peter

    2001-01-01

    Structure-function studies of plasminogen activator inhibitor-1 (PAI-1) have previously been performed mostly with non-glycosylated material expressed in E. coli. We have now studied the importance of PAI-1 glycosylation for its functional properties. PAI-1 has 3 potential sites for N......-linked glycosylation. Biochemical analysis of PAI-1 variants with substitutions of the Asn residues in each of these sites and expression in human embryonic kidney 293 (HEK293) cells showed that only Asn211 and Asn 267, but not Asn331 are glycosylated, and revealed a differential composition of the carbohydrate...... attached at the 2 sites. Analysing the susceptibility of glycosylated and non-glycosylated PAI-1 to activity neutralisation by monoclonal antibodies, we found that the IC50-values for neutralisation by some monoclonal antibodies differed strongly between glycosylated and non-glycosylated PAI-1. The most...

  9. Importance and Functions of Grasslands

    Directory of Open Access Journals (Sweden)

    Lucien CARLIER

    2009-06-01

    Full Text Available Grasslands, mixture of grass, clover and other leguminous species, dicotyledonous, herbs and shrubs, contribute to a high degree to the struggle against erosion and to the regularizing of water regimes, to the purification of fertilizers and pesticides and to biodiversity and they have aesthetic role and recreational function as far as they provide public access that other agricultural uses do not allow. Grassland will continue to be an important form of land use in Europe, but with increased diversity in management objectives and systems used. Besides its role as basic nutrient for herbivores and ruminants, grasslands have opportunities for an adding value by exploiting positive health characteristics in animal products from grassland and through the delivery of environmental benefits. But even for grassland it is very difficult to create a good frame for its different tasks (1 the provision of forage for livestock, (2 protection and conservation of soil and water resources, (3 furnishing a habitat for wildlife, both flora and fauna and (4 contribution to the attractiveness of the landscape. Nevertheless it is the only crop able to fulfil so many tasks and to fit so many requirements. In this article the focus is limited to the grass and clover components of the grasslands.

  10. Clinically important factors influencing endothelial function.

    Science.gov (United States)

    Vapaatalo, H; Mervaala, E

    2001-01-01

    The endothelium, a continuous cellular monolayer lining the blood vessels, has an enormous range of important homeostatic roles. It serves and participates in highly active metabolic and regulatory functions including control of primary hemostasis, blood coagulation and fibrinolysis, platelet and leukocyte interactions with the vessel wall, interaction with lipoprotein metabolism, presentation of histocompatibility antigens, regulation of vascular tone and growth and further of blood pressure. Many crucial vasoactive endogenous compounds like prostacyclin, thromboxane, nitric oxide, endothelin, angiotensin, endothelium derived hyperpolarizing factor, free radicals and bradykinin are formed in the endothelial cells to control the functions of vascular smooth muscle cells and of circulating blood cells. These versatile and complex systems and cellular interactions are extremely vulnerable. The balances may be disturbed by numerous endogenous and exogenous factors including psychological and physical stress, disease states characterized by vasospasm, inflammation, leukocyte and platelet adhesion and aggregation, thrombosis, abnormal vascular proliferation, atherosclerosis and hypertension. The endothelial cells are also the site of action of many drugs and exogenous toxic substances (e.g. smoking, alcohol). As markers and assays for endothelial dysfunction, direct measurement of nitric oxide, its metabolites from plasma and urine, functional measurement of vascular nitric oxide dependent responses and assay of different circulating markers have been used. In numerous pathological conditions (e.g. atherosclerosis, hypertension, congestive heart failure, hyperhomocysteinemia, diabetes, renal failure, transplantation, liver cirrhosis) endothelial dysfunction has been described to exist. Some of them, as well as hormonal and nutritional factors and drug treatment will be discussed in this short review.

  11. The importance of geotechnical studies for siting an ELT

    Science.gov (United States)

    Pescador, German R.

    2004-07-01

    Site selection is, no doubt, one of the most important preliminary studies in any telescope project since the image quality of the telescope will be limited by the site quality. Traditionally, geotechnical studies have had relatively little importance, normally being carried out once the site was already selected. However, with the increase of the telescopes size and mechancial requirements, the geotechnical studies have become increasingly important. Soil characteristics can make a big difference to the cost of an ELT. A thorough geological and geotechnical investigation of the possible site for the erection of an ELT should be carried from the beginning of the site selection process. It is very important to know the geology of the subsoil to determine the geomechanical properties of the materials, to determine the most suitable layers for anchoring the foundations, and to be able to estimate construction costs.

  12. Text Mining Improves Prediction of Protein Functional Sites

    Science.gov (United States)

    Cohn, Judith D.; Ravikumar, Komandur E.

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions. PMID:22393388

  13. Text mining improves prediction of protein functional sites.

    Science.gov (United States)

    Verspoor, Karin M; Cohn, Judith D; Ravikumar, Komandur E; Wall, Michael E

    2012-01-01

    We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites). The structure analysis was carried out using Dynamics Perturbation Analysis (DPA), which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites) in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  14. Text mining improves prediction of protein functional sites.

    Directory of Open Access Journals (Sweden)

    Karin M Verspoor

    Full Text Available We present an approach that integrates protein structure analysis and text mining for protein functional site prediction, called LEAP-FS (Literature Enhanced Automated Prediction of Functional Sites. The structure analysis was carried out using Dynamics Perturbation Analysis (DPA, which predicts functional sites at control points where interactions greatly perturb protein vibrations. The text mining extracts mentions of residues in the literature, and predicts that residues mentioned are functionally important. We assessed the significance of each of these methods by analyzing their performance in finding known functional sites (specifically, small-molecule binding sites and catalytic sites in about 100,000 publicly available protein structures. The DPA predictions recapitulated many of the functional site annotations and preferentially recovered binding sites annotated as biologically relevant vs. those annotated as potentially spurious. The text-based predictions were also substantially supported by the functional site annotations: compared to other residues, residues mentioned in text were roughly six times more likely to be found in a functional site. The overlap of predictions with annotations improved when the text-based and structure-based methods agreed. Our analysis also yielded new high-quality predictions of many functional site residues that were not catalogued in the curated data sources we inspected. We conclude that both DPA and text mining independently provide valuable high-throughput protein functional site predictions, and that integrating the two methods using LEAP-FS further improves the quality of these predictions.

  15. Parameters of importance to determine during geoscientific site investigation

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Johan [QuantiSci AB (Sweden); Almen, K.E. [KEA GEO-Konsult AB (Sweden); Ericsson, Lars O.; Karlsson, Fred; Stroem, A. [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Fredriksson, Anders [ADG Grundteknik AB (Sweden); Stanfors, R. [Roy Stanfors Consulting AB (Sweden)

    1998-06-01

    This document identifies and describes geo-scientific parameters that are of importance in order to carry out performance and safety assessments of a deep repository for spent nuclear fuel, based on the information that can be obtained from a site investigation. The document also discusses data needs for planning and design of the rock works and for description of other environmental aspects. Evaluation of the different parameters is discussed in the document as well. The document was produced by a working group consisting of the authors and various SKB staff and consultants, and comprises a step in the planning of a geo-scientific investigation programme at the sites where site investigations will be conducted. The goals of the work presented in this report can be derived directly from SKBs ongoing RD and D Programme. The programme stipulates that a geo-scientific site investigation programme must be available before a site investigation begins. This programme is supposed to specify the goals, measurement methods and evaluation methodology, as well as the acceptance criteria against which the site is evaluated. It is pointed out that site evaluation is a collective term for an interactive process consisting of different parts 65 refs, 15 figs, 12 tabs

  16. Importance sampling the Rayleigh phase function

    DEFF Research Database (Denmark)

    Frisvad, Jeppe Revall

    2011-01-01

    Rayleigh scattering is used frequently in Monte Carlo simulation of multiple scattering. The Rayleigh phase function is quite simple, and one might expect that it should be simple to importance sample it efficiently. However, there seems to be no one good way of sampling it in the literature. Thi....... This paper provides the details of several different techniques for importance sampling the Rayleigh phase function, and it includes a comparison of their performance as well as hints toward efficient implementation.......Rayleigh scattering is used frequently in Monte Carlo simulation of multiple scattering. The Rayleigh phase function is quite simple, and one might expect that it should be simple to importance sample it efficiently. However, there seems to be no one good way of sampling it in the literature...

  17. Importance and functions of European grasslands.

    Science.gov (United States)

    Carlier, L; De Vliegher, A; Van Cleemput, O; Boeckx, P

    2005-01-01

    The European agricultural policy is not simple and needs to accommodate also social and environmental requirements. Grassland will continue to be an important form of land use in Europe, but with increased diversity in management objectives and systems used. Besides its role as basic nutrient for herbivores and ruminants grasslands have opportunities for adding value by exploiting positive health characteristics in animal products from grassland and through the delivery of environmental benefits. In fact grasslands contribute to a high degree to the struggle against erosion and to the regularizing of water regimes, to the purification of fertilizers and pesticides and to biodiversity. Finally they have aesthetic role and recreational function as far as they provide public access that other agricultural uses do not allow. But even for grassland it is very difficult to create a good frame for its different tasks (1) the provision of forage for livestock, (2) protection and conservation of soil and water resources, (3) furnishing a habitat for wildlife, both flora and fauna and (4) contribution to the attractiveness of the landscape. Nevertheless it is the only crop, able to fulfil so many tasks and to fit so many requirements.

  18. Stereotypy in Autism: The Importance of Function

    Science.gov (United States)

    Cunningham, Allison B.; Schreibman, Laura

    2008-01-01

    We argue for the utility of a functional definition of stereotypy based on evidence of both sensory automatic and socially mediated reinforcement contingencies in the occurrence of stereotypy in children with autism. A predetermined sensory function of stereotypy is often invoked in the behavioral literature and the term "self-stimulatory…

  19. Functional Importance of Mobile Ribosomal Proteins.

    Science.gov (United States)

    Chang, Kai-Chun; Wen, Jin-Der; Yang, Lee-Wei

    2015-01-01

    Although the dynamic motions and peptidyl transferase activity seem to be embedded in the rRNAs, the ribosome contains more than 50 ribosomal proteins (r-proteins), whose functions remain largely elusive. Also, the precise forms of some of these r-proteins, as being part of the ribosome, are not structurally solved due to their high flexibility, which hinders the efforts in their functional elucidation. Owing to recent advances in cryo-electron microscopy, single-molecule techniques, and theoretical modeling, much has been learned about the dynamics of these r-proteins. Surprisingly, allosteric regulations have been found in between spatially separated components as distant as those in the opposite sides of the ribosome. Here, we focus on the functional roles and intricate regulations of the mobile L1 and L12 stalks and L9 and S1 proteins. Conformational flexibility also enables versatile functions for r-proteins beyond translation. The arrangement of r-proteins may be under evolutionary pressure that fine-tunes mass distributions for optimal structural dynamics and catalytic activity of the ribosome.

  20. Estimating the Importance of Differential Item Functioning.

    Science.gov (United States)

    Rudas, Tamas; Zwick, Rebecca

    1997-01-01

    The mixture index of fit (T. Rudas et al, 1994) is used to estimate the fraction of a population for which differential item functioning (DIF) occurs, and this approach is compared to the Mantel Haenszel test of DIF. The proposed noniterative procedure provides information about data portions contributing to DIF. (SLD)

  1. Estimating the Importance of Differential Item Functioning.

    Science.gov (United States)

    Rudas, Tamas; Zwick, Rebecca

    1997-01-01

    The mixture index of fit (T. Rudas et al, 1994) is used to estimate the fraction of a population for which differential item functioning (DIF) occurs, and this approach is compared to the Mantel Haenszel test of DIF. The proposed noniterative procedure provides information about data portions contributing to DIF. (SLD)

  2. IMPORTANCE OF SOUTHAMPTON WOUND GRADING SYSTEM IN SURGICAL SITE INFECTION

    Directory of Open Access Journals (Sweden)

    Shaleen

    2014-05-01

    Full Text Available : Post-operative wound infection is defined as surgical site infection from 0-30 days after surgery, or infection to surgical site till one year in cases of implants like mesh, vascular grafts and prosthesis. This study was done to find out incidence of post-operative wound infection in surgical patients in rural setup. This study of post-operative wound infection was carried out from August 2008 to August 2010. The study is of 3275 patients who underwent surgery in the A.V.B.R.H. Significant association was observed between the nature of surgery and Southampton Wound Grading System. It concluded that severity rate of post-operative wound infection was increased from grade I to grade V which was found to be similar in clean to contaminated nature of surgery and that was found to be statistically significant at P value less than 0.001.

  3. Frequent gain and loss of functional transcription factor binding sites.

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    Scott W Doniger

    2007-05-01

    Full Text Available Cis-regulatory sequences are not always conserved across species. Divergence within cis-regulatory sequences may result from the evolution of species-specific patterns of gene expression or the flexible nature of the cis-regulatory code. The identification of functional divergence in cis-regulatory sequences is therefore important for both understanding the role of gene regulation in evolution and annotating regulatory elements. We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs. We find that a significant fraction of functionally constrained binding sites have been lost in a lineage-specific manner among three closely related yeast species. Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains gene regulation. We estimate that nearly half of all loss events cannot be explained by binding site turnover. Recreating the mutations that led to binding site loss confirms that these sequence changes affect gene expression in some cases. We also estimate that there is a high rate of binding site gain, as more than half of experimentally identified S. cerevisiae binding sites are not conserved across species. The frequent gain and loss of TFBSs implies that cis-regulatory sequences are labile and, in the absence of turnover, may contribute to species-specific patterns of gene expression.

  4. The Importance of Site Familiarity to Landscape Photographic Assessments

    Directory of Open Access Journals (Sweden)

    Joanne Westphal

    2004-12-01

    Full Text Available This paper examines the effect of familiarity on the rating of 28 black and white photographs of landscape scenes from the Old Mission Peninsula, Traverse City, Michigan. Respondents were asked to rate 24 of the 28 scenes on two criteria: scenic beauty and likelihood to visit. Four other scenes were rated for representativeness. Results of the study show that there is a powerful correlation between the rating of scenic beauty and the likelihood of visiting a place. The data also indicates that pictorial captions initially result in higher ratings of scenic beauty. Site visitation to an area will result in the elevation of some photograph ratings while others remain unchanged or lowered.

  5. Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

    Science.gov (United States)

    Huang, Yi-Fei; Golding, G Brian

    2014-01-01

    A critical question in biology is the identification of functionally important amino acid sites in proteins. Because functionally important sites are under stronger purifying selection, site-specific substitution rates tend to be lower than usual at these sites. A large number of phylogenetic models have been developed to estimate site-specific substitution rates in proteins and the extraordinarily low substitution rates have been used as evidence of function. Most of the existing tools, e.g. Rate4Site, assume that site-specific substitution rates are independent across sites. However, site-specific substitution rates may be strongly correlated in the protein tertiary structure, since functionally important sites tend to be clustered together to form functional patches. We have developed a new model, GP4Rate, which incorporates the Gaussian process model with the standard phylogenetic model to identify slowly evolved regions in protein tertiary structures. GP4Rate uses the Gaussian process to define a nonparametric prior distribution of site-specific substitution rates, which naturally captures the spatial correlation of substitution rates. Simulations suggest that GP4Rate can potentially estimate site-specific substitution rates with a much higher accuracy than Rate4Site and tends to report slowly evolved regions rather than individual sites. In addition, GP4Rate can estimate the strength of the spatial correlation of substitution rates from the data. By applying GP4Rate to a set of mammalian B7-1 genes, we found a highly conserved region which coincides with experimental evidence. GP4Rate may be a useful tool for the in silico prediction of functionally important regions in the proteins with known structures.

  6. Organization and function of membrane contact sites.

    Science.gov (United States)

    Helle, Sebastian C J; Kanfer, Gil; Kolar, Katja; Lang, Alexander; Michel, Agnès H; Kornmann, Benoît

    2013-11-01

    Membrane-bound organelles are a wonderful evolutionary acquisition of the eukaryotic cell, allowing the segregation of sometimes incompatible biochemical reactions into specific compartments with tailored microenvironments. On the flip side, these isolating membranes that crowd the interior of the cell, constitute a hindrance to the diffusion of metabolites and information to all corners of the cell. To ensure coordination of cellular activities, cells use a network of contact sites between the membranes of different organelles. These membrane contact sites (MCSs) are domains where two membranes come to close proximity, typically less than 30nm. Such contacts create microdomains that favor exchange between two organelles. MCSs are established and maintained in durable or transient states by tethering structures, which keep the two membranes in proximity, but fusion between the membranes does not take place. Since the endoplasmic reticulum (ER) is the most extensive cellular membrane network, it is thus not surprising to find the ER involved in most MCSs within the cell. The ER contacts diverse compartments such as mitochondria, lysosomes, lipid droplets, the Golgi apparatus, endosomes and the plasma membrane. In this review, we will focus on the common organizing principles underlying the many MCSs found between the ER and virtually all compartments of the cell, and on how the ER establishes a network of MCSs for the trafficking of vital metabolites and information. This article is part of a Special Issue entitled: Functional and structural diversity of endoplasmic reticulum. Copyright © 2013 Elsevier B.V. All rights reserved.

  7. Extra-gonadal sites of estrogen biosynthesis and function.

    Science.gov (United States)

    Barakat, Radwa; Oakley, Oliver; Kim, Heehyen; Jin, Jooyoung; Ko, CheMyong Jay

    2016-09-01

    Estrogens are the key hormones regulating the development and function of reproductive organs in all vertebrates. Recent evidence indicates that estrogens play important roles in the immune system, cancer development, and other critical biological processes related to human well-being. Obviously, the gonads (ovary and testis) are the primary sites of estrogen synthesis, but estrogens synthesized in extra- gonadal sites play an equally important role in controlling biological activities. Understanding non-gonadal sites of estrogen synthesis and function is crucial and will lead to therapeutic interventions targeting estrogen signaling in disease prevention and treatment. Developing a rationale targeting strategy remains challenging because knowledge of extra-gonadal biosynthesis of estrogens, and the mechanism by which estrogen activity is exerted, is very limited. In this review, we will summarize recent discoveries of extra-gonadal sites of estrogen biosynthesis and their local functions and discuss the significance of the most recent novel discovery of intestinal estrogen biosynthesis. [BMB Reports 2016; 49(9): 488-496].

  8. An Autophosphorylation Site of the Protein Kinase SOS2 Is Important for Salt Tolerance in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Hiroaki Fujii; Jian-Kang Zhu

    2009-01-01

    The protein kinase SOS2 (Salt Overly Sensitive 2) is essential for salt-stress signaling and tolerance in Arabidopsis. SOS2 is known to be activated by calcium-SOS3 and by phosphorylation at its activation loop. SOS2 is autophosphorylated in vitro, but the autophosphorylation site and its role in salt tolerance are not known. In this study, we identified an autophosphorylation site in SOS2 and analyzed its role in the responses of Arabidopsis to salt stress. Mass spectrometry analysis showed that Ser 228 of SOS2 is autophosphorylated. When this site was mutated to Ala, the autophosphorylation rate of SOS2 decreased. The substrate phosphorylation by the mutated SOS2 was also less than that by the wild-type SOS2. In contrast, changing Ser228 to Asp to mimic the autophosphorylation enhanced substrate phosphorylation by SOS2. Complementation tests in a sos2 mutant showed that the S228A but not the S228D mutation partially disrupted the function of SOS2 in salt tolerance. We also show that activation loop phosphorylation at Thr168 and autophosphorylation at Ser228 cannot substitute for each other, suggesting that both are required for salt tolerance. Our results indicate that Ser 228 of SOS2 is autophosphorylated and that this autophosphorylation is important for SOS2 function under salt stress.

  9. Adaptive bandwidth measurements of importance functions for speech intelligibility prediction.

    Science.gov (United States)

    Whitmal, Nathaniel A; DeRoy, Kristina

    2011-12-01

    The Articulation Index (AI) and Speech Intelligibility Index (SII) predict intelligibility scores from measurements of speech and hearing parameters. One component in the prediction is the "importance function," a weighting function that characterizes contributions of particular spectral regions of speech to speech intelligibility. Previous work with SII predictions for hearing-impaired subjects suggests that prediction accuracy might improve if importance functions for individual subjects were available. Unfortunately, previous importance function measurements have required extensive intelligibility testing with groups of subjects, using speech processed by various fixed-bandwidth low-pass and high-pass filters. A more efficient approach appropriate to individual subjects is desired. The purpose of this study was to evaluate the feasibility of measuring importance functions for individual subjects with adaptive-bandwidth filters. In two experiments, ten subjects with normal-hearing listened to vowel-consonant-vowel (VCV) nonsense words processed by low-pass and high-pass filters whose bandwidths were varied adaptively to produce specified performance levels in accordance with the transformed up-down rules of Levitt [(1971). J. Acoust. Soc. Am. 49, 467-477]. Local linear psychometric functions were fit to resulting data and used to generate an importance function for VCV words. Results indicate that the adaptive method is reliable and efficient, and produces importance function data consistent with that of the corresponding AI/SII importance function.

  10. Mitochondrial cholesterol: mechanisms of import and effects on mitochondrial function.

    Science.gov (United States)

    Martin, Laura A; Kennedy, Barry E; Karten, Barbara

    2016-04-01

    Mitochondria require cholesterol for biogenesis and membrane maintenance, and for the synthesis of steroids, oxysterols and hepatic bile acids. Multiple pathways mediate the transport of cholesterol from different subcellular pools to mitochondria. In steroidogenic cells, the steroidogenic acute regulatory protein (StAR) interacts with a mitochondrial protein complex to mediate cholesterol delivery to the inner mitochondrial membrane for conversion to pregnenolone. In non-steroidogenic cells, several members of a protein family defined by the presence of a StAR-related lipid transfer (START) domain play key roles in the delivery of cholesterol to mitochondrial membranes. Subdomains of the endoplasmic reticulum (ER), termed mitochondria-associated ER membranes (MAM), form membrane contact sites with mitochondria and may contribute to the transport of ER cholesterol to mitochondria, either independently or in conjunction with lipid-transfer proteins. Model systems of mitochondria enriched with cholesterol in vitro and mitochondria isolated from cells with (patho)physiological mitochondrial cholesterol accumulation clearly demonstrate that mitochondrial cholesterol levels affect mitochondrial function. Increased mitochondrial cholesterol levels have been observed in several diseases, including cancer, ischemia, steatohepatitis and neurodegenerative diseases, and influence disease pathology. Hence, a deeper understanding of the mechanisms maintaining mitochondrial cholesterol homeostasis may reveal additional targets for therapeutic intervention. Here we give a brief overview of mitochondrial cholesterol import in steroidogenic cells, and then focus on cholesterol trafficking pathways that deliver cholesterol to mitochondrial membranes in non-steroidogenic cells. We also briefly discuss the consequences of increased mitochondrial cholesterol levels on mitochondrial function and their potential role in disease pathology.

  11. Designing functional metalloproteins: from structural to catalytic metal sites.

    Science.gov (United States)

    Zastrow, Melissa L; Pecoraro, Vincent L

    2013-09-01

    Metalloenzymes efficiently catalyze some of the most important and difficult reactions in nature. For many years, coordination chemists have effectively used small molecule models to understand these systems. More recently, protein design has been shown to be an effective approach for mimicking metal coordination environments. Since the first designed proteins were reported, much success has been seen for incorporating metal sites into proteins and attaining the desired coordination environment but until recently, this has been with a lack of significant catalytic activity. Now there are examples of designed metalloproteins that, although not yet reaching the activity of native enzymes, are considerably closer. In this review, we highlight work leading up to the design of a small metalloprotein containing two metal sites, one for structural stability (HgS3) and the other a separate catalytic zinc site to mimic carbonic anhydrase activity (ZnN3O). The first section will describe previous studies that allowed for a high affinity thiolate site that binds heavy metals in a way that stabilizes three-stranded coiled coils. The second section will examine ways of preparing histidine rich environments that lead to metal based hydrolytic catalysts. We will also discuss other recent examples of the design of structural metal sites and functional metalloenzymes. Our work demonstrates that attaining the proper first coordination geometry of a metal site can lead to a significant fraction of catalytic activity, apparently independent of the type of secondary structure of the surrounding protein environment. We are now in a position to begin to meet the challenge of building a metalloenzyme systematically from the bottom-up by engineering and analyzing interactions directly around the metal site and beyond.

  12. Importance of predictor variables for models of chemical function

    Data.gov (United States)

    U.S. Environmental Protection Agency — Importance of random forest predictors for all classification models of chemical function. This dataset is associated with the following publication: Isaacs , K., M....

  13. An important base triple anchors the substrate helix recognition surface within the Tetrahymena ribozyme active site.

    Science.gov (United States)

    Szewczak, A A; Ortoleva-Donnelly, L; Zivarts, M V; Oyelere, A K; Kazantsev, A V; Strobel, S A

    1999-09-28

    Key to understanding the structural biology of catalytic RNA is determining the underlying networks of interactions that stabilize RNA folding, substrate binding, and catalysis. Here we demonstrate the existence and functional importance of a Hoogsteen base triple (U300.A97-U277), which anchors the substrate helix recognition surface within the Tetrahymena group I ribozyme active site. Nucleotide analog interference suppression analysis of the interacting functional groups shows that the U300.A97-U277 triple forms part of a network of hydrogen bonds that connect the P3 helix, the J8/7 strand, and the P1 substrate helix. Product binding and substrate cleavage kinetics experiments performed on mutant ribozymes that lack this base triple (C A-U, U G-C) or replace it with the isomorphous C(+).G-C triple show that the A97 Hoogsteen triple contributes to the stabilization of both substrate helix docking and the conformation of the ribozyme's active site. The U300. A97-U277 base triple is not formed in the recently reported crystallographic model of a portion of the group I intron, despite the presence of J8/7 and P3 in the RNA construct [Golden, B. L., Gooding, A. R., Podell, E. R. & Cech, T. R. (1998) Science 282, 259-264]. This, along with other biochemical evidence, suggests that the active site in the crystallized form of the ribozyme is not fully preorganized and that substantial rearrangement may be required for substrate helix docking and catalysis.

  14. Protecting important sites for biodiversity contributes to meeting global conservation targets.

    Directory of Open Access Journals (Sweden)

    Stuart H M Butchart

    Full Text Available Protected areas (PAs are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs (referred to collectively hereafter as 'important sites'. Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites. Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs. While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45-1.14% annually since 1950 for IBAs and 0.79-1.49% annually for AZEs. Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends.

  15. Functional constraints on adaptive evolution of protein ubiquitination sites

    Science.gov (United States)

    Lu, Liang; Li, Yang; Liu, Zhongyang; Liang, Fengji; Guo, Feifei; Yang, Shuai; Wang, Dan; He, Yangzhige; Xiong, Jianghui; Li, Dong; He, Fuchu

    2017-01-01

    It is still unclear whether there exist functional constraints on the evolution of protein ubiquitination sites, because most previous studies regarded all protein ubiquitination sites as a whole or only focused on limited structural properties. We tried to clarify the relation between functional constraints and ubiquitination sites evolution. We investigated the evolutionary conservation of human ubiquitination sites in a broad evolutionary scale from G. gorilla to S. pombe, and we found that in organisms originated after the divergence of vertebrate, ubiquitination sites are more conserved than their flanking regions, while the opposite tendency is observed before this divergence time. By grouping the ubiquitination proteins into different functional categories, we confirm that many functional constraints like certain molecular functions, protein tissue expression specificity and protein connectivity in protein-protein interaction network enhance the evolutionary conservation of ubiquitination sites. Furthermore, by analyzing the gains of ubiquitination sites at different divergence time and their functional characters, we validate that the emergences of ubiquitination sites at different evolutionary time were also affected by the uncovered functional constraints. The above results suggest that functional constraints on the adaptive evolution of ubiquitination sites increase the opportunity for ubiquitination to synthetically regulate various cellular and developmental processes during evolution. PMID:28054638

  16. Protecting Important Sites for Biodiversity Contributes to Meeting Global Conservation Targets

    Science.gov (United States)

    Butchart, Stuart H. M.; Scharlemann, Jörn P. W.; Evans, Mike I.; Quader, Suhel; Aricò, Salvatore; Arinaitwe, Julius; Balman, Mark; Bennun, Leon A.; Bertzky, Bastian; Besançon, Charles; Boucher, Timothy M.; Brooks, Thomas M.; Burfield, Ian J.; Burgess, Neil D.; Chan, Simba; Clay, Rob P.; Crosby, Mike J.; Davidson, Nicholas C.; De Silva, Naamal; Devenish, Christian; Dutson, Guy C. L.; Fernández, David F. Día z; Fishpool, Lincoln D. C.; Fitzgerald, Claire; Foster, Matt; Heath, Melanie F.; Hockings, Marc; Hoffmann, Michael; Knox, David; Larsen, Frank W.; Lamoreux, John F.; Loucks, Colby; May, Ian; Millett, James; Molloy, Dominic; Morling, Paul; Parr, Mike; Ricketts, Taylor H.; Seddon, Nathalie; Skolnik, Benjamin; Stuart, Simon N.; Upgren, Amy; Woodley, Stephen

    2012-01-01

    Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites). Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs). While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45–1.14% annually since 1950 for IBAs and 0.79–1.49% annually for AZEs). Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends. PMID:22457717

  17. Protein function annotation by local binding site surface similarity.

    Science.gov (United States)

    Spitzer, Russell; Cleves, Ann E; Varela, Rocco; Jain, Ajay N

    2014-04-01

    Hundreds of protein crystal structures exist for proteins whose function cannot be confidently determined from sequence similarity. Surflex-PSIM, a previously reported surface-based protein similarity algorithm, provides an alternative method for hypothesizing function for such proteins. The method now supports fully automatic binding site detection and is fast enough to screen comprehensive databases of protein binding sites. The binding site detection methodology was validated on apo/holo cognate protein pairs, correctly identifying 91% of ligand binding sites in holo structures and 88% in apo structures where corresponding sites existed. For correctly detected apo binding sites, the cognate holo site was the most similar binding site 87% of the time. PSIM was used to screen a set of proteins that had poorly characterized functions at the time of crystallization, but were later biochemically annotated. Using a fully automated protocol, this set of 8 proteins was screened against ∼60,000 ligand binding sites from the PDB. PSIM correctly identified functional matches that predated query protein biochemical annotation for five out of the eight query proteins. A panel of 12 currently unannotated proteins was also screened, resulting in a large number of statistically significant binding site matches, some of which suggest likely functions for the poorly characterized proteins.

  18. Protecting important sites for biodiversity contributes to meeting global conservation targets

    DEFF Research Database (Denmark)

    Butchart, Stuart H. M.; Scharlemann, Jörn P.W.; Evans, Mike I.

    2012-01-01

    Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species...... remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter...... as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds...

  19. Talin contains a C-terminal calpain2 cleavage site important in focal adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Neil Bate

    Full Text Available Talin is a large (∼2540 residues dimeric adaptor protein that associates with the integrin family of cell adhesion molecules in cell-extracellular matrix junctions (focal adhesions; FAs, where it both activates integrins and couples them to the actin cytoskeleton. Calpain2-mediated cleavage of talin between the head and rod domains has previously been shown to be important in FA turnover. Here we identify an additional calpain2-cleavage site that removes the dimerisation domain from the C-terminus of the talin rod, and show that an E2492G mutation inhibits calpain cleavage at this site in vitro, and increases the steady state levels of talin1 in vivo. Expression of a GFP-tagged talin1 E2492G mutant in CHO.K1 cells inhibited FA turnover and the persistence of cell protrusion just as effectively as a L432G mutation that inhibits calpain cleavage between the talin head and rod domains. Moreover, incorporation of both mutations into a single talin molecule had an additive effect clearly demonstrating that calpain cleavage at both the N- and C-terminal regions of talin contribute to the regulation of FA dynamics. However, the N-terminal site was more sensitive to calpain cleavage suggesting that lower levels of calpain are required to liberate the talin head and rod fragments than are needed to clip off the C-terminal dimerisation domain. The talin head and rod liberated by calpain2 cleavage have recently been shown to play roles in an integrin activation cycle important in FA turnover and in FAK-dependent cell cycle progression respectively. The half-life of the talin head is tightly regulated by ubiquitination and we suggest that removal of the C-terminal dimerisation domain from the talin rod may provide a mechanism both for terminating the signalling function of the talin rod and indeed for inactivating full-length talin thereby promoting FA turnover at the rear of the cell.

  20. The functional importance of co-evolving residues in proteins.

    Science.gov (United States)

    Sandler, Inga; Zigdon, Nitzan; Levy, Efrat; Aharoni, Amir

    2014-02-01

    Computational approaches for detecting co-evolution in proteins allow for the identification of protein-protein interaction networks in different organisms and the assignment of function to under-explored proteins. The detection of co-variation of amino acids within or between proteins, moreover, allows for the discovery of residue-residue contacts and highlights functional residues that can affect the binding affinity, catalytic activity, or substrate specificity of a protein. To explore the functional impact of co-evolutionary changes in proteins, a combined experimental and computational approach must be recruited. Here, we review recent studies that apply computational and experimental tools to obtain novel insight into the structure, function, and evolution of proteins. Specifically, we describe the application of co-evolutionary analysis for predicting high-resolution three-dimensional structures of proteins. In addition, we describe computational approaches followed by experimental analysis for identifying specificity-determining residues in proteins. Finally, we discuss studies addressing the importance of such residues in terms of the functional divergence of proteins, allowing proteins to evolve new functions while avoiding crosstalk with existing cellular pathways or forming reproductive barriers and hence promoting speciation.

  1. Two putative protein kinase CK2 phosphorylation sites are important for Myf-5 activity

    DEFF Research Database (Denmark)

    Winter, B; Kautzner, I; Issinger, O G;

    1997-01-01

    Myf-5, a member of a family of muscle-specific transcription factors, is important for myogenic cell determination and differentiation. Here, we report that Myf-5 protein constitutes a substrate for phosphorylation in vitro by protein kinase CK2. We identified two potential phosphorylation sites ...

  2. Active chemisorption sites in functionalized ionic liquids for carbon capture.

    Science.gov (United States)

    Cui, Guokai; Wang, Jianji; Zhang, Suojiang

    2016-07-25

    Development of novel technologies for the efficient and reversible capture of CO2 is highly desired. In the last decade, CO2 capture using ionic liquids has attracted intensive attention from both academia and industry, and has been recognized as a very promising technology. Recently, a new approach has been developed for highly efficient capture of CO2 by site-containing ionic liquids through chemical interaction. This perspective review focuses on the recent advances in the chemical absorption of CO2 using site-containing ionic liquids, such as amino-based ionic liquids, azolate ionic liquids, phenolate ionic liquids, dual-functionalized ionic liquids, pyridine-containing ionic liquids and so on. Other site-containing liquid absorbents such as amine-based solutions, switchable solvents, and functionalized ionic liquid-amine blends are also investigated. Strategies have been discussed for how to activate the existent reactive sites and develop novel reactive sites by physical and chemical methods to enhance CO2 absorption capacity and reduce absorption enthalpy. The carbon capture mechanisms of these site-containing liquid absorbents are also presented. Particular attention has been paid to the latest progress in CO2 capture in multiple-site interactions by amino-free anion-functionalized ionic liquids. In the last section, future directions and prospects for carbon capture by site-containing ionic liquids are outlined.

  3. Critical importance of RAB proteins for synaptic function.

    Science.gov (United States)

    Mignogna, Maria Lidia; D'Adamo, Patrizia

    2017-02-01

    Neurons are highly polarized cells that exhibit one of the more complex morphology and function. Neuronal intracellular trafficking plays a key role in dictating the directionality and specificity of vesicle formation, transport and fusion, allowing the transmission of information in sophisticate cellular network. Thus, the integrity of protein trafficking and spatial organization is especially important in neuronal cells. RAB proteins, small monomeric GTPases belonging to the RAS superfamily, spatially and temporally orchestrate specific vesicular trafficking steps. In this review we summarise the known roles of RAB GTPases involved in the maintenance of neuronal vesicular trafficking in the central nervous system. In particular, we discriminate the axonal pre-synaptic trafficking and dendritic post-synaptic trafficking, to better underlie how a correct orchestration of vesicle movement is necessary to maintain neuronal polarity and then, to permit an accurate architecture and functionality of synaptic activity.

  4. Radiative lifetimes and cooling functions for astrophysically important molecules

    CERN Document Server

    Tennyson, Jonathan; Naim, Omree K; Yurchenko, Sergei N

    2016-01-01

    Extensive line lists generated as part of the ExoMol project are used to compute lifetimes for individual rotational, rovibrational and rovibronic excited states, and temperature-dependent cooling functions by summing over all dipole-allowed transitions for the states concerned. Results are presented for SiO, CaH, AlO, ScH, H$_2$O and methane. The results for CH$_4$ are particularly unusual with 4 excited states with no dipole-allowed decay route and several others where these decays lead to exceptionally long lifetimes. These lifetime data should be useful in models of masers and estimates of critical densities, and can provide a link with laboratory measurements. Cooling functions are important in stellar and planet formation.

  5. Minimal functional sites allow a classification of zinc sites in proteins.

    Directory of Open Access Journals (Sweden)

    Claudia Andreini

    Full Text Available Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS. We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design.

  6. Impact of Web Site Functions on E-Business Success in Chinese Wholesale and Retail Industries

    Institute of Scientific and Technical Information of China (English)

    TANG Qian; HUANG Jinghua

    2008-01-01

    Web sites are very important and companies can attract customers by promoting various features of the web site. This paper presents an analysis of the relationship between web site functions and firm performance. A research model based on the DeLone and McLean (D&M) model and customer service life cycle (CSLC) theory was used to investigate the impact of web site functions on e-business success. The research model considers web site functions, web site use, customer satisfaction, and firm performance. According to the CSLC theory, there are three stages in a customer service life cycle. Therefore, the web site functions are divided into three stages: requirements, acquisition, and ownership. The functions in each stage serve to encourage usage and thus, enhance customer satisfaction and firm performance. The theoretical model and hypotheses were tested using data collected from 72 wholesale and retail firms in China using the partial least squares (PLS) method. The results suggest that web site functions in the acquisition stage have the strongest impact on web site use and that the improvement of customer satisfaction can significantly increase firm performance.

  7. A second tubulin binding site on the kinesin-13 motor head domain is important during mitosis.

    Directory of Open Access Journals (Sweden)

    Dong Zhang

    Full Text Available Kinesin-13s are microtubule (MT depolymerases different from most other kinesins that move along MTs. Like other kinesins, they have a motor or head domain (HD containing a tubulin and an ATP binding site. Interestingly, kinesin-13s have an additional binding site (Kin-Tub-2 on the opposite side of the HD that contains several family conserved positively charged residues. The role of this site in kinesin-13 function is not clear. To address this issue, we investigated the in-vitro and in-vivo effects of mutating Kin-Tub-2 family conserved residues on the Drosophila melanogaster kinesin-13, KLP10A. We show that the Kin-Tub-2 site enhances tubulin cross-linking and MT bundling properties of KLP10A in-vitro. Disruption of the Kin-Tub-2 site, despite not having a deleterious effect on MT depolymerization, results in abnormal mitotic spindles and lagging chromosomes during mitosis in Drosophila S2 cells. The results suggest that the additional Kin-Tub-2 tubulin biding site plays a direct MT attachment role in-vivo.

  8. The importance of hydrology in restoration of bottomland hardwood wetland functions

    Science.gov (United States)

    Hunter, R.G.; Faulkner, S.P.; Gibson, K.A.

    2008-01-01

    Bottomland hardwood (BLH) forests have important biogeochemical functions and it is well known that certain structural components, including pulsed hydrology, hydric soils, and hydrophytic vegetation, enhance these functions. It is unclear, however, how functions of restored BLH wetlands compare to mature, undisturbed wetlands. We measured a suite of structural and functional attributes in replicated natural BLH wetlands (NAT), restored BLH wetlands with hydrology re-established (RWH), and restored BLH wetlands without hydrology re-established (RWOH) in this study. Trees were replanted in all restored wetlands at least four years prior to the study and those wetlands with hydrology re-established had flashboard risers placed in drainage ditches to allow seasonal surface flooding. Vegetation, soils, and selected biogeochemical functions were characterized at each site. There was a marked difference in woody vegetation among the wetlands that was due primarily to site age. There was also a difference in herbaceous vegetation among the restored sites that may have been related to differences in age or hydrology. Water table fluctuations of the RWH wetlands were comparable to those of the NAT wetlands. Thus, placing flashboard risers in existing drainage ditches, along with proper management, can produce a hydroperiod that is similar to that of a relatively undisturbed BLH. Average length of saturation within the upper 15 cm of soils was 37, 104, and 97 days for RWOH, RWH, and NAT, respectively. Soil moisture, denitrification potential, and soluble organic carbon concentrations differed among wetland sites, but soil carbon and nitrogen concentrations, heterotrophic microbial activity, and readily mineralizable carbon concentrations did not. Significant linear relationships were also found between soil moisture and heterotrophic microbial activity, readily mineralizable carbon, and soluble organic carbon. In addition, sedimentation rates were higher in NAT and RWH

  9. Emission of volatile organic compounds from solid waste disposal sites and importance of heat management.

    Science.gov (United States)

    Urase, Taro; Okumura, Hiroyuki; Panyosaranya, Samerjai; Inamura, Akihiro

    2008-12-01

    The emission of volatile organic compounds (VOCs) from a solid waste disposal site for municipal solid wastes was quantified. The VOCs contained in the landfill gas taken at the site were benzene, toluene, xylenes, ethyl benzenes, and trimethyl benzenes, while the concentrations of chlorinated compounds were very low. The concentration of benzene in the landfill gas samples ranged from below the detection limit to 20 mg m(-3), and the ratio of benzene to toluene ranged from 0.2 to 8. The higher concentrations of VOCs in landfill gas and in leachates were observed with the samples taken at high temperature areas of the target site. Polystyrene plastic waste was identified as one of the sources of VOCs in solid waste disposal sites at a high temperature condition. The appropriate heat management in landfill sites is an important countermeasure to avoid unusually high emission of VOCs because the heat generated by the biodegradation of organic solid wastes may promote the release of VOCs, especially in the case of sites which receive both biodegradable and plastic wastes.

  10. Site Identity and Importance in Cosubstituted Bixbyite In2O3

    Directory of Open Access Journals (Sweden)

    Karl Rickert

    2017-02-01

    Full Text Available The bixbyite structure of In2O3 has two nonequivalent, 6-coordinate cation sites and, when Sn is doped into In2O3, the Sn prefers the “b-site” and produces a highly conductive material. When divalent/tetravalent cation pairs are cosubstituted into In2O3, however, the conductivity increases to a lesser extent and the site occupancy is less understood. We examine the site occupancy in the MgxIn2−2xSnxO3 and ZnxIn2−2xSnxO3 systems with high resolution X-ray and neutron diffraction and density functional theory computations, respectively. In these sample cases and those that are previously reported in the MxIn2−2xSnxO3 (M = Cu, Ni, or Zn systems, the solubility limit is greater than 25%, ensuring that the b-site cannot be the exclusively preferred site as it is in Sn:In2O3. Prior to this saturation point, we report that the M2+ cation always has at least a partial occupancy on the d-site and the Sn4+ cation has at least a partial occupancy on the b-site. The energies of formation for these configurations are highly favored, and prefer that the divalent and tetravalent substitutes are adjacent in the crystal lattice, which suggests short range ordering. Diffuse reflectance and 4-point probe measurements of MgxIn2−xSnxO3 demonstrate that it can maintain an optical band gap >2.8 eV while surpassing 1000 S/cm in conductivity. Understanding how multiple constituents occupy the two nonequivalent cation sites can provide information on how to optimize cosubstituted systems to increase Sn solubility while maintaining its dopant nature, achieving maximum conductivity.

  11. The importance of site selection for setting up a wind turbine

    Energy Technology Data Exchange (ETDEWEB)

    Raghunandan, A.; Gowda, G.; Pandian, A. [MS RAMAIAH Institute of Technology, Bangalore (India); Ramanan, G. [RV College of Engineering, Bangalore (India)

    2012-07-01

    A wind energy system transforms the kinetic energy of the wind into mechanical or electrical energy that can be harnessed for practical use. Building a wind turbine is far more than simply a matter of finding a field or mountaintop where the wind is blowing and plopping one down. A great deal of attention should be given to finding the proper site for a wind turbine. The main factor one should consider is the average speed of the wind over an extended time. Estimation of the wind power potential for a site is the most important requirement for selecting a site for the installation of a wind turbine. Also wind turbines should be sited well above trees, buildings, and other obstacles else, the result will be poor energy production and increased wear and tear on the turbine. One way to get rid of this is to place the wind turbine on a tall tower. When selecting a place for setting up a wind turbine, engineers consider factors such as wind hazards, characteristics of the land that affect wind speed, and the effects of one turbine on nearby turbines in wind farms. The other factors that are important for selecting a site for installation of wind turbines are Hill effect, Roughness, or the amount of friction that Earth's surface exerts on wind, Tunnel effect, Turbulence, Variations in wind speed, Wind obstacles and Wind shear. This paper will emphasis on the necessary inspections which are to be done on the site before installing a Wind Turbine. (Author)

  12. THE IMPORTANCE OF COMMUNICATION IN THE FUNCTIONING OF AN ORGANIZATION

    Directory of Open Access Journals (Sweden)

    Zvonimir Jurković

    2012-12-01

    Full Text Available Organizations cannot exist without communication. Every human action is a kind of communication, and thus “not communicating” is also a form of communication. Efficient communication is the foundation for the internal organization development, but also a key factor of existence in an uncertain environment. Therefore, communication is an important aspect of manager behaviour as well as of the functioning of the entire organizational system. Business communication takes place both within and outside of organizations. A communication event within an organization can have two routes: a formal and an informal one. To make the organizational communication more successful, it is necessary for all participants and organization employees to have adequate language skills, to conduct interactive exercises and to possess intercultural awareness.

  13. The functional importance of disease-associated mutation

    Directory of Open Access Journals (Sweden)

    Klein Teri E

    2002-09-01

    Full Text Available Abstract Background For many years, scientists believed that point mutations in genes are the genetic switches for somatic and inherited diseases such as cystic fibrosis, phenylketonuria and cancer. Some of these mutations likely alter a protein's function in a manner that is deleterious, and they should occur in functionally important regions of the protein products of genes. Here we show that disease-associated mutations occur in regions of genes that are conserved, and can identify likely disease-causing mutations. Results To show this, we have determined conservation patterns for 6185 non-synonymous and heritable disease-associated mutations in 231 genes. We define a parameter, the conservation ratio, as the ratio of average negative entropy of analyzable positions with reported mutations to that of every analyzable position in the gene sequence. We found that 84.0% of the 231 genes have conservation ratios less than one. 139 genes had eleven or more analyzable mutations and 88.0% of those had conservation ratios less than one. Conclusions These results indicate that phylogenetic information is a powerful tool for the study of disease-associated mutations. Our alignments and analysis has been made available as part of the database at http://cancer.stanford.edu/mut-paper/. Within this dataset, each position is annotated with the analysis, so the most likely disease-causing mutations can be identified.

  14. HANFORD SITE WELDING PROGRAM SUCCESSFULLY PROVIDING A SINGLE SITE FUNCTION FOR USE BY MULTIPLE CONTRACTORS

    Energy Technology Data Exchange (ETDEWEB)

    CANNELL GR

    2009-11-19

    The Department of Energy, Richland Operations (DOE-RL) recently restructured its Hanford work scope, awarding two new contracts over the past several months for a total of three contracts to manage the sites cleanup efforts. DOE-RL met with key contractor personnel prior to and during contract transition to ensure site welding activities had appropriate oversight and maintained code compliance. The transition also provided an opportunity to establish a single site-wide function that would provide welding and materials engineering services to the Hanford site contractors: CH2M HILL Plateau Remediation Company (CHPRC); Mission Support Alliance (MSA); Washington River Protection Solutions (WRPS); and Washington Closure Hanford (WCH). Over the years, multiple and separate welding programs (amongst the several contractors) existed at the Hanford site leading to inefficiencies resulting from duplication of administrative efforts, maintenance of welding procedures, welder performance certifications, etc. The new, single program eliminates these inefficiencies. The new program, co-managed by two of the sites' new contractors, the CHPRC ('owner' of the program and responsible for construction welding services) and the MSA (provides maintenance welding services), provides more than just the traditional construction and maintenance welding services. Also provided, are welding engineering, specialty welding development/qualification for the closure of radioactive materials containers and materials evaluation/failure analysis. The following describes the new Hanford site welding program.

  15. Functional and catalytic active sites prediction and docking analysis ...

    African Journals Online (AJOL)

    Bioinformatics

    2015-07-01

    Jul 1, 2015 ... industrially important azo dyes such as the molecular weight, molecular ... et al., 2010). The software possesses structure-based method to predict active sites in proteins based on a Difference of Gaussian (DoG) approach ...

  16. Identification of a functional hepatocyte nuclear factor 4 binding site in the neutral ceramidase promoter

    DEFF Research Database (Denmark)

    Maltesen, Henrik R; Troelsen, Jesper T; Olsen, Jørgen

    2010-01-01

    in ceramide digestion. It was the purpose of the present work to experimentally verify the functional importance of a HNF-4a binding site predicted by bioinformatic analysis to be present in the Asah2 promoter. Using supershift analysis, HNF-4a overexpression, and HNF-4a knockdown experiments it was confirmed...... that the predicted HNF-4a binding site identified in the Asah2 promoter is functional. The results support the hypothesis that HNF-4a might be important for intestinal glycolipid metabolism....

  17. Ongoing change of site conditions important for sustainable forest management planning

    Science.gov (United States)

    Bidló, András; Horváth, Adrienn; Gulyás, Krisztina; Gálos, Borbála

    2016-04-01

    Observed tree mortality of the last decades has shown that the vulnerable forest ecosystems are especially affected by the recurrent, long lasting droughts, heat waves and their consequences. From all site conditions climate is changing the fastest, in this way it can be the largest threatening factor in the 21st century. Beyond climate, soil characteristics are playing an important influencing role. Until now, silvicultural technologies and species preferences of many countries are prescribed by binding regulation based on climate conditions that are assumed to be constant over time. Therefore the aim of our research was to investigate the ongoing and projected change of site conditions that are considered to be of primary importance in terms of tree species selection. For a case study region in Hungary (Keszthely Mountains, near to Lake Balaton) long-term climate tendencies have been determined for the period 1961-2100, as well as a detailed soil sample analysis has been carried out including ~100 sites. Results show a 0.5 degree increase of temperature and a 6-7 % decrease of the precipitation amount for the summer months in the last decades. For the future, significant warming and drying of summers is expected. Decrease of the summer precipitation sum can exceed 25 % until the end of the century, probability of extreme hot days may increase. These tendencies together with the unfavourable soil conditions and biotic damages can be the reason of the ongoing forest dieback. One of the characteristic soil type of the region is rendzina with a thin topsoil layer and an unfavourable water holding capacity. These properties are limiting the amount of available water for plants, especially in case of intense precipitation events. Black pine stands planted on rendzinas after many years of grazing; therefore erosion may have played a significant role. Not only microclimate conditions but also soil types show a large diversity within a relatively small distance. However

  18. Local structure of multiferroic RMn 2O 5: Important role of the R site

    Science.gov (United States)

    Tyson, T. A.; Chen, Z.; DeLeon, M. A.; Yoong, S.; Cheong, S.-W.

    2009-06-01

    The temperature and magnetic field dependent local structure of RMn 2O 5 systems was examined. While no significant displacements of the Mn ions are observed, it is found that the R-O distribution exhibits changes at low temperature which are possibly related to the changes in the electric polarization. Density functional computations are used to explore the system dynamics and to link the local structural measurements with anomalous changes in the infrared absorption spectra. The anomalous R-O distribution and observed coupling to magnetic fields point to the need to properly treat the 4f electrons on the R sites in these systems.

  19. Holistic marketing and its importance in the functioning of universities

    Directory of Open Access Journals (Sweden)

    I.P. Chajka

    2013-09-01

    Full Text Available The aim of the article is to study holistic marketing concept for its further implementation into activities of national enterprises including universities.The results of the analysis. Implementation of holistic marketing into activities of the company means to move away from traditional, built on a rigid hierarchy and subordination forms of management of production processes. Holistic marketing requires promotion of democracy, decentralization, development initiatives from below, involvement in decision-making of all stakeholders. Another important aspect of holistic marketing is to establish constant feedback to management, interactivity of all elements of the system recognizing the importance of each element.Thus, holistic marketing is a model of integrated planning, development and implementation of marketing programs, processes and activities with deprivation of rigid centralization. Holistic marketing leaves open the possibility for inherent mobility and, consequently, of its internal creative self-configuration potential.The mature state of governance in holistic marketing should be a situation where parts and wholes equal, there is no greater and smaller, important and not important. Each element of the holistic marketing has its meaning, functions that are considered as a whole. The prospect of such a system would be to totality the point where each element of the system becomes equal for the entire system.Authors propose the following principles of holistic marketing implementation into universities activities:independent decision-making;decentralization of management, providing an opportunity to decide the course of individual processes, promotion marketing activity of each participant in the process;the establishment and ongoing support of feedback between elements of the operation of the business;the freedom of each participant in the process, etc.Choosing the strategy of holistic marketing concept at a high school constantly

  20. The importance of measuring psychosocial functioning in schizophrenia

    Directory of Open Access Journals (Sweden)

    Dias Vasco

    2011-06-01

    Full Text Available Abstract Background Schizophrenia is among the most disabling of mental illnesses and frequently causes impaired functioning. We explore issues of definition and terminology, and the relationship between social functioning, cognition, and psychopathology considering relevant research findings. Methods The present article describes measures of social functioning and outlines their psychometric properties. It considers their usefulness in research and clinical settings. Treatment aims and objectives are explored in the context of cognitive and social functioning. Finally, we identify areas for developing research and refining the measurement of social functioning. Results The definition and measurement of social functioning in schizophrenia remains a complex and disputed area. The relationships between symptoms, cognitive functioning and social functioning are complex but we are beginning to understand them better. Scales for measuring functioning in clinical practice must be brief and sensitive to change and the Personal and Social Performance (PSP scale may offer several advantages in these regards. Brief cognitive assessments focusing upon the domains most commonly affected in schizophrenia, such as verbal memory and executive functions, should be coadministered with measures of functioning. Conclusions The use of validated scales for schizophrenia that are sensitive to change over the course of the illness and its treatment, should allow for a better understanding of patients' functional disabilities, enabling better and more comprehensive monitoring and evaluation of both pharmacological and non-pharmacological treatment strategies.

  1. Insect Diversity of the Muni-Pomadze Ramsar Site: An Important Site for Biodiversity Conservation in Ghana

    OpenAIRE

    Rosina Kyerematen; Daniel Acquah-Lamptey; Erasmus Henaku Owusu; Roger Sigismund Anderson; Yaa Ntiamoa-Baidu

    2014-01-01

    An inventory of species diversity of insects of the Muni-Pomadze Ramsar site, with special reference to species of conservation concern, was carried out as part of an evaluation of changes in the ecological character of the site, twenty years after designation. Samples were taken from two protected areas within the Ramsar site, in the wet (July), dry (January), and intermediate (June) seasons. Community diversity was characterized in terms of number of species accumulated, species richness, S...

  2. estimating an aggregate import demand function for ghana

    African Journals Online (AJOL)

    Administrator

    80% of shocks to real exchange rates, merchandise imports and GDP respectively, are attributed to own shocks. ... the United Kingdom and Germany as the main export markets. .... period stock of imported merchandise if posi- tive, and the ...

  3. Importance sampling for Lambda-coalescents in the infinitely many sites model

    CERN Document Server

    Birkner, Matthias; Steinruecken, Matthias; 10.1016/j.tpb.2011.01.005

    2011-01-01

    We present and discuss new importance sampling schemes for the approximate computation of the sample probability of observed genetic types in the infinitely many sites model from population genetics. More specifically, we extend the 'classical framework', where genealogies are assumed to be governed by Kingman's coalescent, to the more general class of Lambda-coalescents and develop further Hobolth et. al.'s (2008) idea of deriving importance sampling schemes based on 'compressed genetrees'. The resulting schemes extend earlier work by Griffiths and Tavar\\'e (1994), Stephens and Donnelly (2000), Birkner and Blath (2008) and Hobolth et. al. (2008). We conclude with a performance comparison of classical and new schemes for Beta- and Kingman coalescents.

  4. Fast dynamics perturbation analysis for prediction of protein functional sites

    Directory of Open Access Journals (Sweden)

    Cohn Judith D

    2008-01-01

    Full Text Available Abstract Background We present a fast version of the dynamics perturbation analysis (DPA algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy Dx. Such regions are associated with functional sites. Results The Fast DPA algorithm, which accelerates DPA calculations, is motivated by an empirical observation that Dx in a normal-modes model is highly correlated with an entropic term that only depends on the eigenvalues of the normal modes. The eigenvalues are accurately estimated using first-order perturbation theory, resulting in a N-fold reduction in the overall computational requirements of the algorithm, where N is the number of residues in the protein. The performance of the original and Fast DPA algorithms was compared using protein structures from a standard small-molecule docking test set. For nominal implementations of each algorithm, top-ranked Fast DPA predictions overlapped the true binding site 94% of the time, compared to 87% of the time for original DPA. In addition, per-protein recall statistics (fraction of binding-site residues that are among predicted residues were slightly better for Fast DPA. On the other hand, per-protein precision statistics (fraction of predicted residues that are among binding-site residues were slightly better using original DPA. Overall, the performance of Fast DPA in predicting ligand-binding-site residues was comparable to that of the original DPA algorithm. Conclusion Compared to the original DPA algorithm, the decreased run time with comparable performance makes Fast DPA well-suited for implementation on a web server and for high-throughput analysis.

  5. The importance of physical function to people with osteoporosis.

    Science.gov (United States)

    Kerr, C; Bottomley, C; Shingler, S; Giangregorio, L; de Freitas, H M; Patel, C; Randall, S; Gold, D T

    2017-03-06

    There is increasing need to understand patient outcomes in osteoporosis. This article discusses that fracture in osteoporosis can lead to a cycle of impairment, driven by complex psychosocial factors, having a profound impact on physical function/activity which accumulates over time. More information is required on how treatments impact physical function.

  6. The Importance of Safety in Construction Sector: Costs of Occupational Accidents in Construction Sites

    Directory of Open Access Journals (Sweden)

    Fatih Yılmaz

    2015-04-01

    Full Text Available Occupational accidents cause important social and economic problems by loss of life and physical injuries. Construction sector involves high risk due to its production processes and labor intensive characteristic and because of occupational accidents the sector brings up against financial loss in large scale. In developing countries, construction sector is one of the most important sectors that have a great contribution to economic development with its employment capacity and added-value to the economy. On the other hand, due to the lack of preventive measures, occupational accidents occur, frequently in construction in Turkey. Major occupational accidents are defined as the cause of serious injuries and a long-term disability; minor occupational accidents are defined as the cause of insignificant injuries and short-term disability. Minor occupational accidents are not considered sufficiently, they are even not kept as a record. It is known that minor occupational accidents, which are not considered sufficiently and even not registered, cause great financial loss in workplaces. The aim of this paper is to investigate the cost of workforce loss caused by the accidents in construction sites by using the statistics of three construction sites in Turkey and to compare the financial losses of minor and major occupational accidents. In this study, three construction project are investigated in Turkey in 2009 and it is obtained that the cost of workday loss caused by major occupational accidents is 19431.75 $ and minor occupational accidents cause a loss of 6924.25 $. The cost of workday loss caused by minor occupational accidents are almost 35 % of major workday losses’. These costs presents the importance of preventive measures for workers’ health and safety in construction.

  7. Attribute-Value Functions as Global Interpretations of Attribute Importance

    NARCIS (Netherlands)

    Ittersum, van K.; Pennings, J.M.E.

    2012-01-01

    In order to better understand decision maker’s perceptions of the importance of attributes, Goldstein (1990) differentiates between global and local interpretations of attribute importance. While the appreciation for the distinction is growing, research on the relationship between measures of global

  8. Protection reduces loss of natural land-cover at sites of conservation importance across Africa.

    Science.gov (United States)

    Beresford, Alison E; Eshiamwata, George W; Donald, Paul F; Balmford, Andrew; Bertzky, Bastian; Brink, Andreas B; Fishpool, Lincoln D C; Mayaux, Philippe; Phalan, Ben; Simonetti, Dario; Buchanan, Graeme M

    2013-01-01

    There is an emerging consensus that protected areas are key in reducing adverse land-cover change, but their efficacy remains difficult to quantify. Many previous assessments of protected area effectiveness have compared changes between sets of protected and unprotected sites that differ systematically in other potentially confounding respects (e.g. altitude, accessibility), have considered only forest loss or changes at single sites, or have analysed changes derived from land-cover data of low spatial resolution. We assessed the effectiveness of protection in reducing land-cover change in Important Bird Areas (IBAs) across Africa using a dedicated visual interpretation of higher resolution satellite imagery. We compared rates of change in natural land-cover over a c. 20-year period from around 1990 at a large number of points across 45 protected IBAs to those from 48 unprotected IBAs. A matching algorithm was used to select sample points to control for potentially confounding differences between protected and unprotected IBAs. The rate of loss of natural land-cover at sample points within protected IBAs was just 42% of that at matched points in unprotected IBAs. Conversion was especially marked in forests, but protection reduced rates of forest loss by a similar relative amount. Rates of conversion increased from the centre to the edges of both protected and unprotected IBAs, but rates of loss in 20-km buffer zones surrounding protected IBAs and unprotected IBAs were similar, with no evidence of displacement of conversion from within protected areas to their immediate surrounds (leakage).

  9. Extensions of PDZ domains as important structural and functional elements

    OpenAIRE

    Wang, Conan K.; Pan, Lifeng; Chen, Jia; Zhang, Mingjie

    2010-01-01

    ‘Divide and conquer’ has been the guiding strategy for the study of protein structure and function. Proteins are divided into domains with each domain having a canonical structural definition depending on its type. In this review, we push forward with the interesting observation that many domains have regions outside of their canonical definition that affect their structure and function; we call these regions ‘extensions’. We focus on the highly abundant PDZ (PSD-95, DLG1 and ZO-1) domain. Us...

  10. Importance of Fragmentation Functions in Determining Polarized Parton Densities

    CERN Document Server

    Leader, Elliot; Stamenov, Dimiter B

    2012-01-01

    New fragmentation functions (FFs) are extracted from a NLO QCD fit to the preliminary COMPASS data on pion and kaon multiplicities. It is shown that the new kaon FFs are very different from those of De Florian at al. (DSS) and Hirai et al. (HKNS). The sensitivity of the extracted polarized PDFs to the new FFs is discussed.

  11. Characterization of heparin-binding site of tissue transglutaminase: its importance in cell surface targeting, matrix deposition, and cell signaling.

    Science.gov (United States)

    Wang, Zhuo; Collighan, Russell J; Pytel, Kamila; Rathbone, Daniel L; Li, Xiaoling; Griffin, Martin

    2012-04-13

    Tissue transglutaminase (TG2) is a multifunctional Ca(2+)-activated protein cross-linking enzyme secreted into the extracellular matrix (ECM), where it is involved in wound healing and scarring, tissue fibrosis, celiac disease, and metastatic cancer. Extracellular TG2 can also facilitate cell adhesion important in wound healing through a nontransamidating mechanism via its association with fibronectin, heparan sulfates (HS), and integrins. Regulating the mechanism how TG2 is translocated into the ECM therefore provides a strategy for modulating these physiological and pathological functions of the enzyme. Here, through molecular modeling and mutagenesis, we have identified the HS-binding site of TG2 (202)KFLKNAGRDCSRRSSPVYVGR(222). We demonstrate the requirement of this binding site for translocation of TG2 into the ECM through a mechanism involving cell surface shedding of HS. By synthesizing a peptide NPKFLKNAGRDCSRRSS corresponding to the HS-binding site within TG2, we also demonstrate how this mimicking peptide can in isolation compensate for the RGD-induced loss of cell adhesion on fibronectin via binding to syndecan-4, leading to activation of PKCα, pFAK-397, and ERK1/2 and the subsequent formation of focal adhesions and actin cytoskeleton organization. A novel regulatory mechanism for TG2 translocation into the extracellular compartment that depends upon TG2 conformation and the binding of HS is proposed.

  12. The importance of team functioning to natural resource planning outcomes.

    Science.gov (United States)

    Stern, Marc J; Predmore, S Andrew

    2012-09-15

    In its recent history, the U.S. Forest Service is among many federal land management agencies struggling with questions concerning why its planning procedures are sometimes inefficient, perform poorly in the eyes of the public, and fail to deliver outputs that advance agency mission. By examining a representative sample of National Environmental Policy Act (NEPA) processes conducted by the agency between 2007 and 2009, we provide new insights into what drives outcomes in these planning processes. We examined team leaders' perceptions of the following outcomes: achievement of agency goals and NEPA mandates, process efficiency, public relations, and team outcomes. The most consistently important predictors of positive outcomes were team harmony and a clearly empowered team leader. Other factors, such as perceptions of the use of best science, a clear and unambiguous purpose and need, team turnover (personnel changes during the process), extra-agency engagement, and intra-agency relations, were also important, but played a less consistent role. The findings suggest the importance of empowering team leaders and team members through enhancing elements of discretion, responsibility, clear role definition, collaborative interdisciplinary deliberation, and perceived self-efficacy. The results also suggest the importance of genuine concern and respect for participating publics and effective inter-agency coordination. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Importance of ventricular function in the election of electro heart mode.

    Science.gov (United States)

    Nicolás-Franco, S; Rodríguez-González, F J; Nicolás-Boluda, A; Sánchez-Martos, A

    2015-04-01

    The integration of the ventricular function is essential when making decisions over a patient subjected to cardiac electrostimulation in order to understand the structure followed in the new cardiac stimulation and resynchronising therapy guides. To support the importance of ventricular function in cardiac electrostimulation it is important to know: (i)the deleterious effect of stimulation on the right ventricle apex; (ii)the effect over the left ventricular function produced by complete blockage of the left branch, and (iii)left ventricular disfunction as arrythmogenic substrate. When it comes to decide what type of cardiac electrostimualtion to apply we will know: the percentage of ventricular stimulation needed and its ventricular function. A normal ventricular function will enable electrostimulation from the right ventricle apex or alternative site. On the contrary, if this value is lower than 50% the most recommended electrostimulation is cardiac resynchronisation (CRT-P), which will be accompanied by defibrillation (CRT-D) if FEVI is lower than 35%. Copyright © 2014 Elsevier España, S.L.U. and SEMICYUC. All rights reserved.

  14. Insect Diversity of the Muni-Pomadze Ramsar Site: An Important Site for Biodiversity Conservation in Ghana

    Directory of Open Access Journals (Sweden)

    Rosina Kyerematen

    2014-01-01

    Full Text Available An inventory of species diversity of insects of the Muni-Pomadze Ramsar site, with special reference to species of conservation concern, was carried out as part of an evaluation of changes in the ecological character of the site, twenty years after designation. Samples were taken from two protected areas within the Ramsar site, in the wet (July, dry (January, and intermediate (June seasons. Community diversity was characterized in terms of number of species accumulated, species richness, Shannon-Weiner indices of diversity, Pielou’s evenness, and Bray-Curtis similarity. A total of 134 families from 19 insect orders were recorded during the entire study period. Yenku Block A recorded the highest species richness (98 and the highest diversity index (14.97, corroborated by the highest Margalef index of 3.82 with a relatively even distribution of species (0.834 during the intermediate season, and recorded the lowest diversity (6.957 and species richness (41 during the dry season. On the whole, the Muni-Pomadzi Ramsar site showed a high diversity of insect species. The presence of species such as Junonia oenone and Papilio demodocus which are specialized in degraded habitats at Yenku Block A in large numbers is a clear indication of degradation of the forest, but the presence of forest species such as Salamis anacardii and Euphaedra crokeri is an indication that some parts of this reserve are still in good shape. A comparison of the butterfly species recorded with findings in a 1997 survey showed a marked increase in numbers from 75 to 130; this may be attributed to the habitat changes that have taken place at the site offering more diverse habitat types.

  15. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.

    Science.gov (United States)

    Frederiksen, John K; Li, Nan-Sheng; Das, Rhiju; Herschlag, Daniel; Piccirilli, Joseph A

    2012-06-01

    Within the three-dimensional architectures of RNA molecules, divalent metal ions populate specific locations, shedding their water molecules to form chelates. These interactions help the RNA adopt and maintain specific conformations and frequently make essential contributions to function. Defining the locations of these site-bound metal ions remains challenging despite the growing database of RNA structures. Metal-ion rescue experiments have provided a powerful approach to identify and distinguish catalytic metal ions within RNA active sites, but the ability of such experiments to identify metal ions that contribute to tertiary structure acquisition and structural stability is less developed and has been challenged. Herein, we use the well-defined P4-P6 RNA domain of the Tetrahymena group I intron to reevaluate prior evidence against the discriminatory power of metal-ion rescue experiments and to advance thermodynamic descriptions necessary for interpreting these experiments. The approach successfully identifies ligands within the RNA that occupy the inner coordination sphere of divalent metal ions and distinguishes them from ligands that occupy the outer coordination sphere. Our results underscore the importance of obtaining complete folding isotherms and establishing and evaluating thermodynamic models in order to draw conclusions from metal-ion rescue experiments. These results establish metal-ion rescue as a rigorous tool for identifying and dissecting energetically important metal-ion interactions in RNAs that are noncatalytic but critical for RNA tertiary structure.

  16. Site and Orbit Repeatabilities using Adaptive Mapping Functions

    Science.gov (United States)

    Desjardins, Camille; Gegout, Pascal; Soudarin, Laurent; Biancale, Richard; Perosanz, Felix

    2015-04-01

    The electromagnetic signals emitted by the satellite positioning systems travel at the speed of light in a straight line in a vacuum but are modified in their propagation through the neutral atmosphere by temporal and spatial changes of density, and composition and refractivity. These waves are slowed down and their trajectories are bent. This presentation summarizes the performances of the modeling of the tropospheric propagation by the ray tracing technique through the assimilations of the European Meteorological Centre (ECMWF) in the framework of realizing the geodetic reference frame. This goal is achieved by modeling the spatial variability of the propagation using the time variable three-dimensional physical parameters of the atmosphere. The tropospheric delays obtained by ray tracing in all directions throughout the meteorological model surrounding the geodetic site, are fitted by Adaptive Mapping Functions (AMF) parameterized by several tens of coefficients. The delays produced by the Horizon software are then experimented, kept unchanged or adjusted, when recovering a reference frame based on hundred sites using the GINS software. Without any adjustments of the tropospheric modeling, the subcentimetric performances of the AMF are demonstrated by the repeatability of sites positions and GPS satellites orbits. When some AMF coefficients are adjusted, the accuracy of orbits recovery in term of quadratic mean is 7 to 8 millimeters. This limit is imposed by the lack or deficiency of other models, such as non-tidal and tidal loading respectively. Hence the repeatability of the vertical position is not enhanced by changing the propagation model. At the contrary, the repeatability of the horizontal position of geodetic sites is greatly enhanced by accounting for the azimuthal variability provided by the realistic 3D shapes of the Atmosphere and the Earth and the rigorous interpolations of atmospheric parameters included in Adaptive Mapping Functions with respect

  17. Impact of the permanent ventricular pacing site on left ventricular function in children : a retrospective multicentre survey

    NARCIS (Netherlands)

    van Geldorp, Irene E.; Delhaas, Tammo; Gebauer, Roman A.; Frias, Patrick; Tomaske, Maren; Friedberg, Mark K.; Tisma-Dupanovic, Svjetlana; Elders, Jan; Fruh, Andreas; Gabbarini, Fulvio; Kubus, Petr; Illikova, Viera; Tsao, Sabrina; Blank, Andreas Christian; Hiippala, Anita; Sluysmans, Thierry; Karpawich, Peter; Clur, Sally-Ann; Ganame, Xavier; Collins, Kathryn K.; Dann, Gisela; Thambo, Jean-Benoit; Trigo, Conceicao; Nagel, Bert; Papagiannis, John; Rackowitz, Annette; Marek, Jan; Nuernberg, Jan-Hendrik; Vanagt, Ward Y.; Prinzen, Frits W.; Janousek, Jan

    2011-01-01

    Background Chronic right ventricular (RV) pacing is associated with deleterious effects on cardiac function. Objective In an observational multicentre study in children with isolated atrioventricular (AV) block receiving chronic ventricular pacing, the importance of the ventricular pacing site on le

  18. Multiplexed site-specific electrode functionalization for multitarget biosensors.

    Science.gov (United States)

    Levrie, Karen; Jans, Karolien; Vos, Rita; Ardakanian, Niyousha; Verellen, Niels; Van Hoof, Chris; Lagae, Liesbet; Stakenborg, Tim

    2016-12-01

    Multitarget biosensors hold great promise to improve point-of-care diagnostics as they enable simultaneous detection of different biomolecular markers. Multiplexed detection of different markers, like genes, proteins, or a combination of both, propels advancement in numerous fields such as genomics, medical diagnosis and therapy monitoring. The functionalization of these biosensors, however, necessitates patterned immobilization of different bioreceptors, which remains challenging and time-consuming. We demonstrate a simple method for the patterned multiplexing of bioreceptors on a multi-electrode chip. By using the lithographically defined electrodes for surface functionalization, additional patterning steps become obsolete. Using the electrodes for self-aligned immobilization provides a spatial resolution that is limited by the electrode patterning process and that cannot be easily obtained by alternative dispensing or coating techniques. Via electrochemical reduction of diazonium salts combined with click chemistry, we achieved site-specific immobilization of two different ssDNA probes side by side on a single chip. This method was experimentally verified by cyclic voltammetry (CV), Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS), and specific target recognition was visualized by fluorescence microscopy. The combination of the electroaddressability of electrografting with the chemoselectivity of click chemistry, offers a versatile platform for highly efficient site-specific functionalization of multitarget biosensors.

  19. Is recreational hunting important for landscape multi-functionality?

    DEFF Research Database (Denmark)

    Lund, Jens Friis; Jensen, Frank Søndergaard

    2017-01-01

    , and preservation of valued and/or threatened animal and plant species. Recreational hunting may thus contribute to preserve and enhance landscape multifunctionality. Yet, little is known about the importance of hunting interests in motivating such landscape management. In this article, we seek to shed light...... on these issues on the basis of data from a nationally representative survey of Danish landowners. Our findings show a mixed picture of the role of recreational hunting in supporting multifunctional landscapes. We observe a broad swathe of landscape changes for multifunctionality cross properties with different...

  20. Prevalence of feral swine disturbance at important archaeological sites over a large landscape in Florida

    Science.gov (United States)

    Engeman, Richard M.; Meyer, Joseph S.; Allen, John B.

    2017-01-01

    Feral swine are globally known as one of the most destructive invasive vertebrates, damaging native habitats, native plants and animals, agriculture, infrastructure, spreading diseases. There has been little quantification on their disturbance to archaeological sites across a broad landscape. Over 6 years we inspected 293 significant archaeological sites for swine disturbance across a vast area. We found a 42% prevalence of swine disturbance among all sites, with prevalence not distinguishable among prehistoric sites, historic sites, and sites with both components. The areas of disturbance mapped within three historic homestead sites showed 5–26% of total site surface area rooted. Disturbance was not evident upon re-inspection of one of these sites after 18 months, indicating how evidence of disturbance can be obscured in this environment. Thus, our observed 42% prevalence of disturbance should be considered a minimum for disturbance occurring through time. Artifacts depths were <10 cm of the surface at 85% of the sites and <20 cm of the surface for 90% of the sites. Feral swine rooting commonly exceeds 20 cm in depth, especially in soft sandy substrates typical of Florida, making the great majority of the studied sites highly vulnerable to artifact damage or displacement.

  1. Proteins of the corneal stroma: importance in visual function.

    Science.gov (United States)

    Xuan, Meng; Wang, Shurong; Liu, Xin; He, Yuxi; Li, Ying; Zhang, Yan

    2016-04-01

    The human cornea, consisting of five layers, is the transparent tissue that refracts and transmits light to the lens and retina, providing about two thirds of the refractive power of the eye. The stroma layer comprises nearly 90 % of the thickness of the cornea and thus plays a pivotal role in normal visual function. The bulk of this layer is constituted by proteins in the extracellular martrix secreted by the corneal epithelial, stroma, and endothelial cells. Clinical research has shown that corneal stroma diseases are common and involve conditions such as infections, injuries, and genetic defects, which cause severe visual disturbances or even blindness. To improve our understanding of the basic molecular mechanisms involved in the physiological and pathological activities of the corneal stroma, its proteins have been brought into the limelight to determine their crucial and irreplaceable roles. The data presented in a previous study have demonstrated the presence of 1679 proteins in the stroma, and this data set has subsequently been perfected by utilizing a highly sensitive isobaric peptide-labeling approach. According to their manifestations, these proteins can be classified as a gel-like organic material composed of proteoglycans, enzymes, and hemocyanin-binding proteins and a network of filaments composed of collagen, elastin, keratin, vimentin, and interconnected filaments comprising fibronectin and laminin. The aim of this review is to describe some corneal stroma proteins by highlighting their major functions and valuable applications in ophthalmologic research toward the better characterization and treatment of eye diseases.

  2. Executive Functions in Tobacco Dependence: Importance of Inhibitory Capacities.

    Directory of Open Access Journals (Sweden)

    Valentin Flaudias

    Full Text Available Executive functions are linked to tobacco dependence and craving. In this cross-sectional study, we assessed the impact of three executive functions: updating, inhibition and shifting processes on tobacco craving and dependence.134 tobacco consumers were included in this study: 81 moderately (Fagerström score 7. Dependence was assessed with the Fagerström test and craving with the tobacco craving questionnaire (TCQ 12. We used the Stroop test and the Hayling test to measure inhibition, the Trail Making Test to measure shifting processes and the n-back test to measure updating processes. A multivariate logistic model was used to assess which variables explained best the level of nicotine dependence.Inhibition (p = 0.002 and updating (p = 0.014 processes, but not shifting processes, were associated with higher tobacco dependence. Inhibition capacity had a significant effect on the nicotine dependence level independently of age, education, time since last cigarette, intellectual quotient, craving, updating and shifting process.Nicotine dependence level seems better explained by inhibition capacities than by craving and updating effects. The capacity to inhibit our behaviours is a good predictor of the severity of tobacco dependence. Our results suggest a prefrontal cortex dysfunction affecting the inhibitory capacities of heavy tobacco dependent smokers. Further studies are needed to investigate the application of these findings in the treatment of tobacco dependence.

  3. Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites.

    Directory of Open Access Journals (Sweden)

    Tzong-Yi Lee

    Full Text Available Ubiquitin (Ub is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3 enzymes. Three major enzymes participate in ubiquitin conjugation. They are E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF network to identify protein ubiquitin conjugation (ubiquitylation sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (-20∼+20 revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information, which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence

  4. Incorporating distant sequence features and radial basis function networks to identify ubiquitin conjugation sites.

    Science.gov (United States)

    Lee, Tzong-Yi; Chen, Shu-An; Hung, Hsin-Yi; Ou, Yu-Yen

    2011-03-09

    Ubiquitin (Ub) is a small protein that consists of 76 amino acids about 8.5 kDa. In ubiquitin conjugation, the ubiquitin is majorly conjugated on the lysine residue of protein by Ub-ligating (E3) enzymes. Three major enzymes participate in ubiquitin conjugation. They are E1, E2 and E3 which are responsible for activating, conjugating and ligating ubiquitin, respectively. Ubiquitin conjugation in eukaryotes is an important mechanism of the proteasome-mediated degradation of a protein and regulating the activity of transcription factors. Motivated by the importance of ubiquitin conjugation in biological processes, this investigation develops a method, UbSite, which uses utilizes an efficient radial basis function (RBF) network to identify protein ubiquitin conjugation (ubiquitylation) sites. This work not only investigates the amino acid composition but also the structural characteristics, physicochemical properties, and evolutionary information of amino acids around ubiquitylation (Ub) sites. With reference to the pathway of ubiquitin conjugation, the substrate sites for E3 recognition, which are distant from ubiquitylation sites, are investigated. The measurement of F-score in a large window size (-20∼+20) revealed a statistically significant amino acid composition and position-specific scoring matrix (evolutionary information), which are mainly located distant from Ub sites. The distant information can be used effectively to differentiate Ub sites from non-Ub sites. As determined by five-fold cross-validation, the model that was trained using the combination of amino acid composition and evolutionary information performs best in identifying ubiquitin conjugation sites. The prediction sensitivity, specificity, and accuracy are 65.5%, 74.8%, and 74.5%, respectively. Although the amino acid sequences around the ubiquitin conjugation sites do not contain conserved motifs, the cross-validation result indicates that the integration of distant sequence features of Ub

  5. Remarkable difference in catalytic performance of an organoamino-functionalized MCM-41-HPA composite with controlled site-isolation and site-aggregation

    Science.gov (United States)

    Chu, Xiaofeng; Le, Ying-Yi; Zhu, Quanjing; Fan, Kangnian; Dai, Wei-Lin

    2011-08-01

    The organoamino-functionalized mesoporous silicas with different distribution patterns—site-isolation or site-aggregation are prepared using post-grafting method. We have investigated the effects of the solvents and the catalytic reactivity of these catalysts. It is found that, using the polar ethanol as solvent, the catalytic center is site-isolated. Contrarily, the catalytic center is site-aggregated with the non-polar toluene. Characterization techniques, including transmission electron microscopy, nitrogen sorption experiments, thermogravimetric analysis, and ultraviolet-visible absorbance spectroscopy, demonstrate the most important dependencies of the distribution pattern on the polarity of solvent.

  6. Importance of quantification of local site effects based on wave propagation in seismic microzonation

    Indian Academy of Sciences (India)

    S Kumar; J P Narayan

    2008-11-01

    This paper presents the three most important aspects of seismic microzonation namely prediction of fundamental frequency (F0) of soil deposit, aggravation factor (aggravation factor is simply the extra spectral amplification due to complex 2D site effects over the 1D response of the soil column) and the spatial variability of the ground motion caused by the basin-edge induced Love waves. The predicted F0 of single, double and three-soil-layered models revealed that the available empirical relations to predict the F0 of layered soil deposits are inadequate. We recommend the use of analytical or numerical methods to predict such an important parameter based on wave propagation effects. An increase of amplitude of Love wave, strain level and average aggravation factor (AAF) with increase of impedance contrast was obtained. Based on the trend of rate of decrease of AAF and maximum strain with offset from the basin-edge, we can qualitatively infer that the effects of induced Love wave may reduce to a negligible value after a traveled distance of 6.5–10.0 (where is the wavelength corresponding to the 0 of soil layer). The obtained increase of strain level with the decrease of distance between two receiver points used for the computation of strain reflects that structures having spatial extent smaller than the may suffer damage due to the basin-edge induced surface waves. The fast rate of decrease of strain with the offset from the strong lateral discontinuity (SLD)/basin-edge may be attributed to the dispersive nature of Love wave. We can incorporate the increased spectral amplification due to the induced surface waves in the form of aggravation factor but till date we have no effective way to incorporate the effects of developed strain by induced surface waves in seismic microzonation or in building codes.

  7. Functional Analysis of PKC Phosphorylation Sites on Myelin Protein Zero

    Institute of Scientific and Technical Information of China (English)

    GangXu; MichaelShy; JohnKamhoz; JanneBalsamo

    2003-01-01

    Objective To analyze the function of Protein kinase C(PKC) phosphorylation sites on mylelin protein zero (P0) at adhesion and myelination.Methods Mutations of p0 cyto-plasmic domain motif (RSTK) and adjacent sequence which are targeted by PKC were studied.Results The point mutations in this region or an adjacent serine residue could abolish P0 adhe-sion function. PKCα,along with the PKC binding protein RACK1,were associated with wild type P0.Inhibition of PKC activity abolished the P0 mediated adhesion.Point mutation in the RSTKtarget site that abolished adhesion did not alter the association of PKC with P0,but deletion of a 14 amino acid region,which included the PSTK motif,could abolish the association.Conclusion PKC mediated phosphorylation of specific residues within the cytoplasmic domain of P0 is neces-sary for P0 mediated adhesion.The alteration of this phoporylation can cause demyelinating neu-ropathy in human.

  8. Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

    Directory of Open Access Journals (Sweden)

    Chen Brian Y

    2008-01-01

    Full Text Available Abstract Background Structural genomics projects such as the Protein Structure Initiative (PSI yield many new structures, but often these have no known molecular functions. One approach to recover this information is to use 3D templates – structure-function motifs that consist of a few functionally critical amino acids and may suggest functional similarity when geometrically matched to other structures. Since experimentally determined functional sites are not common enough to define 3D templates on a large scale, this work tests a computational strategy to select relevant residues for 3D templates. Results Based on evolutionary information and heuristics, an Evolutionary Trace Annotation (ETA pipeline built templates for 98 enzymes, half taken from the PSI, and sought matches in a non-redundant structure database. On average each template matched 2.7 distinct proteins, of which 2.0 share the first three Enzyme Commission digits as the template's enzyme of origin. In many cases (61% a single most likely function could be predicted as the annotation with the most matches, and in these cases such a plurality vote identified the correct function with 87% accuracy. ETA was also found to be complementary to sequence homology-based annotations. When matches are required to both geometrically match the 3D template and to be sequence homologs found by BLAST or PSI-BLAST, the annotation accuracy is greater than either method alone, especially in the region of lower sequence identity where homology-based annotations are least reliable. Conclusion These data suggest that knowledge of evolutionarily important residues improves functional annotation among distant enzyme homologs. Since, unlike other 3D template approaches, the ETA method bypasses the need for experimental knowledge of the catalytic mechanism, it should prove a useful, large scale, and general adjunct to combine with other methods to decipher protein function in the structural proteome.

  9. The soft palate is an important site of adaptation for transmissible influenza viruses.

    Science.gov (United States)

    Lakdawala, Seema S; Jayaraman, Akila; Halpin, Rebecca A; Lamirande, Elaine W; Shih, Angela R; Stockwell, Timothy B; Lin, Xudong; Simenauer, Ari; Hanson, Christopher T; Vogel, Leatrice; Paskel, Myeisha; Minai, Mahnaz; Moore, Ian; Orandle, Marlene; Das, Suman R; Wentworth, David E; Sasisekharan, Ram; Subbarao, Kanta

    2015-10-01

    Influenza A viruses pose a major public health threat by causing seasonal epidemics and sporadic pandemics. Their epidemiological success relies on airborne transmission from person to person; however, the viral properties governing airborne transmission of influenza A viruses are complex. Influenza A virus infection is mediated via binding of the viral haemagglutinin (HA) to terminally attached α2,3 or α2,6 sialic acids on cell surface glycoproteins. Human influenza A viruses preferentially bind α2,6-linked sialic acids whereas avian influenza A viruses bind α2,3-linked sialic acids on complex glycans on airway epithelial cells. Historically, influenza A viruses with preferential association with α2,3-linked sialic acids have not been transmitted efficiently by the airborne route in ferrets. Here we observe efficient airborne transmission of a 2009 pandemic H1N1 (H1N1pdm) virus (A/California/07/2009) engineered to preferentially bind α2,3-linked sialic acids. Airborne transmission was associated with rapid selection of virus with a change at a single HA site that conferred binding to long-chain α2,6-linked sialic acids, without loss of α2,3-linked sialic acid binding. The transmissible virus emerged in experimentally infected ferrets within 24 hours after infection and was remarkably enriched in the soft palate, where long-chain α2,6-linked sialic acids predominate on the nasopharyngeal surface. Notably, presence of long-chain α2,6-linked sialic acids is conserved in ferret, pig and human soft palate. Using a loss-of-function approach with this one virus, we demonstrate that the ferret soft palate, a tissue not normally sampled in animal models of influenza, rapidly selects for transmissible influenza A viruses with human receptor (α2,6-linked sialic acids) preference.

  10. Important geosites and parks in the UNESCO World Heritage Site of the Dolomites

    Energy Technology Data Exchange (ETDEWEB)

    Nossing, L.; Forti, S.

    2016-10-01

    In the geological complexity of the south Tyrol, the Dolomites play a fundamental role, as they are now included in the UNESCO World Heritage (2009) because of their exceptional beauty and unique landscape, together with numerous scientific discoveries. The name of Dolomite comes from the famous mineral dolomite (double calcium magnesium carbonate) discovered by Déodat De Dolomieu in 1789. The dolomitic rocks constitute a large area of the Triassic mountains and many studies have contributed to the discovery of the fundamental stratotypes for the signature of the Permian/Triassic boundary. The steep walls of the Permian volcanic formations and the Sciliar Mountain have always been a great attraction for scientists from all over the world to study the open book of nature in the Dolomites. We will illustrate three sites: 1. The Bula Geotrail. A geological trail through one of the best-preserved sedimentary series in which we can observe one of the most important stratotypes to touch the Permian/Triassic boundary. 2. The Siusi-Alpe di Siusi Geological Trail. This trail starts just above the Permian/Triassic boundary and is characterized by some unique basaltic columnar formations and other significant outcrops of Lower and Medium Triassic. 3. The Bletterbach Geopark. In this sequence the stratotype, which represents the boundary, is a dark coloured continuous layer (organic matter) 5cm thick, and contains some paleobotanical evidence which is unique in the world. The preservation and added value of the natural and geological patrimony of a region through guided and documented trails are at the origin of a new kind of tourism: geotourism. The modern tourist is more and more interested and stimulated by getting to knowing nature in depth. The trails are the best instruments for scientific divulgation and education, allowing a better understanding of the landscape and stimulating new discoveries. (Author)

  11. The importance of environmental quality and catch potential to fishing site selection by freshwater anglers in Mississippi

    Science.gov (United States)

    Schramm, H.L.; Gerard, P.D.; Gill, D.A.

    2003-01-01

    We measured the importance of 24 fishing site attributes to Mississippi freshwater anglers. Factor analysis identified four multiattribute factors as important in the selection of fishing location: CLEAN ENVIRONMENT CATCH, COST AND HARVEST and AMENITIES AND SAFETY. In general, the importance of site selection factors differed little among anglers grouped by preferred type of fish, preferred fishing location (lakes and reservoirs, rivers and streams, ponds, or reservoir tailwaters), usual manner of fishing (engine-powered boat, nonpowered boat, or shore), or change in fishing frequency. COST AND HARVEST was more important to anglers with high harvest orientations. We found low correlations between site selection factor importance scores and angler age, fishing frequency, fishing expenditures, or fishing motivation factors. We suggest that the general lack of differences in site selection factors among angler groups indicates that management strategies to improve fishing site attributes should benefit all angler groups. Clean fishing environments and awareness of the availability of desired sport fishes were "very" or "extremely" important to fishing site selection by more than 70% of Mississippi freshwater anglers and should be priority management objectives.

  12. Energy benchmarking in wastewater treatment plants: the importance of site operation and layout.

    Science.gov (United States)

    Belloir, C; Stanford, C; Soares, A

    2015-01-01

    Energy benchmarking is a powerful tool in the optimization of wastewater treatment plants (WWTPs) in helping to reduce costs and greenhouse gas emissions. Traditionally, energy benchmarking methods focused solely on reporting electricity consumption, however, recent developments in this area have led to the inclusion of other types of energy, including electrical, manual, chemical and mechanical consumptions that can be expressed in kWh/m3. In this study, two full-scale WWTPs were benchmarked, both incorporated preliminary, secondary (oxidation ditch) and tertiary treatment processes, Site 1 also had an additional primary treatment step. The results indicated that Site 1 required 2.32 kWh/m3 against 0.98 kWh/m3 for Site 2. Aeration presented the highest energy consumption for both sites with 2.08 kWh/m3 required for Site 1 and 0.91 kWh/m3 in Site 2. The mechanical energy represented the second biggest consumption for Site 1 (9%, 0.212 kWh/m3) and chemical input was significant in Site 2 (4.1%, 0.026 kWh/m3). The analysis of the results indicated that Site 2 could be optimized by constructing a primary settling tank that would reduce the biochemical oxygen demand, total suspended solids and NH4 loads to the oxidation ditch by 55%, 75% and 12%, respectively, and at the same time reduce the aeration requirements by 49%. This study demonstrated that the effectiveness of the energy benchmarking exercise in identifying the highest energy-consuming assets, nevertheless it points out the need to develop a holistic overview of the WWTP and the need to include parameters such as effluent quality, site operation and plant layout to allow adequate benchmarking.

  13. Site-to-site interdomain communication may mediate different loss-of-function mechanisms in a cancer-associated NQO1 polymorphism

    Science.gov (United States)

    Medina-Carmona, Encarnación; Neira, Jose L.; Salido, Eduardo; Fuchs, Julian E.; Palomino-Morales, Rogelio; Timson, David J.; Pey, Angel L.

    2017-01-01

    Disease associated genetic variations often cause intracellular enzyme inactivation, dysregulation and instability. However, allosteric communication of mutational effects to distant functional sites leading to loss-of-function remains poorly understood. We characterize here interdomain site-to-site communication by which a common cancer-associated single nucleotide polymorphism (c.C609T/p.P187S) reduces the activity and stability in vivo of NAD(P)H:quinone oxidoreductase 1 (NQO1). NQO1 is a FAD-dependent, two-domain multifunctional stress protein acting as a Phase II enzyme, activating cancer pro-drugs and stabilizing p53 and p73α oncosuppressors. We show that p.P187S causes structural and dynamic changes communicated to functional sites far from the mutated site, affecting the FAD binding site located at the N-terminal domain (NTD) and accelerating proteasomal degradation through dynamic effects on the C-terminal domain (CTD). Structural protein:protein interaction studies reveal that the cancer-associated polymorphism does not abolish the interaction with p73α, indicating that oncosuppressor destabilization largely mirrors the low intracellular stability of p.P187S. In conclusion, we show how a single disease associated amino acid change may allosterically perturb several functional sites in an oligomeric and multidomain protein. These results have important implications for the understanding of loss-of-function genetic diseases and the identification of novel structural hot spots as targets for pharmacological intervention. PMID:28291250

  14. Quality, Range, and Legibility in Web Sites Related to Orofacial Functions

    Directory of Open Access Journals (Sweden)

    Corrêa, Camila de Castro

    2013-09-01

    Full Text Available Introduction: Plenty of information about health is available on the Internet; however, quality and legibility are not always evaluated. Knowledge regarding orofacial functions can be considered important for the population because it allows proper stimulus, early diagnosis, and prevention of the oral myofunctional alterations during early infancy. Objective: The aim was evaluate the quality, legibility, and range of Web sites available in Brazilian Portuguese regarding the orofacial functions. Methods: Selected Web sites with information directed to parents/caregivers of babies regarding breast-feeding, feeding after 6 months, deleterious oral habits, and breathing and speech were studied. The Web sites were evaluated through the application of Flesch Reading Ease Test and aspects of the Health on the Net (HON modified code (HONCode; the range of the subjects addressed was compared with other aspects of infant development. Results: From the access of 350 pages of the Internet, 35 Web sites were selected and 315 excluded because they did not meet the inclusion criteria. In relation to legibility, Web sites scored an average of 61.23% in the Flesch Test, and the application of the modified HONCode showed an average of 6.43 points; an average of 2.49 subjects were found per Web site evaluated, with information on breast-feeding being more frequent and subjects such as breathing and speech less frequent. Conclusions: Web sites that deal with orofacial functions presented standard legibility classification. Only half of the ethical principles were considered by the modified HONCode in their majority, and most addressed subjects after “breast-feeding” were presented with restricted range.

  15. Tailoring biocontrol to maximize top-down effects: on the importance of underlying site fertility.

    Science.gov (United States)

    Hovick, Stephen M; Carson, Walter P

    2015-01-01

    The degree to which biocontrol agents impact invasive plants varies widely across landscapes, often for unknown reasons. Understanding this variability can help optimize invasive species management while also informing our understanding of trophic linkages. To address these issues, we tested three hypotheses with contrasting predictions regarding the likelihood of biocontrol success. (1) The biocontrol effort hypothesis: invasive populations are regulated primarily by top-down effects, predicting that increased biocontrol efforts alone (e.g., more individuals of a given biocontrol agent or more time since agent release) will enhance biocontrol success. (2) The relative fertility hypothesis: invasive populations are regulated primarily by bottom-up effects, predicting that nutrient enrichment will increase dominance by invasives and thus reduce biocontrol success, regardless of biocontrol efforts. (3) The fertility-dependent biocontrol effort hypothesis: top-down effects will only regulate invasive populations if bottom-up effects are weak. It predicts that greater biocontrol efforts will increase biocontrol success, but only in low-nutrient sites. To test these hypotheses, we surveyed 46 sites across three states with prior releases of Galerucella beetles, the most common biocontrol agents used against invasive purple loosestrife (Lythrum salicaria). We found strong support for the fertility-dependent biocontrol effort hypothesis, as biocontrol success occurred most often with greater biocontrol efforts, but only in low-fertility sites. This result held for early stage metrics of biocontrol success (higher Galerucella abundance) and ultimate biocontrol outcomes (decreased loosestrife plant size and abundance). Presence of the invasive grass Phalaris arundinacea was also inversely related to loosestrife abundance, suggesting that biocontrol-based reductions in loosestrife made secondary invasion by P. arundinacea more likely. Our data suggest that low-nutrient sites

  16. Identification of functionally important TonB-ExbD periplasmic domain interactions in vivo.

    Science.gov (United States)

    Ollis, Anne A; Postle, Kathleen

    2012-06-01

    In gram-negative bacteria, the cytoplasmic membrane proton-motive force energizes the active transport of TonB-dependent ligands through outer membrane TonB-gated transporters. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD couple the proton-motive force to conformational changes in TonB, which are hypothesized to form the basis of energy transduction through direct contact with the transporters. While the role of ExbB is not well understood, contact between periplasmic domains of TonB and ExbD is required, with the conformational response of TonB to presence or absence of proton motive force being modulated through ExbD. A region (residues 92 to 121) within the ExbD periplasmic domain was previously identified as being important for TonB interaction. Here, the specific sites of periplasmic domain interactions between that region and the TonB carboxy terminus were identified by examining 270 combinations of 45 TonB and 6 ExbD individual cysteine substitutions for disulfide-linked heterodimer formation. ExbD residues A92C, K97C, and T109C interacted with multiple TonB substitutions in four regions of the TonB carboxy terminus. Two regions were on each side of the TonB residues known to interact with the TonB box of TonB-gated transporters, suggesting that ExbD positions TonB for correct interaction at that site. A third region contained a functionally important glycine residue, and the fourth region involved a highly conserved predicted amphipathic helix. Three ExbD substitutions, F103C, L115C, and T121C, were nonreactive with any TonB cysteine substitutions. ExbD D25, a candidate to be on a proton translocation pathway, was important to support efficient TonB-ExbD heterodimerization at these specific regions.

  17. Site or Size of Waist Circumference, Which one is More important in Metabolic Syndrome?

    OpenAIRE

    Syed Mohd Razi; Gutch Manish; Gupta Kumar Keshav; Kumar Sukriti; Abhinav Gupta

    2016-01-01

    Abdominal obesity is one of the pivotal factors in defining the metabolic syndrome. Abdominal obesity is assessed by the various clinical surrogates among which waist circumference is considered to be simple, inexpensive & sensitive tool. But various controversies surround the exact cut offs and the ideal sites of waist circumference measurement, so in this review we discussed these issues.

  18. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  19. Conserved functional motifs and homology modelling to predict hidden moonlighting functional sites

    Directory of Open Access Journals (Sweden)

    Helen R Irving

    2015-06-01

    Full Text Available Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here we review how hidden moonlighting functional centers which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico which in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  20. Not on my block you don't - facilities siting and the strategic importance of compensation

    Energy Technology Data Exchange (ETDEWEB)

    O' Hare, M.

    1977-03-01

    An important failing of current practice in siting locally noxious facilities is the strategic problem which results from failure to pay compensation to neighbors who suffer costs (loss in property values or less measurable amenity costs) not found to be a taking under law. Unless such compensation is paid, socially beneficial projects will be blocked or stalled on each possible site, thus failing entirely. If local costs are compensated, choosing the right amount to pay is more important than accurately estimating (uncompensated) social costs for purposes of cost-benefit analysis. Auctioning facilities (for presumable negative prices - compensation) among communities effects correct compensation and overcomes important strategic, efficiency, and equity problems in the siting process; some feasible ways to conduct such auctions are outlined and reviewed.

  1. The importance of previous fracture site on osteoporosis diagnosis and incident fractures in women.

    Science.gov (United States)

    Morin, Suzanne N; Lix, Lisa M; Leslie, William D

    2014-07-01

    Previous fracture increases the risk of subsequent fractures regardless of the site of the initial fracture. Fracture risk assessment tools have been developed to guide clinical management; however, no discrimination is made as to the site of the prior fracture. Our objective was to determine which sites of previous nontraumatic fractures are most strongly associated with a diagnosis of osteoporosis, defined by a bone mineral density (BMD) T-score of ≤ -2.5 at the femoral neck, and an incident major osteoporotic fracture. Using administrative health databases, we conducted a retrospective historical cohort study of 39,991 women age 45 years and older who had BMD testing with dual-energy X-ray absorptiometry (DXA). Logistic regression and Cox proportional multivariate models were used to test the association of previous fracture site with risk of osteoporosis and incident fractures. Clinical fractures at the following sites were strongly and independently associated with higher risk of an osteoporotic femoral neck T-score after adjustment for age: hip (odds ratio [OR], 3.58; 95% confidence interval [CI], 3.04-4.21), pelvis (OR, 2.23; 95% CI, 1.66-3.0), spine (OR, 2.16; 95% CI, 1.77-2.62), and humerus (OR, 1.74; 95% CI, 1.49-2.02). Cox proportional hazards models, with adjustment for age and femoral neck BMD, showed the greatest increase in risk for a major osteoporotic fracture for women who had sustained previous fractures of the spine (hazard ratio [HR], 2.08; 95% CI, 1.72-2.53), humerus (HR, 1.70; 95% CI, 1.44-2.01), patella (HR, 1.54; 95% CI, 1.10-2.18), and pelvis (HR, 1.45; 95% CI, 1.04-2.02). In summary, our results confirm that nontraumatic fractures in women are associated with osteoporosis at the femoral neck and that the site of previous fracture impacts on future osteoporotic fracture risk, independent of BMD.

  2. The Ironbridge Gorge Heritage Site and its local and regional functions

    Directory of Open Access Journals (Sweden)

    Cudny Waldemar

    2017-06-01

    Full Text Available The article is devoted to the issue of heritage and its functions. Based on the existing literature, the author presents the definition of heritage, the classification of heritage resources, and its most important impacts. The aim of the article was to show the functions that may be performed by a heritage site, locally and regionally. The example used by the author is the Ironbridge Gorge Heritage Site in the United Kingdom. Most heritage functions described by other authors are confirmed in this case study. The cultural heritage of the Ironbridge Gorge creates an opportunity to undertake various local and regional activities, having first of all an educational influence on the inhabitants, school youth and tourists. We must not ignore the economicinfluences, such as financing the activity of the Ironbridge Trust (the institution administering the site, generating income for local firms providing service to tourists, or for construction companies. This income helps to preserve and conserve the tangible heritage of the Ironbridge Gorge, as well as to generate jobs in heritage management, conservation and heritage tourism. Other effects of the Ironbridge Gorge Site include a socio-cultural impact or that related to sustainable development.

  3. Prediction of biological functions on glycosylation site migrations in human influenza H1N1 viruses.

    Science.gov (United States)

    Sun, Shisheng; Wang, Qinzhe; Zhao, Fei; Chen, Wentian; Li, Zheng

    2012-01-01

    Protein glycosylation alteration is typically employed by various viruses for escaping immune pressures from their hosts. Our previous work had shown that not only the increase of glycosylation sites (glycosites) numbers, but also glycosite migration might be involved in the evolution of human seasonal influenza H1N1 viruses. More importantly, glycosite migration was likely a more effectively alteration way for the host adaption of human influenza H1N1 viruses. In this study, we provided more bioinformatics and statistic evidences for further predicting the significant biological functions of glycosite migration in the host adaptation of human influenza H1N1 viruses, by employing homology modeling and in silico protein glycosylation of representative HA and NA proteins as well as amino acid variability analysis at antigenic sites of HA and NA. The results showed that glycosite migrations in human influenza viruses have at least five possible functions: to more effectively mask the antigenic sites, to more effectively protect the enzymatic cleavage sites of neuraminidase (NA), to stabilize the polymeric structures, to regulate the receptor binding and catalytic activities and to balance the binding activity of hemagglutinin (HA) with the release activity of NA. The information here can provide some constructive suggestions for the function research related to protein glycosylation of influenza viruses, although these predictions still need to be supported by experimental data.

  4. Functional identification of catalytic metal ion binding sites within RNA.

    Directory of Open Access Journals (Sweden)

    James L Hougland

    2005-09-01

    Full Text Available The viability of living systems depends inextricably on enzymes that catalyze phosphoryl transfer reactions. For many enzymes in this class, including several ribozymes, divalent metal ions serve as obligate cofactors. Understanding how metal ions mediate catalysis requires elucidation of metal ion interactions with both the enzyme and the substrate(s. In the Tetrahymena group I intron, previous work using atomic mutagenesis and quantitative analysis of metal ion rescue behavior identified three metal ions (MA, MB, and MC that make five interactions with the ribozyme substrates in the reaction's transition state. Here, we combine substrate atomic mutagenesis with site-specific phosphorothioate substitutions in the ribozyme backbone to develop a powerful, general strategy for defining the ligands of catalytic metal ions within RNA. In applying this strategy to the Tetrahymena group I intron, we have identified the pro-SP phosphoryl oxygen at nucleotide C262 as a ribozyme ligand for MC. Our findings establish a direct connection between the ribozyme core and the functionally defined model of the chemical transition state, thereby extending the known set of transition-state interactions and providing information critical for the application of the recent group I intron crystallographic structures to the understanding of catalysis.

  5. The importance of relationship closeness expectations in brand-page communication in social networking sites

    OpenAIRE

    Frias, Rui Alberto Móia Praça

    2013-01-01

    While there is extensive research regarding the way users in social networking sites (SNSs) connect and communicate with each other, literature on consumer-brand relationships in SNSs is scarce. This paper hypothesizes and tests the impact of varying the source of communication in Facebook brand pages on key characteristics of brand equity, examining whether this impact is conditioned by relationship closeness expectations. More specifically, two experiments assess how relationship closeness ...

  6. Safety leadership at construction sites: the importance of rule-oriented and participative leadership.

    Science.gov (United States)

    Grill, Martin; Pousette, Anders; Nielsen, Kent; Grytnes, Regine; Törner, Marianne

    2017-07-01

    Objectives The construction industry accounted for >20% of all fatal occupational accidents in Europe in 2014. Leadership is an essential antecedent to occupational safety. The aim of the present study was to assess the influence of transformational, active transactional, rule-oriented, participative, and laissez-faire leadership on safety climate, safety behavior, and accidents in the Swedish and Danish construction industry. Sweden and Denmark are similar countries but have a large difference in occupational accidents rates. Methods A questionnaire study was conducted among a random sample of construction workers in both countries: 811 construction workers from 85 sites responded, resulting in site and individual response rates of 73% and 64%, respectively. Results The results indicated that transformational, active transactional, rule-oriented and participative leadership predict positive safety outcomes, and laissez-faire leadership predict negative safety outcomes. For example, rule-oriented leadership predicts a superior safety climate (β=0.40, Pconstruction industry, which may partly explain the difference in occupational accident rates. Conclusions Applying less laissez-faire leadership and more transformational, active transactional, participative and rule-oriented leadership appears to be an effective way for construction site managers to improve occupational safety in the industry.

  7. The Importance of Safety in Construction Sector: Costs of Occupational Accidents in Construction Sites

    OpenAIRE

    Fatih Yılmaz; Uğur Buğra Çelebi

    2015-01-01

    Occupational accidents cause important social and economic problems by loss of life and physical injuries. Construction sector involves high risk due to its production processes and labor intensive characteristic and because of occupational accidents the sector brings up against financial loss in large scale. In developing countries, construction sector is one of the most important sectors that have a great contribution to economic development with its employment capacity and added-value t...

  8. Methods for studying seed dispersal and its importance for colonization of new sites

    OpenAIRE

    Vlasta, Tomáš

    2015-01-01

    Study of seed dispersal is crucial for understanding of several processes in life of plants and landscape. Seed dispesal is very important for persistence of local populations in fragmented landscape, it plays an important role in succession, it helps to protect plant populations againts loss of genetic variability. We usually recognize several types of seed dispersal depending on vector (dispersal by wind, animals and water.) In nature, it is very common that seed can be independently disper...

  9. The vital importance of GIS : a workshop in project siting and development

    Energy Technology Data Exchange (ETDEWEB)

    Warner, D. [Ortech International, Mississauga, ON (Canada); EDF Energies Nouvelles, Nanterre (France)

    2010-07-01

    Geographic information system (GIS) technology is now being used by wind energy developers who are required to consider and accommodate a wide variety of environmental and social considerations. This poster presentation discussed some of the new features available in current GIS technologies. High resolution imagery from satellites is being used to verify the accuracy of collected spatial data, as well as to investigate potential locations for meteorological towers, turbine sites, and roads. Slopes are easily calculated using GIS software tools, and digital elevation data can be used with high resolution aerial photography to determine routes for new roads and to establish available sites for crane pads. The GIS tools allow developers to consider protected ecological areas, wetlands and forests, and gives them the ability to better report project development considerations at public consultations. Wind resource grid outputs can also be projected using GIS software. The ability to combine all available information on a single map can assist landowners, stakeholders, and investors in understanding the scope and potential impacts of wind power projects. tabs., figs.

  10. Regional chemical setting of the Apollo 16 landing site and the importance of the Kant Plateau

    Science.gov (United States)

    Andre, C. G.; El-Baz, F.

    1982-01-01

    Orbital X-ray data from the Apollo 16 region indicate that physiographic units identified before the lunar mission can be classified as chemical units as well. The Descartes Mountains, however, appear to be an extension of the Kant Plateau composition that is unusually anorthositic and resembles farside terra. The Cayley Plains have closer affinities to basaltic materials than terra materials, physically, spectrally and chemically. The Theophilus impact, 330 km east of the landing site, excavated magnesium-rich basalts from below less-magnesian flows in Mare Nectaris; but, mafic ejecta was substantially blocked from the Apollo 16 site by the Kant Plateau that rises 5 km above the level of the mare. Apollo 16 soil samples from stations selected to collect either Descartes Mountains material or Cayley Plains material were surprisingly similar. However, they do, indeed, show the chemical trends indicative of the two units as defined by the orbiting geochemistry detectors. The Kant Plateau and Descartes Mountains material may be among the rare nearside examples of a plagioclase-rich cumulate of the primordial magma ocean.

  11. Towards a risk map of malaria for Sri Lanka: the importance of house location relative to vector breeding sites

    DEFF Research Database (Denmark)

    Van Der Hoek, Wim; Konradsen, Flemming; Amerasinghe, Priyanie H

    2003-01-01

    collections. RESULTS: People living within 750 m of the local stream, which was the established vector-breeding site, were at much higher risk for malaria than people living further away (odds ratio adjusted for confounding by other variables 5.93, 95% CI: 3.50-8.91). Houses close to the stream also had more......BACKGROUND: In Sri Lanka, the major malaria vector Anopheles culicifacies breeds in pools formed in streams and river beds and it is likely that people living close to such breeding sites are at higher risk of malaria than people living further away. This study was done to quantify the importance...... of house location relative to vector breeding sites for the occurrence of malaria in order to assess the usefulness of this parameter in future malaria risk maps. Such risk maps could be important tools for planning efficient malaria control measures. METHODS: In a group of seven villages in north central...

  12. Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters.

    Directory of Open Access Journals (Sweden)

    Fu-Jou Lai

    Full Text Available Transcription factor binding site (TFBS identification plays an important role in deciphering gene regulatory codes. With comprehensive knowledge of TFBSs, one can understand molecular mechanisms of gene regulation. In the recent decades, various computational approaches have been proposed to predict TFBSs in the genome. The TFBS dataset of a TF generated by each algorithm is a ranked list of predicted TFBSs of that TF, where top ranked TFBSs are statistically significant ones. However, whether these statistically significant TFBSs are functional (i.e. biologically relevant is still unknown. Here we develop a post-processor, called the functional propensity calculator (FPC, to assign a functional propensity to each TFBS in the existing computationally predicted TFBS datasets. It is known that functional TFBSs reveal strong positional preference towards the transcriptional start site (TSS. This motivates us to take TFBS position relative to the TSS as the key idea in building our FPC. Based on our calculated functional propensities, the TFBSs of a TF in the original TFBS dataset could be reordered, where top ranked TFBSs are now the ones with high functional propensities. To validate the biological significance of our results, we perform three published statistical tests to assess the enrichment of Gene Ontology (GO terms, the enrichment of physical protein-protein interactions, and the tendency of being co-expressed. The top ranked TFBSs in our reordered TFBS dataset outperform the top ranked TFBSs in the original TFBS dataset, justifying the effectiveness of our post-processor in extracting functional TFBSs from the original TFBS dataset. More importantly, assigning functional propensities to putative TFBSs enables biologists to easily identify which TFBSs in the promoter of interest are likely to be biologically relevant and are good candidates to do further detailed experimental investigation. The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/.

  13. Are Synonymous Sites in Primates and Rodents Functionally Constrained?

    Science.gov (United States)

    Price, Nicholas; Graur, Dan

    2016-01-01

    It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.

  14. Parallel sites implicate functional convergence of the hearing gene prestin among echolocating mammals.

    Science.gov (United States)

    Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Ren, Hai-Qing; Shi, Peng

    2014-09-01

    Echolocation is a sensory system whereby certain mammals navigate and forage using sound waves, usually in environments where visibility is limited. Curiously, echolocation has evolved independently in bats and whales, which occupy entirely different environments. Based on this phenotypic convergence, recent studies identified several echolocation-related genes with parallel sites at the protein sequence level among different echolocating mammals, and among these, prestin seems the most promising. Although previous studies analyzed the evolutionary mechanism of prestin, the functional roles of the parallel sites in the evolution of mammalian echolocation are not clear. By functional assays, we show that a key parameter of prestin function, 1/α, is increased in all echolocating mammals and that the N7T parallel substitution accounted for this functional convergence. Moreover, another parameter, V1/2, was shifted toward the depolarization direction in a toothed whale, the bottlenose dolphin (Tursiops truncatus) and a constant-frequency (CF) bat, the Stoliczka's trident bat (Aselliscus stoliczkanus). The parallel site of I384T between toothed whales and CF bats was responsible for this functional convergence. Furthermore, the two parameters (1/α and V1/2) were correlated with mammalian high-frequency hearing, suggesting that the convergent changes of the prestin function in echolocating mammals may play important roles in mammalian echolocation. To our knowledge, these findings present the functional patterns of echolocation-related genes in echolocating mammals for the first time and rigorously demonstrate adaptive parallel evolution at the protein sequence level, paving the way to insights into the molecular mechanism underlying mammalian echolocation. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. In Vivo Phosphorylation Site Mapping and Functional Characterization of Arabidopsis Phototropin 1

    Institute of Scientific and Technical Information of China (English)

    Stuart Sullivan; Catriona E. Thomson; Douglas J.Lamont; Matthew A. Jones; John M.Christie

    2008-01-01

    Phototropins (phot1 and phot2) are blue-light receptor kinases controlling a range of responses that optimize the photosynthetic efficiency of plants. Light sensing is mediated by two flavin-binding motifs, known as LOV1 and LOV2,located within the N-terminal region of the protein. Photoexcitation via LOV2 leads to activation of the C-terminal kinase domain and consequently receptor autophosphorylation. However, knowledge of the in-vivo phosphorylation sites for Arabidopsis phototropins is lacking and has impeded progress in elucidating the functional significance of receptor phosphorylation. We have purified phot1 from Arabidopsis and identified the in-vivo sites of receptor phosphorylation by liquid chromatography tandem mass spectrometry. Arabidopsis-derived phot1 binds flavin mononucleotide as chromophore and is phosphorylated at four major sites located upstream of LOV2 (Ser58, Ser85, Ser350, and Ser410), three of which are induced by blue light. Nevertheless, structure-function analysis indicates that the biological activity of phot1 can be attributed to a modular unit comprising the LOV2-kinase region of the protein. Thus, peptide regions upstream of LOV2, including the sites of receptor phosphorylation identified here, do not appear to be important for receptor signaling. By contrast, these regions may be necessary for maximizing stomatal performance and possibly light-induced relocalization of phot1.

  16. Imported Items Found at the Uvek Site (Accidental Finds Kept at the Saratov Regional Museum of Local Lore

    Directory of Open Access Journals (Sweden)

    Kubankin Dmitriy A.

    2013-12-01

    Full Text Available A collection of 396 imported items found on the Uvek fortified settlement site as accidental discoveries is discussed in the article. Among them, the majority of ceramic products are mostly ceremonial utensils. Mirrors, jewelry, glass and metal vessels are also represented. Most finds relevant to external imports come from Iran, Byzantium, Trebizond, the Mamluk State, China and Central Asia (with the exception of Khwarezm. Domestic import is dominated by products from South-Eastern Crimea, Khwarezm and the Lower Volga area. The peak of trade routes development is dated by the period from the 1270s through to the 1330s.

  17. The Functionality of Facial Appearance and Its Importance to a Korean Population

    Directory of Open Access Journals (Sweden)

    Young Jun Kim

    2013-11-01

    Full Text Available BackgroundMany people have an interest in the correction of facial scars or deformities caused by trauma. The increasing ability to correct such flaws has been one of the reasons for the increase in the popularity of facial plastic surgery. In addition to its roles in communication, breathing, eating, olfaction and vision, the appearance of the face also plays an important role in human interactions, including during social activities. However, studies on the importance of the functional role of facial appearance. As a function of the face are scare. Therefore, in the present study, we evaluated the importance of the functions of the face in Korea.MethodsWe conducted an online panel survey of 300 participants (age range, 20-70 years. Each respondent was administered the demographic data form, Facial Function Assessment Scale, Rosenberg Self-Esteem Scale, and standard gamble questionnaires.ResultsIn the evaluation on the importance of facial functions, a normal appearance was considered as important as communication, breathing, speech, and vision. Of the 300 participants, 85% stated that a normal appearance is important in social activities.ConclusionsThe results of this survey involving a cross-section of the Korean population indicated that a normal appearance was considered one of the principal facial functions. A normal appearance was considered more important than the functions of olfaction and expression. Moreover, a normal appearance was determined to be an important facial function for leading a normal life in Korea.

  18. Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation.

    Science.gov (United States)

    Smith, Steven D; Bridou, Romain; Johs, Alexander; Parks, Jerry M; Elias, Dwayne A; Hurt, Richard A; Brown, Steven D; Podar, Mircea; Wall, Judy D

    2015-05-01

    Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative "cap helix" region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.

  19. Dynamics of a recovering Arctic bird population: the importance of climate, density dependence, and site quality.

    Science.gov (United States)

    Bruggeman, Jason E; Swem, Ted; Andersen, David E; Kennedy, Patricia L; Nigro, Debora

    2015-10-01

    indicative of higher-quality habitat), are a priority for continued protection from potential nearby development and disturbance to minimize population-level impacts. Climate change. may affect Arctic peregrines in multiple ways, including through access to more snow-free nest sites and a lengthened breeding season that may increase likelihood of nest success. Our work provides insight into factors affecting a population during and after recovery, and demonstrates how the Dail-Madsen model can be used for any unmarked population with multiple years of abundance data collected through repeated surveys.

  20. Facilitating Structure-Function Studies of CFTR Modulator Sites with Efficiencies in Mutagenesis and Functional Screening.

    Science.gov (United States)

    Molinski, Steven V; Ahmadi, Saumel; Hung, Maurita; Bear, Christine E

    2015-12-01

    There are nearly 2000 mutations in the CFTR gene associated with cystic fibrosis disease, and to date, the only approved drug, Kalydeco, has been effective in rescuing the functional expression of a small subset of these mutant proteins with defects in channel activation. However, there is currently an urgent need to assess other mutations for possible rescue by Kalydeco, and further, definition of the binding site of such modulators on CFTR would enhance our understanding of the mechanism of action of such therapeutics. Here, we describe a simple and rapid one-step PCR-based site-directed mutagenesis method to generate mutations in the CFTR gene. This method was used to generate CFTR mutants bearing deletions (p.Gln2_Trp846del, p.Ser700_Asp835del, p.Ile1234_Arg1239del) and truncation with polyhistidine tag insertion (p.Glu1172-3Gly-6-His*), which either recapitulate a disease phenotype or render tools for modulator binding site identification, with subsequent evaluation of drug responses using a high-throughput (384-well) membrane potential-sensitive fluorescence assay of CFTR channel activity within a 1 wk time frame. This proof-of-concept study shows that these methods enable rapid and quantitative comparison of multiple CFTR mutants to emerging drugs, facilitating future large-scale efforts to stratify mutants according to their "theratype" or most promising targeted therapy.

  1. The importance of species identity and interactions for multifunctionality depends on how ecosystem functions are valued.

    Science.gov (United States)

    Slade, Eleanor M; Kirwan, Laura; Bell, Thomas; Philipson, Christopher D; Lewis, Owen T; Roslin, Tomas

    2017-10-01

    Studies investigating how biodiversity affects ecosystem functioning increasingly focus on multiple functions measured simultaneously ("multifunctionality"). However, few such studies assess the role of species interactions, particularly under alternative environmental scenarios, despite interactions being key to ecosystem functioning. Here we address five questions of central importance to ecosystem multifunctionality using a terrestrial animal system. (1) Does the contribution of individual species differ for different ecosystem functions? (2) Do inter-species interactions affect the delivery of single functions and multiple functions? (3) Does the community composition that maximizes individual functions also maximize multifunctionality? (4) Is the functional role of individual species, and the effect of interspecific interactions, modified by changing environmental conditions? (5) How do these roles and interactions change under varying scenarios where ecosystem services are weighted to reflect different societal preferences? We manipulated species' relative abundance in dung beetle communities and measured 16 functions contributing to dung decomposition, plant productivity, nutrient recycling, reduction of greenhouse gases, and microbial activity. Using the multivariate diversity-interactions framework, we assessed how changes in species identity, composition, and interspecific interactions affected these functions in combination with an environmental driver (increased precipitation). This allowed us to identify key species and interactions across multiple functions. We then developed a desirability function approach to examine how individual species and species mixtures contribute to a desired state of overall ecosystem functioning. Species contributed unequally to individual functions, and to multifunctionality, and individual functions were maximized by different community compositions. Moreover, the species and interactions important for maintaining

  2. Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site.

    Directory of Open Access Journals (Sweden)

    Yuval Tabach

    Full Text Available BACKGROUND: Transcription factors (TF regulate expression by binding to specific DNA sequences. A binding event is functional when it affects gene expression. Functionality of a binding site is reflected in conservation of the binding sequence during evolution and in over represented binding in gene groups with coherent biological functions. Functionality is governed by several parameters such as the TF-DNA binding strength, distance of the binding site from the transcription start site (TSS, DNA packing, and more. Understanding how these parameters control functionality of different TFs in different biological contexts is a must for identifying functional TF binding sites and for understanding regulation of transcription. METHODOLOGY/PRINCIPAL FINDINGS: We introduce a novel method to screen the promoters of a set of genes with shared biological function (obtained from the functional Gene Ontology (GO classification against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. More than 8,000 human (and 23,000 mouse genes, were assigned to one of 134 GO sets. Their promoters were searched (from 200 bp downstream to 1,000 bp upstream the TSS for 414 known DNA motifs. We optimized the sequence similarity score threshold, independently for every location window, taking into account nucleotide heterogeneity along the promoters of the target genes. The method, combined with binding sequence and location conservation between human and mouse, identifies with high probability functional binding sites for groups of functionally-related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were tested experimentally. CONCLUSIONS/SIGNIFICANCE: We identified reliably functional TF binding sites. This is an essential step towards constructing regulatory networks. The promoter region proximal to the TSS is of central

  3. Aspartic acid 413 is important for the normal allosteric functioning of ADP-glucose pyrophosphorylase

    Energy Technology Data Exchange (ETDEWEB)

    Greene, T.W.; Woodbury, R.L.; Okita, T.W. [Washington State Univ., Pullman, WA (United States)

    1996-11-01

    As part of a structure-function analysis of the higher-plant ADP-glucose pyrophosphorylase (AGP), we used a random mutagenesis approach in combination with a novel bacterial complementation system to isolate over 100 mutants that were defective in glycogen production. One mutant of the large subunit M27 was identified by its capacity to only partially complement a mutation in the structural gene for the bacterial AGP (glg C), as determined by its light-staining phenotype when cells were exposed to I{sub 2} vapors. Enzyme-linked immunosorbent assay and enzymatic pyrophosphorylysis assays of M27 cell extracts showed that the level of expression and AGP activity was comparable to those of cells that expressed the wildtype recombinant enzyme. Kinetic analysis indicated that the M27 AGP displays normal Michaelis constant values for the substrates glucose-1-phosphate and ATP but requires 6- to 10-fold greater levels of 3-phosphoglycerate (3-PGA) than the wild-type recombinant enzyme for maximum activation. DNA sequence analysis showed that M27 contains a single point mutation that resulted in the replacement of aspartic acid 413 to alanine. Substitution of a lysine residue at this site almost completely abolished activation by 3-PGA. Aspartic acid 413 is adjacent to a lysine residue that was previously identified by chemical modification studies to be important in the binding of 3-PGA. The kinetic properties of M27 corroborate the importance of this region in the allosteric regulation of a higher-plant AGP. 28 refs., 3 figs., 1 tab.

  4. Aspartic acid 413 is important for the normal allosteric functioning of ADP-glucose pyrophosphorylase.

    Science.gov (United States)

    Greene, T W; Woodbury, R L; Okita, T W

    1996-01-01

    As part of a structure-function analysis of the higher-plant ADP-glucose pyrophosphorylase (AGP), we used a random mutagenesis approach in combination with a novel bacterial complementation system to isolate over 100 mutants that were defective in glycogen production (T.W. Greene, S.E. Chantler, M.L. Khan, G.F. Barry, J. Preiss, T.W. Okita [1996] Proc Natl Acad Sci USA 93: 1509-1513). One mutant of the large subunit M27 was identified by its capacity to only partially complement a mutation in the structural gene for the bacterial AGP (glg C), as determined by its light-staining phenotype when cells were exposed to l3 vapors. Enzyme-linked immunosorbent assay and enzymatic pyrophosphorylysis assays of M27 cell extracts showed that the level of expression and AGP activity was comparable to those of cells that expressed the wild-type recombinant enzyme. Kinetic analysis indicated that the M27 AGP displays normal Michaelis constant values for the substrates glucose-1-phosphate and ATP but requires 6- to 10-fold greater levels of 3-phosphoglycerate (3-PGA) than the wild-type recombinant enzyme for maximum activation. DNA sequence analysis showed that M27 contains a single point mutation that resulted in the replacement of aspartic acid 413 to alanine. Substitution of a lysine residue at this site almost completely abolished activation by 3-PGA. Aspartic acid 413 is adjacent to a lysine residue that was previously identified by chemical modification studies to be important in the binding of 3-PGA (K. Ball, J. Preiss [1994] J Biol Chem 269: 24706-24711). The kinetic properties of M27 corroborate the importance of this region in the allosteric regulation of a higher-plant AGP. PMID:8938421

  5. Logic minimization and rule extraction for identification of functional sites in molecular sequences

    Directory of Open Access Journals (Sweden)

    Cruz-Cano Raul

    2012-08-01

    Full Text Available Abstract Background Logic minimization is the application of algebraic axioms to a binary dataset with the purpose of reducing the number of digital variables and/or rules needed to express it. Although logic minimization techniques have been applied to bioinformatics datasets before, they have not been used in classification and rule discovery problems. In this paper, we propose a method based on logic minimization to extract predictive rules for two bioinformatics problems involving the identification of functional sites in molecular sequences: transcription factor binding sites (TFBS in DNA and O-glycosylation sites in proteins. TFBS are important in various developmental processes and glycosylation is a posttranslational modification critical to protein functions. Methods In the present study, we first transformed the original biological dataset into a suitable binary form. Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset. These rules were used to predict TFBS and O-glycosylation sites. The TFBS dataset is obtained from the TRANSFAC database, while the glycosylation dataset was compiled using information from OGLYCBASE and the Swiss-Prot Database. We performed the same predictions using two standard classification techniques, Artificial Neural Networks (ANN and Support Vector Machines (SVM, and used their sensitivities and positive predictive values as benchmarks for the performance of our proposed algorithm. SVM were also used to reduce the number of variables included in the logic minimization approach. Results For both TFBS and O-glycosylation sites, the prediction performance of the proposed logic minimization method was generally comparable and, in some cases, superior to the standard ANN and SVM classification methods with the advantage of providing intelligible rules to describe the datasets. In TFBS prediction, logic minimization produced a very small set of simple rules. In

  6. Arabidopsis AtADF1 is Functionally Affected by Mutations on Actin Binding Sites

    Institute of Scientific and Technical Information of China (English)

    Chun-Hai Dong; Wei-Ping Tang; Jia-Yao Liu

    2013-01-01

    The plant actin depolymerizing factor (ADF) binds to both monomeric and filamentous actin,and is directly involved in the depolymerization of actin filaments.To better understand the actin binding sites of the Arabidopsis thaliana L.AtADF1,we generated mutants of AtADF1 and investigated their functions in vitro and in vivo.Analysis of mutants harboring amino acid substitutions revealed that charged residues (Arg98 and Lys100) located at the α-helix 3 and forming an actin binding site together with the N-terminus are essential for both G-and F-actin binding.The basic residues on the β-strand 5 (K82/A) and the α-helix 4 (R135/A,R137/A) form another actin binding site that is important for F-actin binding.Using transient expression of CFP-tagged AtADF1 mutant proteins in onion (Allium cepa) peel epidermal cells and transgenic Arabidopsis thaliana L.plants overexpressing these mutants,we analyzed how these mutant proteins regulate actin organization and affect seedling growth.Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional,unless the affinity foractin monomers is also affected.The G-actin binding activity of the ADF plays an essential role in actin binding,depolymerization of actin polymers,and therefore in the control of actin organization.

  7. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function

    Directory of Open Access Journals (Sweden)

    Deng W-M

    2009-02-01

    Full Text Available Abstract Background Dystroglycan (Dg is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C-terminal PPXY motif has been established as a binding site for Dystrophin (Dys WW-domain. However, our previous studies indicate that both Dystroglycan PPXY motives, WWbsI and WWbsII can bind Dystrophin protein in vitro. Results We now find that both WW binding sites are important for maintaining full Dg function in the establishment of oocyte polarity in Drosophila. If either WW binding site is mutated, the Dg protein can still be active. However, simultaneous mutations in both WW binding sites abolish the Dg activities in both overexpression and loss-of-function oocyte polarity assays in vivo. Additionally, sequence comparisons of WW binding sites in 12 species of Drosophila, as well as in humans, reveal a high level of conservation. This preservation throughout evolution supports the idea that both WW binding sites are functionally required. Conclusion Based on the obtained results we propose that the presence of the two WW binding sites in Dystroglycan secures the essential interaction between Dg and Dys and might further provide additional regulation for the cytoskeletal interactions of this complex.

  8. A new functional site W115 in CdtA is critical for Aggregatibacter actinomycetemcomitans cytolethal distending toxin.

    Directory of Open Access Journals (Sweden)

    Lu Li

    Full Text Available Aggregatibacter actinomycetemcomitans, a specific pathogen of localized aggressive periodontitis, produces a cytolethal distending toxin (CDT that arrests eukaryotic cells irreversibly in G0/G1 or G2/M phase of the cell cycle. Although structural studies show that the aromatic patch region of CdtA plays an important role in its biological activity, the functional sites of CdtA have not been firmly established. In this study, site-specific mutagenesis strategy was employed for cdtA point mutations construction so as to examine the contributions of individual amino acids to receptor binding and the biological activity of holotoxin. The binding ability was reduced in CdtA(Y181ABC holotoxin and the biological function of CDT was not weaken in CdtA(Y105ABC, CdtA(Y125ABC, CdtA(F109ABC and CdtA(S106NBC holotoxin suggesting that these sites were not critical to CDT. But the binding activity and cell cycle arrest ability of holotoxin complexes were inhibited in CdtA(W115GBC. And this site did not affect the holotoxin assembly by size exclusion chromatography. Therefore, W115 might be a critical site of CdtA binding ability. These findings suggest that the functional sites of CdtA are not only in the aromatic patch region. W115, the new functional site is critical for receptor binding and cell cycle arrest, which provides potential targets for pharmacological disruption of CDT activity.

  9. Importance of native grassland habitat for den-site selection of Indian foxes in a fragmented landscape.

    Directory of Open Access Journals (Sweden)

    Girish Arjun Punjabi

    Full Text Available Fragmentation of native habitats is now a ubiquitous phenomenon affecting wildlife at various scales. We examined selection of den-sites (n = 26 by Indian foxes (Vulpes bengalensis in a highly modified short-grassland landscape in central India (Jan-May, 2010. At the scale of the home-range, defined by an 800 m circular buffer around den sites, we examined the effect of land-cover edges and roads on selection of sites for denning using a distance-based approach. At the smaller den-area scale, defined by a 25 m x 25 m plot around den and paired available sites, the effect of microhabitat characteristics was examined using discrete-choice models. Indian foxes selected den-sites closer to native grasslands (t = -9.57, P < 0.001 and roads (t = -2.04, P = 0.05 than random at the home-range scale. At the smaller scale, abundance of rodents and higher visibility increased the odds of selection of a site by eight and four times respectively, indicating resource availability and predator avoidance to be important considerations for foxes. Indian foxes largely chose to den in human-made structures, indicated by the proportion of dens found in earthen bunds (0.69 and boulder piles (0.27 in the study area. With agricultural expansion and human modification threatening native short-grassland habitats, their conservation and effective management in human-dominated landscapes will benefit the Indian fox. The presence of some human-made structures within native grasslands would also be beneficial for this den-dependent species. We suggest future studies examine the impact of fragmentation and connectivity of grasslands on survival and reproductive success of the Indian fox.

  10. Options and Functions of the Revised IVS Combination Web Site

    Science.gov (United States)

    Messerschmitt, Linda; Bachmann, Sabine; Thaller, Daniela

    2016-12-01

    The World Wide Web is one of the most important communication and information exchange platforms today. Because of the high amount of users and the global accessibility, every business is interested in the Internet. It opens up new possibilities of international cooperation. In geodesy, this aspect of international cooperation is of prime importance.

  11. Functional mimicry of a discontinuous antigenic site by a designed synthetic peptide

    NARCIS (Netherlands)

    Villen, J.; Borras, E.; Schaaper, W.M.M.; Meloen, R.H.; Davila, M.; Domingo, E.; Giralt, E.; Andreu, D.

    2002-01-01

    Functional reproduction of the discontinuous antigenic site D of foot-and-mouth disease virus (FMDV) has been achieved by means of synthetic peptide constructions that integrate each of the three protein loops that define the antigenic site into a single molecule. The site D mimics were designed on

  12. Large-scale information entropy analysis of important sites in mature and precursor miRNA sequences

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In order to find evidence of consistent sequence conservation or the base correlation degree in miRNA,some important sites in the sequences of reported miRNA and their precursors(pre-miRNA) were investigated via information entropy analysis.Twelve different groups of sites were obtained from special locations(head,tail) in miRNAs of different sources according to taxonomy(animal,plant and virus) and then analyzed by measuring the single base information redundancy(D1(L)) and the adjacent base related information redundancy(D2(L)).The results showed that D2(L) has more information than D1(L),though D1(L) changes roughly consistently with D2(L) in each group.Viral pre-miRNAs are more conservative than those belonging to animals or plants.In addition,U is dominant in most sites compared with other nucleotides.It was also found that in the middle of several groups,there were sites where miRNAs were cut down from pre-miRNAs by Enzyme Dicer which were significantly conservative.This phenomenon shows that the conservatism is an aspect of the of miRNA and may be involved in the recognition and cutting by the Dicer.Those results provided another perspective for understanding more about the primary structure of pre-miRNA.

  13. Polymorphisms at activated protein C cleavage sites of factor V: Are they important in the absence of factor V Leiden?

    Directory of Open Access Journals (Sweden)

    Ehsan Kheradmand

    2017-01-01

    Full Text Available Background: Activated protein C (APC inactivates factor V (FV by cleavage of its heavy chain at Arg306, Arg506, Arg679, and Lys994. Mutational changes, which abolish APC cleavage sites, may predispose thrombosis by altering the inactivation process of FV. FV Leiden (FVL (Arg506Glu has been demonstrated as a strong risk factor for thrombosis. In the current study, we have studied whether mutations in the cleavage sites of FV for APC, not due to FVL, would have a role in presenting APC resistance (APCR and initiation of a cerebral thrombotic event.Methods: A group of 22 patients with a history of cerebral venous thrombosis (CVT, who were not carriers of FVL enrolled in the study. The patients who had conditions associated with acquired APCR were excluded from the study. APCR test was performed on the remaining 16 patients, which showed APCR in 4 plasma samples. DNA sequencing was performed on four exons of FV of APCR patients, encoding Arg306, Arg506, Arg679, and Lys994.Results: Mutations were not found within nucleotides encoding the cleavage sites; neither was found within their close upstream and downstream sequences.Conclusion: Our results show that polymorphisms affecting cleavage sites of FV other than Arg506Glu it would be less likely to be the basis for APCR and its increased thrombosis susceptibility. In addition, it emphasizes on the importance of screening for APCR in the patients diagnosed with CVT.

  14. Molybdenum and tungsten oxygen transferases--and functional diversity within a common active site motif.

    Science.gov (United States)

    Pushie, M Jake; Cotelesage, Julien J; George, Graham N

    2014-01-01

    Molybdenum and tungsten are the only second and third-row transition elements with a known function in living organisms. The molybdenum and tungsten enzymes show common structural features, with the metal being bound by a pyranopterin-dithiolene cofactor called molybdopterin. They catalyze a variety of oxygen transferase reactions coupled with two-electron redox chemistry in which the metal cycles between the +6 and +4 oxidation states usually with water, either product or substrate, providing the oxygen. The functional roles filled by the molybdenum and tungsten enzymes are diverse; for example, they play essential roles in microbial respiration, in the uptake of nitrogen in green plants, and in human health. Together, the enzymes form a superfamily which is among the most prevalent known, being found in all kingdoms of life. This review discusses what is known of the active site structures and the mechanisms, together with some recent insights into the evolution of these important enzyme systems.

  15. The prognostic importance of lung function in patients admitted with heart failure

    DEFF Research Database (Denmark)

    Iversen, Kasper Karmark; Kjaergaard, Jesper; Akkan, Dilek

    2010-01-01

    The purpose of the present study was to determine the prognostic importance for all-cause mortality of lung function variables obtained by spirometry in an unselected group of patients admitted with heart failure (HF).......The purpose of the present study was to determine the prognostic importance for all-cause mortality of lung function variables obtained by spirometry in an unselected group of patients admitted with heart failure (HF)....

  16. Perceived difficulty, importance, and satisfaction with physical function in COPD patients

    Directory of Open Access Journals (Sweden)

    Berry Michael J

    2004-03-01

    Full Text Available Abstract Background Research suggests that patients' satisfaction with their physical functioning (SPF is a critical component of HRQL. This study was designed to examine the extent to which perceptions of physical function and the value placed on physical function are related to satisfaction ratings. The sample consisted of older adults suffering from a progressively debilitating disease, chronic obstructive pulmonary disease (COPD. Methods During baseline assessments, COPD patients participating in a randomized controlled physical activity trial completed measures of SPF, perceived difficulty, and perceived importance. Results An ANCOVA controlling for age and gender indicated that perceived difficulty, perceived importance, and their interaction accounted for 43% of the variance in SPF. Additionally, participants were most satisfied with important tasks that they performed with little difficulty. Participants were least satisfied with important tasks that they perceived as highly difficult. Conclusion The results of the present study indicate that not being able to perform valued tasks produces discontent that is reflected in lower rating of satisfaction with physical functioning. Clearly, the significance of loss in function to individual patients is related to the importance of the functional activities that may be compromised. These data have implications for the scope of patient assessment in clinical care and for the conceptual basis of future research in the area of physical functioning.

  17. Sustainable tourism development of globally important agricultural heritage sites: a case study of "traditional rice-fish agriculture system"

    Institute of Scientific and Technical Information of China (English)

    Li Yongle; Sun Yehong; Min Qingwen; Cheng Shengkui

    2008-01-01

    Traditional rice-fish agricultural heritage site in Qingtian County, China, one of the pilot sites of Glob-ally Important Agricultural Heritage Systems (GIAHS), is of great value in tourism development. This paper aims to explore how to realize sustainable tourism development in agricultural heritage site through identifying current problems in GIAHS site, and making constructive recommendations for coupled development of heritage preserva-tion and economic development. Field survey was carried out and data was collected through field questionnaire surveys of tourists and residents' in Longxian Village of Qingtian County, as well as interviews of residents with semi-structured questionnaires for their perceptions and attitudes to tourism development. The following results are got.(1) the tourism industry is still at its early state of Nongjiale tourism (enjoy and experience authentic country life-style), under very limited administrative management; (2) what attracts visitors most are delicious fish and beautiful natural environment, but not agricultural heritage itself; (3) most tourists come from adjacent areas and stay only half a day, many of whom pay their visits twice or more; (4) a few local residents take part in the activities of tourism industry, but in very limited manners even if they do.Current patterns of tourism development are casting negative impacts on agricultural heritage. Conservation agricultural heritage should be put in the first place for sustainable tourism development. Agricultural heritage, as a key attraction, should be taken as the focus for tourism development. The important thing is to change the present Nongjiale tourism into real heritage tourism, to establish a cooperative mechanism among different stakeholders,and to increase local residents' income through engaging in tourism industry.

  18. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins

    Directory of Open Access Journals (Sweden)

    Harrison Alan J

    2010-02-01

    Full Text Available Abstract Background Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. Results We show that selective pressures on reproductive proteins are highly varied. Of the 10 genes analyzed in detail, all contain signatures of positive selection either across specific sites or in specific lineages or a combination of both. Our analysis of SP56 and Col1a1 are entirely novel and the results show positively selected sites present in each gene. Our findings for the Col1a1 gene are suggestive of a link between positive selection and severe disease type. We find evidence in our dataset to suggest that interacting proteins are evolving in symphony: most likely to maintain interacting functionality. Conclusion Our in silico analyses show positively selected sites are occurring near catalytically important regions suggesting selective pressure to maximize efficient fertilization. In those cases where a mechanism of protein function is not fully understood, the sites presented here represent ideal candidates for mutational study. This work has highlighted the widespread rate heterogeneity in mutational rates across the mammalia and specifically has shown that the evolution of reproductive proteins is highly varied depending on the species and interacting partners. We have shown that positive selection and disease are closely linked in the Col1a1 gene.

  19. Positive selection neighboring functionally essential sites and disease-implicated regions of mammalian reproductive proteins.

    LENUS (Irish Health Repository)

    Morgan, Claire C

    2010-01-01

    ABSTRACT: BACKGROUND: Reproductive proteins are central to the continuation of all mammalian species. The evolution of these proteins has been greatly influenced by environmental pressures induced by pathogens, rival sperm, sexual selection and sexual conflict. Positive selection has been demonstrated in many of these proteins with particular focus on primate lineages. However, the mammalia are a diverse group in terms of mating habits, population sizes and germ line generation times. We have examined the selective pressures at work on a number of novel reproductive proteins across a wide variety of mammalia. RESULTS: We show that selective pressures on reproductive proteins are highly varied. Of the 10 genes analyzed in detail, all contain signatures of positive selection either across specific sites or in specific lineages or a combination of both. Our analysis of SP56 and Col1a1 are entirely novel and the results show positively selected sites present in each gene. Our findings for the Col1a1 gene are suggestive of a link between positive selection and severe disease type. We find evidence in our dataset to suggest that interacting proteins are evolving in symphony: most likely to maintain interacting functionality. CONCLUSION: Our in silico analyses show positively selected sites are occurring near catalytically important regions suggesting selective pressure to maximize efficient fertilization. In those cases where a mechanism of protein function is not fully understood, the sites presented here represent ideal candidates for mutational study. This work has highlighted the widespread rate heterogeneity in mutational rates across the mammalia and specifically has shown that the evolution of reproductive proteins is highly varied depending on the species and interacting partners. We have shown that positive selection and disease are closely linked in the Col1a1 gene.

  20. Synthesis and application of functional branched macromolecules: From site isolation and energy harvesting to catalysis

    Science.gov (United States)

    Hecht, Stefan

    polymers is described in Chapters 3, 4, and 5. Among the key findings of these chapters are: the important role of core size and structure for encapsulation, the superior ability of the dendrimer backbone to serve as an insulating shell and energy harvesting building block, as well as the practical and versatile use of dendritic initiators to generate functional star polymers with a high degree of site isolation. Following a short description of hyperbranched porphyrin architectures having multiple active sites (Chapter 6), the encapsulation of benzophenone-based singlet oxygen sensitizers at the core of a regular dendritic micelle is described in Chapter 7. The utilized amphiphilic design leads to the first example of light-driven catalysis within dendrimers. In the context of light-harvesting dendrimers, this finding represents the unique opportunity to convert the excitation energy that is funneled to the core into chemical energy, thereby truly mimicking natural photosynthesis. The design of first systems capable of combining light harvesting and excited state catalysis is outlined in Chapter 8. Finally, Chapter 9 illustrates an alternative, more practical approach towards light-harvesting photocatalytic polymers involving the use of monolithic materials.

  1. A method of synthesis magnetotelluric time-series combining interstation transfer functions and a reference site

    Science.gov (United States)

    Wang, Hui; Campanyà, Joan

    2016-04-01

    A new method to Synthesis magnetotelluric (MT) data is proposed whereby the MT Time-series of local site are derived using an Inverse Fourier transform of electric and magnetic fields spectrum of local site, which are computed by Combining Interstation transfer functions and a Reference horizontal magnetic time series (STICIR). The method is based on the stability of interstation transfer function, assuming that the geoelectrical structures of the subsurface independent of time. Applying the suggested method, two interstation transfer functions need to be estimated: the quasi-MT impedance tensor and the interstation geomagnetic transfer functions, which are used to compute the horizontal electric fields and the vertical magnetic field at the local site, respectively. The interstation transfer functions can be estimated by single site robust or remote reference (RR) method if another reference site existed. STICIR provides a new way to synthesis MT time-series at the local site combining interstation transfer functions and the magnetic fields at a reference site. Due to this property, STICIR provides significant improvements processing MT data when time-series at the local site are affected by local noise or are truncated. A test with good quality of MT data shows that synthetic time-series are similar to natural electric and magnetic time series. For contaminated data example, when this method is used to remove noise present at the local site, the scatter of MT sounding curves are clear reduced, and the low frequency data quality are improved.

  2. Predicting enzymatic function from global binding site descriptors.

    Science.gov (United States)

    Volkamer, Andrea; Kuhn, Daniel; Rippmann, Friedrich; Rarey, Matthias

    2013-03-01

    Due to the rising number of solved protein structures, computer-based techniques for automatic protein functional annotation and classification into families are of high scientific interest. DoGSiteScorer automatically calculates global descriptors for self-predicted pockets based on the 3D structure of a protein. Protein function predictors on three levels with increasing granularity are built by use of a support vector machine (SVM), based on descriptors of 26632 pockets from enzymes with known structure and enzyme classification. The SVM models represent a generalization of the available descriptor space for each enzyme class, subclass, and substrate-specific sub-subclass. Cross-validation studies show accuracies of 68.2% for predicting the correct main class and accuracies between 62.8% and 80.9% for the six subclasses. Substrate-specific recall rates for a kinase subset are 53.8%. Furthermore, application studies show the ability of the method for predicting the function of unknown proteins and gaining valuable information for the function prediction field. Copyright © 2012 Wiley Periodicals, Inc.

  3. Bioprospecting at former mining sites across Europe: microbial and functional diversity in soils.

    Science.gov (United States)

    Sprocati, Anna Rosa; Alisi, Chiara; Tasso, Flavia; Fiore, Alessia; Marconi, Paola; Langella, Francesca; Haferburg, Götz; Nicoara, Andrei; Neagoe, Aurora; Kothe, Erika

    2014-01-01

    The planetary importance of microbial function requires urgently that our knowledge and our exploitation ability is extended, therefore every occasion of bioprospecting is welcome. In this work, bioprospecting is presented from the perspective of the UMBRELLA project, whose main goal was to develop an integral approach for remediation of soil influenced by mining activity, by using microorganisms in association with plants. Accordingly, this work relies on the cultivable fraction of microbial biodiversity, native to six mining sites across Europe, different for geographical, climatic and geochemical characteristics but similar for suffering from chronic stress. The comparative analysis of the soil functional diversity, resulting from the metabolic profiling at community level (BIOLOG ECOPlates) and confirmed by the multivariate analysis, separates the six soils in two clusters, identifying soils characterised by low functional diversity and low metabolic activity. The microbial biodiversity falls into four major bacterial phyla: Actinobacteria, Proteobacteria, Firmicutes and Bacteroidetes, including a total of 47 genera and 99 species. In each soil, despite harsh conditions, metabolic capacity of nitrogen fixation and plant growth promotion were quite widespread, and most of the strains showed multiple resistances to heavy metals. At species-level, Shannon's index (alpha diversity) and Sørensen's Similarity (beta diversity) indicates the sites are indeed diverse. Multivariate analysis of soil chemical factors and biodiversity identifies for each soil well-discriminating chemical factors and species, supporting the assumption that cultured biodiversity from the six mining sites presents, at phylum level, a convergence correlated to soil factors rather than to geographical factors while, at species level, reflects a remarkable local characterisation.

  4. A spider population in flux: selection and abandonment of artificial web-sites and the importance of intraspecific interactions in Lephthyphantes tenuis (Araneae: Linyphiidae) in wheat.

    Science.gov (United States)

    Samu, Ferenc; Sunderland, Keith D; Topping, Chris J; Fenlon, John S

    1996-04-01

    Lepthyphantes tenuis, a small sheet-webbuilding linyphiid spider is one of the most abundant spider species of cereal fields in Europe. In the present study we examined the process of web-site selection and web-site tenacity by adult females of this species in a winter wheat field. Spiders were selective in their choice of web-site. Different immigration rates into various manipulated web-sites, in field and laboratory, suggested that structural support and suitable micro-climate (high humidity) are the most important factors in the selection. Small holes dug in the ground were the most favoured web-sites. Web-site occupation was influenced by the presence of other conspecific spiders. Territorial contests occurred between spiders attempting to occupy the same web, these almost invariably led to the take-over of the web when the intruder was heavier. Interference, but also a certain level of tolerance, between spiders within the same web-site but in different webs was suggested by direct and indirect evidence. Many holes supported two or even three spiders in vertically stratified webs. Leaving probability of marked spiders was significantly higher in multiply occupied holes than in holes with a single web. Comparison with the results of a no-interference stochastic model showed that multiple occupancy in nature is less frequent than predicted by the model. There was further evidence for weak extra-web-interference between spiders in that multiple occupancy was even less frequent and overall occupancy was lower in web-sites which were packed close to each other. However, a level of tolerance for crowding is shown by the fact that closely packed hole colonies supported a spider density 13 times higher than in natural web-sites in the field. A marking experiment was carried out to gain information on web-site tenacity (i.e. the length of time a spider spends in a web-site) and abandonment. The average duration of tenacity was less than 2 days. A random loss function

  5. Zinc cysteine active sites of metalloproteins: A density functional theory and x-ray absorption fine structure study

    Science.gov (United States)

    Dimakis, Nicholas; Farooqi, Mohammed Junaid; Garza, Emily Sofia; Bunker, Grant

    2008-03-01

    Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)4-n(Cys)n sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

  6. Zinc cysteine active sites of metalloproteins: a density functional theory and x-ray absorption fine structure study.

    Science.gov (United States)

    Dimakis, Nicholas; Farooqi, Mohammed Junaid; Garza, Emily Sofia; Bunker, Grant

    2008-03-21

    Density functional theory (DFT) and x-ray absorption fine structure (XAFS) spectroscopy are complementary tools for the biophysical study of active sites in metalloproteins. DFT is used to compute XAFS multiple scattering Debye Waller factors, which are then employed in genetic algorithm-based fitting process to obtain a global fit to the XAFS in the space of fitting parameters. Zn-Cys sites, which serve important functions as transcriptional switches in Zn finger proteins and matrix metalloproteinases, previously have proven intractable by this method; here these limitations are removed. In this work we evaluate optimal DFT nonlocal functionals and basis sets for determining optimal geometries and vibrational densities of states of mixed ligation Zn(His)(4-n)(Cys)(n) sites. Theoretical results are compared to experimental XAFS measurements and Raman spectra from the literature and tabulated for use.

  7. Structure-Function of CD36 and Importance of Fatty Acid Signal Transduction in Fat Metabolism

    OpenAIRE

    Pepino, Marta Yanina; Kuda, Ondrej; Samovski, Dmitri; Abumrad, Nada A.

    2014-01-01

    CD36 is a scavenger receptor that functions in high affinity tissue uptake of long chain fatty acids (FA) and contributes under excessive fat supply to lipid accumulation and metabolic dysfunction. This review describes recent evidence regarding the CD36 FA binding site and a potential mechanism for FA transfer. It also presents the view that CD36 and FA signaling coordinate fat utilization based on newly identified CD36 actions that involve oral fat perception, intestinal fat absorption, sec...

  8. Structure/Function/Dynamics of Photosystem II Plastoquinone Binding Sites

    Science.gov (United States)

    Lambreva, Maya D.; Russo, Daniela; Polticelli, Fabio; Scognamiglio, Viviana; Antonacci, Amina; Zobnina, Veranika; Campi, Gaetano; Rea, Giuseppina

    2014-01-01

    Photosystem II (PSII) continuously attracts the attention of researchers aiming to unravel the riddle of its functioning and efficiency fundamental for all life on Earth. Besides, an increasing number of biotechnological applications have been envisaged exploiting and mimicking the unique properties of this macromolecular pigment-protein complex. The PSII organization and working principles have inspired the design of electrochemical water splitting schemes and charge separating triads in energy storage systems as well as biochips and sensors for environmental, agricultural and industrial screening of toxic compounds. An intriguing opportunity is the development of sensor devices, exploiting native or manipulated PSII complexes or ad hoc synthesized polypeptides mimicking the PSII reaction centre proteins as bio-sensing elements. This review offers a concise overview of the recent improvements in the understanding of structure and function of PSII donor side, with focus on the interactions of the plastoquinone cofactors with the surrounding environment and operational features. Furthermore, studies focused on photosynthetic proteins structure/function/dynamics and computational analyses aimed at rational design of high-quality bio-recognition elements in biosensor devices are discussed. PMID:24678671

  9. Structural descriptor database: a new tool for sequence-based functional site prediction

    Directory of Open Access Journals (Sweden)

    Vasconcelos Ana

    2008-11-01

    Full Text Available Abstract Background The Structural Descriptor Database (SDDB is a web-based tool that predicts the function of proteins and functional site positions based on the structural properties of related protein families. Structural alignments and functional residues of a known protein set (defined as the training set are used to build special Hidden Markov Models (HMM called HMM descriptors. SDDB uses previously calculated and stored HMM descriptors for predicting active sites, binding residues, and protein function. The database integrates biologically relevant data filtered from several databases such as PDB, PDBSUM, CSA and SCOP. It accepts queries in fasta format and predicts functional residue positions, protein-ligand interactions, and protein function, based on the SCOP database. Results To assess the SDDB performance, we used different data sets. The Trypsion-like Serine protease data set assessed how well SDDB predicts functional sites when curated data is available. The SCOP family data set was used to analyze SDDB performance by using training data extracted from PDBSUM (binding sites and from CSA (active sites. The ATP-binding experiment was used to compare our approach with the most current method. For all evaluations, significant improvements were obtained with SDDB. Conclusion SDDB performed better when trusty training data was available. SDDB worked better in predicting active sites rather than binding sites because the former are more conserved than the latter. Nevertheless, by using our prediction method we obtained results with precision above 70%.

  10. Investigation of the metal binding site in methionine aminopeptidase by density functional theory

    DEFF Research Database (Denmark)

    Jørgensen, Anne Techau; Norrby, Per-Ola; Liljefors, Tommy

    2002-01-01

    All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co2+ ions or Zn2+ ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions...... oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based...

  11. Toward a Functional Definition of Methane Super-Emitters: Application to Natural Gas Production Sites.

    Science.gov (United States)

    Zavala-Araiza, Daniel; Lyon, David; Alvarez, Ramón A; Palacios, Virginia; Harriss, Robert; Lan, Xin; Talbot, Robert; Hamburg, Steven P

    2015-07-07

    Emissions from natural gas production sites are characterized by skewed distributions, where a small percentage of sites-commonly labeled super-emitters-account for a majority of emissions. A better characterization of super-emitters is needed to operationalize ways to identify them and reduce emissions. We designed a conceptual framework that functionally defines superemitting sites as those with the highest proportional loss rates (methane emitted relative to methane produced). Using this concept, we estimated total methane emissions from natural gas production sites in the Barnett Shale; functionally superemitting sites accounted for roughly three-fourths of total emissions. We discuss the potential to reduce emissions from these sites, under the assumption that sites with high proportional loss rates have excess emissions resulting from abnormal or otherwise avoidable operating conditions, such as malfunctioning equipment. Because the population of functionally superemitting sites is not expected to be static over time, continuous monitoring will likely be necessary to identify them and improve their operation. This work suggests that achieving and maintaining uniformly low emissions across the entire population of production sites will require mitigation steps at a large fraction of sites.

  12. Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor

    Directory of Open Access Journals (Sweden)

    Kareem Mohideen-Abdul

    2017-06-01

    Full Text Available Most nuclear receptors (NRs bind DNA as dimers, either as hetero- or as homodimers on DNA sequences organized as two half-sites with specific orientation and spacing. The dimerization of NRs on their cognate response elements (REs involves specific protein–DNA and protein–protein interactions. The estrogen-related receptor (ERR belongs to the steroid hormone nuclear receptor (SHR family and shares strong similarity in its DNA-binding domain (DBD with that of the estrogen receptor (ER. In vitro, ERR binds with high affinity inverted repeat REs with a 3-bps spacing (IR3, but in vivo, it preferentially binds to single half-site REs extended at the 5′-end by 3 bp [estrogen-related response element (ERREs], thus explaining why ERR was often inferred as a purely monomeric receptor. Since its C-terminal ligand-binding domain is known to homodimerize with a strong dimer interface, we investigated the binding behavior of the isolated DBDs to different REs using electrophoretic migration, multi-angle static laser light scattering (MALLS, non-denaturing mass spectrometry, and nuclear magnetic resonance. In contrast to ER DBD, ERR DBD binds as a monomer to EREs (IR3, such as the tff1 ERE-IR3, but we identified a DNA sequence composed of an extended half-site embedded within an IR3 element (embedded ERRE/IR3, where stable dimer binding is observed. Using a series of chimera and mutant DNA sequences of ERREs and IR3 REs, we have found the key determinants for the binding of ERR DBD as a dimer. Our results suggest that the sequence-directed DNA shape is more important than the exact nucleotide sequence for the binding of ERR DBD to DNA as a dimer. Our work underlines the importance of the shape-driven DNA readout mechanisms based on minor groove recognition and electrostatic potential. These conclusions may apply not only to ERR but also to other members of the SHR family, such as androgen or glucocorticoid, for which a strong well-conserved half-site

  13. An importance of the muscular imbalance in the context of functional disorders of the spine

    OpenAIRE

    JOZOVÁ, Kateřina

    2010-01-01

    ABSTRACT A topic of my thesis is an importance of the muscular imbalance in the context of functional disorders of the spine. The topic has been very up-to-date, because a large proportion of the population suffers from vertebral disorders of functional nature, which are just caused by muscular imbalances. A goal of the first part of the thesis was a theoretic analysis of the problem of muscular imbalances and functional disorders of the spine. A content of that chapter is an introduction to ...

  14. Skin Barrier Function and Its Importance at the Start of the Atopic March

    Science.gov (United States)

    Hogan, Mary Beth; Peele, Kathy; Wilson, Nevin W.

    2012-01-01

    Atopic dermatitis can be due to a variety of causes from nonatopic triggers to food allergy. Control of egress of water and protection from ingress of irritants and allergens are key components of cutaneous barrier function. Current research suggests that a degraded barrier function of the skin allows the immune system inappropriate access to environmental allergens. Epidermal aeroallergen exposure may allow sensitization to allergen possibly initiating the atopic march. Further research into connections between epidermal barrier function and possible allergen sensitization will be important to undertake. Future clinical trials focused on skin barrier protection may be of value as a possible intervention in prevention of the initiation of the atopic march. PMID:22619686

  15. Site-selective and stereoselective functionalization of unactivated C-H bonds

    Science.gov (United States)

    Liao, Kuangbiao; Negretti, Solymar; Musaev, Djamaladdin G.; Bacsa, John; Davies, Huw M. L.

    2016-05-01

    The laboratory synthesis of complex organic molecules relies heavily on the introduction and manipulation of functional groups, such as carbon-oxygen or carbon-halogen bonds; carbon-hydrogen bonds are far less reactive and harder to functionalize selectively. The idea of C-H functionalization, in which C-H bonds are modified at will instead of the functional groups, represents a paradigm shift in the standard logic of organic synthesis. For this approach to be generally useful, effective strategies for site-selective C-H functionalization need to be developed. The most practical solutions to the site-selectivity problem rely on either intramolecular reactions or the use of directing groups within the substrate. A challenging, but potentially more flexible approach, would be to use catalyst control to determine which site in a particular substrate would be functionalized. Here we describe the use of dirhodium catalysts to achieve highly site-selective, diastereoselective and enantioselective C-H functionalization of n-alkanes and terminally substituted n-alkyl compounds. The reactions proceed in high yield, and functional groups such as halides, silanes and esters are compatible with this chemistry. These studies demonstrate that high site selectivity is possible in C-H functionalization reactions without the need for a directing or anchoring group present in the molecule.

  16. Nitrate removal in a restored riparian groundwater system: functioning and importance of individual riparian zones

    Directory of Open Access Journals (Sweden)

    S. Peter

    2012-11-01

    Full Text Available For the design and the assessment of river restoration projects, it is important to know to what extent the elimination of reactive nitrogen (N can be improved in the riparian groundwater. We investigated the effectiveness of different riparian zones, characterized by a riparian vegetation succession, for nitrate (NO3 removal from infiltrating river water in a restored and a still channelized section of the river Thur, Switzerland. Functional genes of denitrification (nirS and nosZ were relatively abundant in groundwater from willow bush and mixed forest dominated zones, where oxygen concentrations remained low compared to the main channel and other riparian zones. After flood events, a substantial decline in NO3 concentration (> 50% was observed in the willow bush zone but not in the other riparian zones closer to the river. In addition, the characteristic enrichment of 15N and 18O in the residual NO3 pool (by up to 22‰ for δ15N and up to 12‰ for δ18O provides qualitative evidence that the willow bush and forest zones were sites of active denitrification and, to a lesser extent, NO3 removal by plant uptake. Particularly in the willow bush zone during a period of water table elevation after a flooding event, substantial input of organic carbon into the groundwater occurred, thereby fostering post-flood denitrification activity that reduced NO3 concentration with a rate of ~21 μmol N l−1 d−1. Nitrogen removal in the forest zone was not sensitive to flood pulses, and overall NO3 removal rates were lower (~6 μmol l−1 d−1. Hence, discharge-modulated vegetation–soil–groundwater coupling was found to be a key driver for riparian NO3 removal. We estimated that

  17. Nitrate removal in a restored riparian groundwater system: functioning and importance of individual riparian zones

    Science.gov (United States)

    Peter, S.; Rechsteiner, R.; Lehmann, M. F.; Brankatschk, R.; Vogt, T.; Diem, S.; Wehrli, B.; Tockner, K.; Durisch-Kaiser, E.

    2012-11-01

    For the design and the assessment of river restoration projects, it is important to know to what extent the elimination of reactive nitrogen (N) can be improved in the riparian groundwater. We investigated the effectiveness of different riparian zones, characterized by a riparian vegetation succession, for nitrate (NO3-) removal from infiltrating river water in a restored and a still channelized section of the river Thur, Switzerland. Functional genes of denitrification (nirS and nosZ) were relatively abundant in groundwater from willow bush and mixed forest dominated zones, where oxygen concentrations remained low compared to the main channel and other riparian zones. After flood events, a substantial decline in NO3- concentration (> 50%) was observed in the willow bush zone but not in the other riparian zones closer to the river. In addition, the characteristic enrichment of 15N and 18O in the residual NO3- pool (by up to 22‰ for δ15N and up to 12‰ for δ18O) provides qualitative evidence that the willow bush and forest zones were sites of active denitrification and, to a lesser extent, NO3- removal by plant uptake. Particularly in the willow bush zone during a period of water table elevation after a flooding event, substantial input of organic carbon into the groundwater occurred, thereby fostering post-flood denitrification activity that reduced NO3- concentration with a rate of ~21 μmol N l-1 d-1. Nitrogen removal in the forest zone was not sensitive to flood pulses, and overall NO3- removal rates were lower (~6 μmol l-1 d-1). Hence, discharge-modulated vegetation-soil-groundwater coupling was found to be a key driver for riparian NO3- removal. We estimated that, despite higher rates in the fairly constrained willow bush hot spot, total NO3- removal from the groundwater is lower than in the extended forest area. Overall, the aquifer in the restored section was more effective and removed ~20% more NO3- than the channelized section.

  18. The dynamic dielectric at a brain functional site and an EM wave approach to functional brain imaging.

    Science.gov (United States)

    Li, X P; Xia, Q; Qu, D; Wu, T C; Yang, D G; Hao, W D; Jiang, X; Li, X M

    2014-11-04

    Functional brain imaging has tremendous applications. The existing methods for functional brain imaging include functional Magnetic Resonant Imaging (fMRI), scalp electroencephalography (EEG), implanted EEG, magnetoencephalography (MEG) and Positron Emission Tomography (PET), which have been widely and successfully applied to various brain imaging studies. To develop a new method for functional brain imaging, here we show that the dielectric at a brain functional site has a dynamic nature, varying with local neuronal activation as the permittivity of the dielectric varies with the ion concentration of the extracellular fluid surrounding neurons in activation. Therefore, the neuronal activation can be sensed by a radiofrequency (RF) electromagnetic (EM) wave propagating through the site as the phase change of the EM wave varies with the permittivity. Such a dynamic nature of the dielectric at a brain functional site provides the basis for an RF EM wave approach to detecting and imaging neuronal activation at brain functional sites, leading to an RF EM wave approach to functional brain imaging.

  19. Kinetic Mechanism of Uracil Phosphoribosyltransferase from Escherichia coli and Catalytic Importance of the Conserved Proline in the PRPP Binding Site

    DEFF Research Database (Denmark)

    Lundegaard, Claus; Jensen, Kaj Frank

    1999-01-01

    catalytic properties with the properties of the wild-type protein. We found that UPRTase of E. coli obeyed the kinetics of a sequential mechanism with the binding of PRPP preceding the binding of uracil. The basic kinetic constants were derived from initial velocity measurements, product inhibition......, and ligand binding assays. The change of Pro 131 to Asp caused a 50-60-fold reduction of the catalytic rate (kcat) in both directions of the reaction and approximately a 100-fold increase in the KM for uracil. The KM for PRPP was strongly diminished by the mutation, but kcat/KM,PRPP and the dissociation...... constant (KD,PRPP) were nearly unaffected. We conclude that the proline in the PRPP binding site of UPRTase is of only little importance for binding of PRPP to the free enzyme, but is critical for binding of uracil to the enzyme-PRPP complex and for the catalytic rate....

  20. Optimizing health system response to patient's needs: an argument for the importance of functioning information.

    Science.gov (United States)

    Hopfe, Maren; Prodinger, Birgit; Bickenbach, Jerome E; Stucki, Gerold

    2017-06-06

    Current health systems are increasingly challenged to meet the needs of a growing number of patients living with chronic and often multiple health conditions. The primary outcome of care, it is argued, is not merely curing disease but also optimizing functioning over a person's life span. According to the World Health Organization, functioning can serve as foundation for a comprehensive picture of health and augment the biomedical perspective with a broader and more comprehensive picture of health as it plays out in people's lives. The crucial importance of information about patient's functioning for a well-performing health system, however, has yet to be sufficiently appreciated. This paper argues that functioning information is fundamental in all components of health systems and enhances the capacity of health systems to optimize patients' health and health-related needs. Beyond making sense of biomedical disease patterns, health systems can profit from using functioning information to improve interprofessional collaboration and achieve cross-cutting disease treatment outcomes. Implications for rehabilitation Functioning is a key health outcome for rehabilitation within health systems. Information on restoring, maintaining, and optimizing human functioning can strengthen health system response to patients' health and rehabilitative needs. Functioning information guides health systems to achieve cross-cutting health outcomes that respond to the needs of the growing number of individuals living with chronic and multiple health conditions. Accounting for individuals functioning helps to overcome fragmentation of care and to improve interprofessional collaboration across settings.

  1. Predicting functional divergence in protein evolution by site-specific rate shifts

    Science.gov (United States)

    Gaucher, Eric A.; Gu, Xun; Miyamoto, Michael M.; Benner, Steven A.

    2002-01-01

    Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

  2. Effective Boolean dynamics analysis to identify functionally important genes in large-scale signaling networks.

    Science.gov (United States)

    Trinh, Hung-Cuong; Kwon, Yung-Keun

    2015-11-01

    Efficiently identifying functionally important genes in order to understand the minimal requirements of normal cellular development is challenging. To this end, a variety of structural measures have been proposed and their effectiveness has been investigated in recent literature; however, few studies have shown the effectiveness of dynamics-based measures. This led us to investigate a dynamic measure to identify functionally important genes, and the effectiveness of which was verified through application on two large-scale human signaling networks. We specifically consider Boolean sensitivity-based dynamics against an update-rule perturbation (BSU) as a dynamic measure. Through investigations on two large-scale human signaling networks, we found that genes with relatively high BSU values show slower evolutionary rate and higher proportions of essential genes and drug targets than other genes. Gene-ontology analysis showed clear differences between the former and latter groups of genes. Furthermore, we compare the identification accuracies of essential genes and drug targets via BSU and five well-known structural measures. Although BSU did not always show the best performance, it effectively identified the putative set of genes, which is significantly different from the results obtained via the structural measures. Most interestingly, BSU showed the highest synergy effect in identifying the functionally important genes in conjunction with other measures. Our results imply that Boolean-sensitive dynamics can be used as a measure to effectively identify functionally important genes in signaling networks.

  3. Estimating the Importance of Differential Item Functioning. Program Statistics Research Technical Report No. 95-3.

    Science.gov (United States)

    Rudas, Tamas; Zwick, Rebecca

    A method is proposed to assess the importance of differential item functioning (DIF) by estimating the largest possible fraction of the population in which DIF does not occur, or equivalently, the smallest possible portion of the population in which DIF may occur. The approach is based on latent class (C. C. Clogg, 1981) or mixture concepts, and…

  4. Automatic determination of important mode-mode correlations in many-mode vibrational wave functions.

    Science.gov (United States)

    König, Carolin; Christiansen, Ove

    2015-04-14

    We introduce new automatic procedures for parameterizing vibrational coupled cluster (VCC) and vibrational configuration interaction wave functions. Importance measures for individual mode combinations in the wave function are derived based on upper bounds to Hamiltonian matrix elements and/or the size of perturbative corrections derived in the framework of VCC. With a threshold, this enables an automatic, system-adapted way of choosing which mode-mode correlations are explicitly parameterized in the many-mode wave function. The effect of different importance measures and thresholds is investigated for zero-point energies and infrared spectra for formaldehyde and furan. Furthermore, the direct link between important mode-mode correlations and coordinates is illustrated employing water clusters as examples: Using optimized coordinates, a larger number of mode combinations can be neglected in the correlated many-mode vibrational wave function than with normal coordinates for the same accuracy. Moreover, the fraction of important mode-mode correlations compared to the total number of correlations decreases with system size. This underlines the potential gain in efficiency when using optimized coordinates in combination with a flexible scheme for choosing the mode-mode correlations included in the parameterization of the correlated many-mode vibrational wave function. All in all, it is found that the introduced schemes for parameterizing correlated many-mode vibrational wave functions lead to at least as systematic and accurate calculations as those using more standard and straightforward excitation level definitions. This new way of defining approximate calculations offers potential for future calculations on larger systems.

  5. Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity.

    Science.gov (United States)

    Kristensen, David M; Chen, Brian Y; Fofanov, Viacheslav Y; Ward, R Matthew; Lisewski, Andreas Martin; Kimmel, Marek; Kavraki, Lydia E; Lichtarge, Olivier

    2006-06-01

    The annotation of protein function has not kept pace with the exponential growth of raw sequence and structure data. An emerging solution to this problem is to identify 3D motifs or templates in protein structures that are necessary and sufficient determinants of function. Here, we demonstrate the recurrent use of evolutionary trace information to construct such 3D templates for enzymes, search for them in other structures, and distinguish true from spurious matches. Serine protease templates built from evolutionarily important residues distinguish between proteases and other proteins nearly as well as the classic Ser-His-Asp catalytic triad. In 53 enzymes spanning 33 distinct functions, an automated pipeline identifies functionally related proteins with an average positive predictive power of 62%, including correct matches to proteins with the same function but with low sequence identity (the average identity for some templates is only 17%). Although these template building, searching, and match classification strategies are not yet optimized, their sequential implementation demonstrates a functional annotation pipeline which does not require experimental information, but only local molecular mimicry among a small number of evolutionarily important residues.

  6. ER import sites and their relationship to ER exit sites: a new model for bidirectional ER-Golgi transport in higher plants

    Directory of Open Access Journals (Sweden)

    Alexander eLerich

    2012-07-01

    Full Text Available The plant Golgi apparatus is polydisperse and COPII fluorescence localizes to the interface between the ER and the overlying Golgi stack rather than the surface of the ER. Per definition, ER exit sites (ERES are COPII vesiculation events at the surface of the ER and are only visualizable in the electron microscope through cryofixation techniques. Nevertheless, ERES is always associated with Golgi stacks and both move together. We have asked whether the domain of the ER where retrograde COPI vesicles fuse, i.e. ER import sites, (ERIS, is also coupled to Golgi stack motility and therefore spatially associated with ERES? As ERIS markers we have investigated ER-located SNAREs and tethering factors. We screened several SNAREs (SYP81, the SYP7 family, and USE1 to find a SNARE whose overexpression did not disrupt ER-Golgi traffic and which gave rise to discrete fluorescent punctae when expressed with an XFP tag. Only the Qc SNARE SYP72 fulfilled these criteria, and, based on quantitative protein transport assays with the retrograde reporter α-amylase-HDEL, even appeared to enhance retrograde traffic. When coexpressed with SYP72-YFP, the type I membrane protein RFP-p24δ5 whose ER localization is due to an efficient COPI-mediated recycling, forms nodules along the tubular ER network. SYP72 colocalizes with these nodules which are not seen when RFP-p24δ5 is expressed alone or when SYP72-YFP is coexpressed with a mutant form of RFP-p24δ5 that cannot exit the ER. Immobilized Golgi stacks show a perfect colocalization between SYP72-YFP and fluorescent COPII/Golgi markers. Endogenous SYP72, also colocalizes with COPII/Golgi. Fluorescently tagged versions of plant homologs to TIP20 of the Dsl1 COPI-tethering factor complex, and to the COPII-tethering factor p115 both colocalize perfectly with Golgi stacks. These data suggest that ERES, ERIS and Golgi stacks are closely associated thereby constituting a mobile secretory and recycling unit: a unique feature

  7. Frequency band-importance functions for auditory and auditory-visual speech recognition

    Science.gov (United States)

    Grant, Ken W.

    2005-04-01

    In many everyday listening environments, speech communication involves the integration of both acoustic and visual speech cues. This is especially true in noisy and reverberant environments where the speech signal is highly degraded, or when the listener has a hearing impairment. Understanding the mechanisms involved in auditory-visual integration is a primary interest of this work. Of particular interest is whether listeners are able to allocate their attention to various frequency regions of the speech signal differently under auditory-visual conditions and auditory-alone conditions. For auditory speech recognition, the most important frequency regions tend to be around 1500-3000 Hz, corresponding roughly to important acoustic cues for place of articulation. The purpose of this study is to determine the most important frequency region under auditory-visual speech conditions. Frequency band-importance functions for auditory and auditory-visual conditions were obtained by having subjects identify speech tokens under conditions where the speech-to-noise ratio of different parts of the speech spectrum is independently and randomly varied on every trial. Point biserial correlations were computed for each separate spectral region and the normalized correlations are interpreted as weights indicating the importance of each region. Relations among frequency-importance functions for auditory and auditory-visual conditions will be discussed.

  8. Functions of synapsins in corticothalamic facilitation: important roles of synapsin I.

    Science.gov (United States)

    Nikolaev, Maxim; Heggelund, Paul

    2015-10-01

    The synaptic vesicle associated proteins synapsin I and synapsin II have important functions in synaptic short-term plasticity. We investigated their functions in cortical facilitatory feedback to neurons in dorsal lateral geniculate nucleus (dLGN), feedback that has important functions in state-dependent regulation of thalamic transmission of visual input to cortex. We compared results from normal wild-type (WT) mice and synapsin knockout (KO) mice in several types of synaptic plasticity, and found clear differences between the responses of neurons in the synapsin I KO and the WT, but no significant differences between the synapsin II KO and the WT. These results are in contrast to the important role of synapsin II previously demonstrated in similar types of synaptic plasticity in other brain regions, indicating that the synapsins can have different roles in similar types of STP in different parts of the brain. The synaptic vesicle associated proteins synapsin I (SynI) and synapsin II (SynII) have important functions in several types of synaptic short-term plasticity in the brain, but their separate functions in different types of synapses are not well known. We investigated possible distinct functions of the two synapsins in synaptic short-term plasticity at corticothalamic synapses on relay neurons in the dorsal lateral geniculate nucleus. These synapses provide excitatory feedback from visual cortex to the relay cells, feedback that can facilitate transmission of signals from retina to cortex. We compared results from normal wild-type (WT), SynI knockout (KO) and SynII KO mice, in three types of synaptic plasticity mainly linked to presynaptic mechanism. In SynI KO mice, paired-pulse stimulation elicited increased facilitation at short interpulse intervals compared to the WT. Pulse-train stimulation elicited weaker facilitation than in the WT, and also post-tetanic potentiation was weaker in SynI KO than in the WT. Between SynII KO and the WT we found no

  9. Distribution dynamics and functional importance of NHERF1 in regulation of Mrp-2 trafficking in hepatocytes.

    Science.gov (United States)

    Karvar, Serhan; Suda, Jo; Zhu, Lixin; Rockey, Don C

    2014-10-15

    Na(+)/H(+) exchanger regulatory factor 1 (NHERF1) is a multifunctional scaffolding protein that interacts with receptors and ion transporters in its PDZ domains and with the ezrin-radixin-moesin (ERM) family of proteins in its COOH terminus. The role of NHERF1 in hepatocyte function remains largely unknown. We examine the distribution and physiological significance of NHERF1 and multidrug resistance-associated protein 2 (Mrp-2) in hepatocytes. A WT radixin binding site mutant (F355R) and NHERF1 PDZ1 and PDZ2 domain adenoviral mutant constructs were tagged with yellow fluorescent protein and expressed in polarized hepatocytes to study localization and function of NHERF1. Cellular distribution of NHERF1 and radixin was visualized by fluorescence microscopy. A 5-chloromethylfluorescein diacetate (CMFDA) assay was used to characterize Mrp-2 function. Similar to Mrp-2, WT NHERF1 and the NHERF1 PDZ2 deletion mutant were localized to the canalicular membrane. In contrast, the radixin binding site mutant (F355R) and the NHERF1 PDZ1 deletion mutant, which interacts poorly with Mrp-2, were rarely associated with the canalicular membrane. Knockdown of NHERF1 led to dramatically impaired CMFDA secretory response. Use of CMFDA showed that the NHERF1 PDZ1 and F355R mutants were devoid of a secretory response, while WT NHERF1-infected cells exhibited increased secretion of glutathione-methylfluorescein. The data indicate that NHERF1 interacts with Mrp-2 via the PDZ1 domain of NHERF1 and, furthermore, that NHERF1 is essential for maintaining the localization and function of Mrp-2.

  10. Social network sites in the corporate communication of the IBEX 35: uses, development and importance according to its leaders

    Directory of Open Access Journals (Sweden)

    Patricia DURÁNTEZ-STOLLE

    2017-01-01

    Full Text Available Social media offer an opportunity for corporate communication in the context of Web 2.0, where image and reputation are affected by the delogue/conversations within virtual communities. Previous research on this issue, based on content analysis, points out the interest of companies to have a corporate presence in social networks, but at the same time they emphasize the lack of harnessing of the interactive and dialogical potential. In this article, we have conducted a survey to know the opinion of the most important Spanish companies about social network sites. With this method, we pretend to find out which professional profiles are in charge of the planning and management of the corporate presence in social media, to understand their uses and relevance and to study how the big companies are answering to the possibility of having dialogue relations with their publics. The results show that the IBEX 35 companies consider of great relevance their corporate profiles on social networks, as well as their frequent updating and professionalized management. Also, the respondents understand the conversational nature of social networks, however, they are using these channels mainly for informative goals. The findings allow us to see the lack of consistency between the understanding of the dialogical context, the importance given to social networking and the informational purposes that prevail in most of the cases.

  11. Fresh steam-flaked corn in cattle feedlots is an important site for fecal coliform contamination by house flies.

    Science.gov (United States)

    Ghosh, Anuradha; Zurek, Ludek

    2015-03-01

    House flies are a common pest at food animal facilities, including cattle feedlots. Previously, house flies were shown to play an important role in the ecology of Escherichia coli O157:H7; house flies in cattle feedlots carried this zoonotic pathogen and were able to contaminate cattle through direct contact and/or by contamination of drinking water and feed. Because house flies aggregate in large numbers on fresh ( # 6 h) steam-flaked corn (FSFC) used in cattle feed, the aim of this study was to assess FSFC in a cattle feedlot as a potentially important site of fecal coliform contamination by house flies. House flies and FSFC samples were collected, homogenized, and processed for culturing of fecal coliforms on membrane fecal coliform agar. Selected isolates were identified by 16S rRNA gene sequencing, and representative isolates from each phylogenetic group were genotyped by pulsed-field gel electrophoresis. Fecal coliforms were undetectable in FSFC shortly (0 h) after flaking; however, in summer, after 4 to 6 h, the concentrations of fecal coliforms ranged from 1.9 × 10(3) to 3.7 × 10(4) CFU/g FSFC (mean, 1.1 ± 3.0 × 10(4) CFU/g). House flies from FSFC carried between 7.6 × 10(2) and 4.1 × 10(6) CFU of fecal coliforms per fly (mean, 6.0 ± 2.3 × 10(5) CFU per fly). Fecal coliforms were represented by E. coli (85.1%), Klebsiella spp. (10.6%), and Citrobacter spp. (4.3%). Pulsed-field gel electrophoresis demonstrated clonal matches of E. coli and Klebsiella spp. between house flies and FSFC. In contrast, in winter and in the absence of house flies, the contamination of corn by fecal coliforms was significantly (∼10-fold) lower. These results indicate that FSFC is an important site for bacterial contamination by flies and possible exchange of E. coli and other bacteria among house flies. Further research is needed to evaluate the potential use of screens or blowers to limit the access of house flies to FSFC and therefore their effectiveness in preventing

  12. Quantifying the importance of plant functional diversity for ecosystem functioning and resilience under scenarios of climate change (Invited)

    Science.gov (United States)

    Pavlick, R.; Drewry, D.; Kleidon, A.

    2013-12-01

    Dynamic Global Vegetation Models (DGVMs) typically employ only a small set of Plant Functional Types (PFTs) to represent the vast diversity of observed vegetation forms and functioning. There is growing evidence, however, that this abstraction may not adequately represent the observed variation in plant functional traits, which is thought to play an important role for many ecosystem functions and for ecosystem resilience to environmental change. The geographic distribution of PFTs in these models is also often based on empirical relationships between present-day climate and vegetation patterns. Projections of future climate change, however, point toward the possibility of novel regional climates, which could lead to no-analog vegetation compositions incompatible with the PFT paradigm. Here, we present results from the Jena Diversity-DGVM (JeDi-DGVM), a novel traits-based vegetation model, which simulates a large number of hypothetical plant growth strategies constrained by functional tradeoffs, thereby allowing for a more flexible temporal and spatial representation of the terrestrial biosphere. We run two sets of model experiments forced with the latest bias-corrected climate change scenarios from several different global climate models. In the first set, we simulate a diverse biosphere using a large number of plant growth strategies, allowing the modelled ecosystems to adapt through emergent changes in ecosystem composition. We then aggregate the surviving growth strategies from the first set of diverse simulations to a small number of biome-averaged growth strategies, recreating something akin to PFTs. We use this smaller set of PFT-like growth strategies to represent a sparse or low-diversity biosphere in the second set of model experiments. We quantify the importance of functional diversity by comparing key metrics of ecosystem functioning across the two sets of simulations. The results reveal the implications of using the common PFT vegetation modelling

  13. Improving ATLAS grid site reliability with functional tests using HammerCloud

    CERN Document Server

    Legger, F; The ATLAS collaboration

    2012-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short light-weight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site...

  14. Analysis of mammalian cytochrome P450 structure and function by site-directed mutagenesis.

    Science.gov (United States)

    Domanski, T L; Halpert, J R

    2001-06-01

    Over the past decade, site-directed mutagenesis has become an essential tool in the study of mammalian cytochrome P450 structure-function relationships. Residues affecting substrate specificity, cooperativity, membrane localization, and interactions with redox partners have been identified using a combination of amino-acid sequence alignments, homology modeling, chimeragenesis, and site-directed mutagenesis. As homology modeling and substrate docking technology continue to improve, the ability to predict more precise functions for specific residues will also advance, making it possible to utilize site-directed mutagenesis to test these predictions. Future studies will employ site-directed mutagenesis to learn more about cytochrome P450 substrate access channels, to define the role of residues that do not lie within substrate recognition sites, to engineer additional soluble forms of microsomal cytochromes P450 for x-ray crystallography, and to engineer more efficient enzymes for drug activation and/or bioremediation.

  15. Microscopic investigations of site and functional selectivity of triazole for CO2 capture and catalytic applications.

    Science.gov (United States)

    Boulmène, Reda; Prakash, Muthuramalingam; Hochlaf, Majdi

    2016-11-02

    Ab initio and DFT studies on CO2 interacting with different tautomers and isomers of triazole (TZ) are carried out to understand the adsorption mechanism and their mutual preferential sites. We used post Hartree-Fock methods (MP2, CCSD(T), and CCSD(T)-F12) and various DFTs (PBE, PBE0, M05-2X, and M11) with and without considering the dispersion correction for comparison. We determined hence the equilibrium structures, vibrational frequencies and binding energies of TZ-CO2 clusters and mapped their potential energy surfaces along the intermonomer coordinates. We find that the most stable TZ-CO2 clusters, some of them are already known, are not relevant for CO2 capture in porous materials. In addition, we show that the bonding between TZ and CO2 is due to various kinds of noncovalent interactions such as π-stacking, acid-base pair electron donor-electron acceptor (EDA) interactions along with N-HO and C-HO H-bonds with CO2. Our analysis reveals the existence of site selectivity effects when CO2 binds to TZ. These effects are related to the magnitude of the interaction potentials, in the order EDA (+N-HO) > EDA (+C-HO) > C(δ+)N[double bond, length as m-dash]N > π-stacking > σ type N-HO > C-HO H-bonds. This is the first report on the importance of competition between EDA, π-stacking and σ-bonds for CO2 capture and catalytic applications. Findings from this work may be used to give insights into the site specific CO2 capture ability of porous materials such as metal organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs) or functionalized polymers. Finally, we show that IR spectroscopy of CO2 within the pores is neither a specific nor an efficient marker in probe-molecule experiments.

  16. [Epidemiology of imported malaria and entomological study of breeding sites of potential risk areas in the province of Khemisset (Morocco)].

    Science.gov (United States)

    Larhbali, Y; Belghyti, D; El Guamri, Y; Lahlou, O; El Kharrim, K; Kirami, A; Khamri, Z

    2014-01-01

    No case of autochthonous malaria has been detected in Morocco since 2004. This achievement is due to a national strategy to combat the disease by appropriate and well-organized disease detection and treatment, as well as control of the mosquito vector of the disease, the female Anopheles mosquito. Nonetheless, imported malaria cases have been increasing (75 in 2007), due to the rise in international travel and migration from countries where the disease is endemic. This work is divided into two parts: the first part is a retrospective study of the cases of imported malaria identified by optical microscopy in the Laboratory of Medical Entomology of the Khemisset Provincial Delegation of Health from 2000 to 2010. The second part is an entomological study conducted in 2010 of the Culicidae insect family, especially the Anopheles genus. The results show that of 176,457 requests for parasite testing, 14 were positive. All positive samples came from men older than 23 years. The cases identified are imported from two African countries: the Democratic Republic of Congo (86%) and Ivory Coast (14%). The years of high incidence were 2003 with four cases and 2000, 2004 and 2006 with two cases. The species found are Plasmodium falciparum in 13 cases (93%) and Plasmodium ovale in one case (7%). The vector of autochthonous malaria, which was eliminated in 2004, is Anopheles (Anopheles) labranchiae Fallerouni 1926, and it was the dominant species found in our entomological study (424 larvae). The other species were found in breeding sites in potential at-risk locations in the study area.

  17. Executive function is an important consideration for coping strategy use in people with multiple sclerosis.

    Science.gov (United States)

    Grech, Lisa B; Kiropoulos, Litza A; Kirby, Katherine M; Butler, Ernest; Paine, Mark; Hester, Robert

    2017-10-01

    Executive function deficits are prevalent in people with multiple sclerosis (PwMS), and PwMS use less adaptive coping than healthy controls. This cross-sectional study assessed whether there is a relationship between executive function and coping in PwMS. One hundred and seven participants with relapsing remitting or secondary progressive MS (n = 83 and 24, respectively; age M = 48.8 ± 11.1 years) completed measures of coping and executive function. A positive relationship was found between verbal fluency and use of active, emotional, and instrumental social support coping, and total executive function and substance abuse coping. There was a negative relationship between coping strategies and core (social support, acceptance, religion, restraint, and total coping), higher order (denial and humor), and total executive function indices (acceptance, religion, behavioral disengagement, denial, and total coping). These directional differences provide support for the importance of specific executive functions in coping strategy utilization. Understanding these relationships will assist psychologists and neuropsychologists with patient psychoeducation, adaptive coping strategy intervention and management for PwMS with reduced executive function ability.

  18. Spectral Data Captures Important Variability Between and Among Species and Functional Types

    Science.gov (United States)

    Townsend, P. A.; Serbin, S. P.; Kingdon, C.; Singh, A.; Couture, J. J.; Gamon, J. A.

    2013-12-01

    Narrowband spectral data in the visible, near and shortwave infrared (400-2500 nm) are being used increasingly in plant ecology to characterize the biochemical, physiological and water status of vegetation, as well as community composition. In particular, spectroscopic data have recently received considerable attention for their capacity to discriminate plants according to functional properties or 'optical types.' Such measurements can be acquired from airborne/satellite remote sensing imagery or field spectrometers and are commonly used to directly estimate or infer properties important to photosynthesis, carbon and water fluxes, nutrient dynamics, phenology, and disturbance. Spectral data therefore represent proxies for measurements that are otherwise time consuming or expensive to make, and - more importantly - provide the opportunity to characterize the spatial and temporal variability of taxonomic or functional groups. We have found that spectral variation within species and functional types can in fact exceed the variation between types. As such, we recommend that the traditional quantification of characteristics defining species and/or functional types must be modified to include the range of variability in those properties. We provide four examples of the importance of spectral data for describing within-species/functional type variation. First, within temperate forests, the spectral properties of foliage vary considerably with canopy position. This variability is strongly related to differences in specific leaf area between shade- and sun-lit leaves, and the resulting differences among leaves in strategies for light harvesting, photosynthesis, and leaf longevity. These results point to the need to better characterize leaf optical properties throughout a canopy, rather than basing the characterization of ecosystem functioning on only the sunlit portion of the canopy crown. Second, we show considerable differences in optical properties of foliage from

  19. Mutational analysis of a plant defensin from radish (Raphanus sativus L.) reveals two adjacent sites important for antifungal activity.

    Science.gov (United States)

    De Samblanx, G W; Goderis, I J; Thevissen, K; Raemaekers, R; Fant, F; Borremans, F; Acland, D P; Osborn, R W; Patel, S; Broekaert, W F

    1997-01-10

    Mutational analysis of Rs-AFP2, a radish antifungal peptide belonging to a family of peptides referred to as plant defensins, was performed using polymerase chain reaction-based site-directed mutagenesis and yeast as a system for heterologous expression. The strategy followed to select candidate amino acid residues for substitution was based on sequence comparison of Rs-AFP2 with other plant defensins exhibiting differential antifungal properties. Several mutations giving rise to peptide variants with reduced antifungal activity against Fusarium culmorum were identified. In parallel, an attempt was made to construct variants with enhanced antifungal activity by substituting single amino acids by arginine. Two arginine substitution variants were found to be more active than wild-type Rs-AFP2 in media with high ionic strength. Our data suggest that Rs-AFP2 possesses two adjacent sites that appear to be important for antifungal activity, namely the region around the type VI beta-turn connecting beta-strands 2 and 3, on the one hand, and the region formed by residues on the loop connecting beta-strand 1 and the alpha-helix and contiguous residues on the alpha-helix and beta-strand 3, on the other hand. When added to F. culmorum in a high ionic strength medium, Rs-AFP2 stimulated Ca2+ uptake by up to 20-fold. An arginine substitution variant with enhanced antifungal activity caused increased Ca2+ uptake by up to 50-fold, whereas a variant that was virtually devoid of antifungal activity did not stimulate Ca2+ uptake.

  20. The complex and important cellular and metabolic functions of saturated fatty acids.

    Science.gov (United States)

    Legrand, Philippe; Rioux, Vincent

    2010-10-01

    This review summarizes recent findings on the metabolism and biological functions of saturated fatty acids (SFA). Some of these findings show that SFA may have important and specific roles in the cells. Elucidated biochemical mechanisms like protein acylation (N-myristoylation, S-palmitoylation) and regulation of gene transcription are presented. In terms of physiology, SFA are involved for instance in lipogenesis, fat deposition, polyunsaturated fatty acids bioavailability and apoptosis. The variety of their functions demonstrates that SFA should no longer be considered as a single group.

  1. Physical Function Assessment of a Mayan Population Living With Osteoarthritis: The Importance of Considering Different Aspects of Functioning

    Directory of Open Access Journals (Sweden)

    Adalberto Loyola-Sanchez

    2017-06-01

    Full Text Available Objectives: To assess the physical function of people living with osteoarthritis in a Maya-Yucateco rural community from 3 perspectives and explore factors associated with the presence of disability. Design: Physical function and social, physical, psychological, and behavioral factors were evaluated in all adults detected with hand, hip, and/or knee osteoarthritis (n = 144 through a Community-Oriented Program for the Control of Rheumatic Diseases–based census in the Mayan community of Chankom, Yucatán. All cases fulfilled the American College of Rheumatology criteria. Physical function was assessed from 3 perspectives: hypothetical or “what people think they can do” (Health Assessment Questionnaire-Disability Index [HAQ-DI], experimental or “what people could do in standardized conditions” (6-minute walk test [6MWT] + the Functional Dexterity Test and enacted or “what people actually do” (personal care, work, and leisure activities’ self-report. Results: About 80% of participants reported “mild” disability (HAQ-DI ≤ 1 in the hypothetical function perspective, whereas average experimental function scores were low (6MWT: 206 m, Functional Dexterity Test: 64 seconds, and 78% of participants reported problems with enacted function (ie, work. Pain was significantly associated with disability in the hypothetical perspective (odds ratio [OR] = 3 [95% confidence interval [CI]: 1-4]; levels of wealth (β = 5 [95% CI: 1-9] and muscle strength (β = 54 [95% CI: 20-87] were significantly associated with functioning in the experimental perspective; and lower levels of self-efficacy (OR = 12 [95% CI: 6-27] and physical activity (OR = 12 [95% CI: 6-27] were significantly associated with work disability in the enacted function perspective. Conclusions: People living with osteoarthritis in Chankom show important issues when assessing physical function at the experimental and enacted perspectives, which

  2. Application of a biotin functionalized QD assay for determining available binding sites on electrospun nanofiber membrane

    Directory of Open Access Journals (Sweden)

    Magnone Joshua

    2011-10-01

    Full Text Available Abstract Background The quantification of surface groups attached to non-woven fibers is an important step in developing nanofiber biosensing detection technologies. A method utilizing biotin functionalized quantum dots (QDs 655 for quantitative analysis of available biotin binding sites within avidin immobilized on electrospun nanofiber membranes was developed. Results A method for quantifying nanofiber bound avidin using biotin functionalized QDs is presented. Avidin was covalently bound to electrospun fibrous polyvinyl chloride (PVC 1.8% COOH w/w containing 10% w/w carbon black membranes using primary amine reactive EDC-Sulfo NHS linkage chemistry. After a 12 h exposure of the avidin coated membranes to the biotin-QD complex, fluorescence intensity was measured and the total amount of attached QDs was determined from a standard curve of QD in solution (total fluorescence vs. femtomole of QD 655. Additionally, fluorescence confocal microscopy verified the labeling of avidin coated nanofibers with QDs. The developed method was tested against 2.4, 5.2, 7.3 and 13.7 mg spray weights of electrospun nanofiber mats. Of the spray weight samples tested, maximum fluorescence was measured for a weight of 7.3 mg, not at the highest weight of 13.7 mg. The data of total fluorescence from QDs bound to immobilized avidin on increasing weights of nanofiber membrane was best fit with a second order polynomial equation (R2 = .9973 while the standard curve of total fluorescence vs. femtomole QDs in solution had a linear response (R2 = .999. Conclusion A QD assay was developed in this study that provides a direct method for quantifying ligand attachment sites of avidin covalently bound to surfaces. The strong fluorescence signal that is a fundamental characteristic of QDs allows for the measurement of small changes in the amount of these particles in solution or attached to surfaces.

  3. The importance of Asn47 for structure and reactivity of azurin from Alcaligenes denitrificans as studied by site-directed mutagenesis and spectroscopy.

    Science.gov (United States)

    Hoitink, C W; Canters, G W

    1992-07-15

    To study the importance of a rigid copper site for the structure and function of azurin, a mutant with a reduced number of internal hydrogen bonds around the copper has been prepared and characterized. To this purpose, the previously cloned azu gene from Alcaligenes denitrificans (Hoitink, C. W. G., Woudt, L. P., Turenhout, J. C. M., Van de Kamp, M., and Canters, G. W. (1990) Gene (Amst.) 90, 15-20) was expressed in Escherichia coli and an isolation and purification procedure for the azurin was developed. The azurin obtained after heterologous expression in E. coli appears spectroscopically indistinguishable from azurin derived from A. denitrificans. The hydrogen bonding network around the copper site was altered by replacing Asn47 by a leucine by means of site-directed mutagenesis. Asn47 is a conserved residue in all blue copper proteins of which the primary structure has been reported. Characterization of the mutant protein with UV-visible, electron spin resonance, and NMR spectroscopy, and comparison with the wild type azurin revealed that the structure of the copper site as well as the overall structure of the protein have been largely retained. The redox activity as measured by the electron self-exchange rate appears not to have changed either. However, the mutant differs from the wild type azurin with respect to stability and midpoint potential. Midpoint potentials of mutant and wild type azurin amount to 396 and 286 mV, respectively. The difference is due to sizable entropic and enthalpic contributions which to a large extent cancel. Possible explanations for the outcome of these experiments are discussed.

  4. Rat Islet Isograft Function. Effect of Graft Volume and Transplantation Site

    NARCIS (Netherlands)

    Suylichem, Paul T.R. van; Strubbe, Jan H.; Houwing, Harmina; Wolters, Gerrit H.J.; Schilfgaarde, Reinout van

    1994-01-01

    Islet isograft function was analyzed after transplantation of 4 well-defined endocrine volumes (12.5%, 25%, 50%, and 100% of the endocrine volume in the normal adult rat pancreas) to 3 different sites (kidney, liver, and spleen). Graft function was tested in unanesthetized, unstressed rats by the re

  5. The complex and important cellular and metabolic functions of saturated fatty acids

    OpenAIRE

    Legrand, Philippe; Rioux, Vincent

    2010-01-01

    This review summarizes recent findings on the metabolism and biological functions of saturated fatty acids (SFA). Some of these findings show that SFA may have important and specific roles in the cells. Elucidated biochemical mechanisms like protein acylation (N-myristoylation, S-palmitoylation) and regulation of gene transcription are presented. In terms of physiology, SFA are involved for instance in lipogenesis, fat deposition, polyunsaturated fatty acids bioavailability and apoptosis. The...

  6. Inulin and Oligofructosis: a review about functional properties, prebiotic effects and importance for food industry

    OpenAIRE

    Maria Celia de Oliveira Hauly; Janaína Andréa Moscatto

    2002-01-01

    Nowadays consumers are more conscious about the relation between food and health. Therefore food industry has been looking for food that has a lot of benefits besides good flavor and appearance. Inulin and oligofructose are fructose polimers, vastly found in plants as storage carbohydrates. They present important functional for the food industry. Both inulin and oligofructose have been used as fiber bulk in food products. Differently from other fibers, they do not add flavor, allowing the foo...

  7. Method and system to reclaim functional sites on a sorbent contaminated by heat stable salts

    Science.gov (United States)

    Krutka, Holly; Sjostrom, Sharon; Morris, William J.

    2016-03-08

    The objective of this invention is to develop a method to reclaim functional sites on a CO.sub.2 sorbent that have reacted with an acid gas (other than CO.sub.2) to form heat stable salts (HSS). HSS are a significant concern for dry sorbent based CO.sub.2 capture because over time the buildup of HSS will reduce the overall functionality of the CO.sub.2 sorbent. A chemical treatment can remove the non-CO.sub.2 acid gas and reclaim functional sites that can then be used for further CO.sub.2 adsorption.

  8. Objective measures for predicting speech intelligibility in noisy conditions based on new band-importance functions.

    Science.gov (United States)

    Ma, Jianfen; Hu, Yi; Loizou, Philipos C

    2009-05-01

    The articulation index (AI), speech-transmission index (STI), and coherence-based intelligibility metrics have been evaluated primarily in steady-state noisy conditions and have not been tested extensively in fluctuating noise conditions. The aim of the present work is to evaluate the performance of new speech-based STI measures, modified coherence-based measures, and AI-based measures operating on short-term (30 ms) intervals in realistic noisy conditions. Much emphasis is placed on the design of new band-importance weighting functions which can be used in situations wherein speech is corrupted by fluctuating maskers. The proposed measures were evaluated with intelligibility scores obtained by normal-hearing listeners in 72 noisy conditions involving noise-suppressed speech (consonants and sentences) corrupted by four different maskers (car, babble, train, and street interferences). Of all the measures considered, the modified coherence-based measures and speech-based STI measures incorporating signal-specific band-importance functions yielded the highest correlations (r=0.89-0.94). The modified coherence measure, in particular, that only included vowel/consonant transitions and weak consonant information yielded the highest correlation (r=0.94) with sentence recognition scores. The results from this study clearly suggest that the traditional AI and STI indices could benefit from the use of the proposed signal- and segment-dependent band-importance functions.

  9. Structure and magnetism in S r1 -xAxTc O3 perovskites: Importance of the A -site cation

    Science.gov (United States)

    Reynolds, Emily; Avdeev, Maxim; Thorogood, Gordon J.; Poineau, Frederic; Czerwinski, Kenneth R.; Kimpton, Justin A.; Yu, Michelle; Kayser, Paula; Kennedy, Brendan J.

    2017-02-01

    The S r1 -xB axTc O3 (x =0 , 0.1, 0.2) oxides were prepared and their solid-state and magnetic structure studied as a function of temperature by x-ray and neutron powder diffraction. The refined Tc moments at room temperature and Néel temperatures for B a0.1S r0.9Tc O3 and B a0.2S r0.8Tc O3 were 2.32 (14 ) μβ and 2.11 (13 ) μβ and 714 ∘C and 702 ∘C , respectively. In contrast to expectations, the Néel temperature in the series S r1 -xAxTc O3 decreases with increasing Ba content. This observation is consistent with previous experimental measurements for the two series A M O3 (M =Ru , Mn; A =Ca , Sr, Ba) where the maximum magnetic ordering temperature was observed for A =Sr . Taken with these previous results the current work demonstrates the critical role of the A -site cation in the broadening of the π* bandwidth and ultimately the magnetic ordering temperature.

  10. Skin Barrier Function and Its Importance at the Start of the Atopic March

    Directory of Open Access Journals (Sweden)

    Mary Beth Hogan

    2012-01-01

    Full Text Available Atopic dermatitis can be due to a variety of causes from nonatopic triggers to food allergy. Control of egress of water and protection from ingress of irritants and allergens are key components of cutaneous barrier function. Current research suggests that a degraded barrier function of the skin allows the immune system inappropriate access to environmental allergens. Epidermal aeroallergen exposure may allow sensitization to allergen possibly initiating the atopic march. Further research into connections between epidermal barrier function and possible allergen sensitization will be important to undertake. Future clinical trials focused on skin barrier protection may be of value as a possible intervention in prevention of the initiation of the atopic march.

  11. Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase.

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    Sandeep Chakraborty

    Full Text Available Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - CataLytic Active Site Prediction (CLASP. In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP, one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP, where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in

  12. Active site detection by spatial conformity and electrostatic analysis--unravelling a proteolytic function in shrimp alkaline phosphatase.

    Science.gov (United States)

    Chakraborty, Sandeep; Minda, Renu; Salaye, Lipika; Bhattacharjee, Swapan K; Rao, Basuthkar J

    2011-01-01

    Computational methods are increasingly gaining importance as an aid in identifying active sites. Mostly these methods tend to have structural information that supplement sequence conservation based analyses. Development of tools that compute electrostatic potentials has further improved our ability to better characterize the active site residues in proteins. We have described a computational methodology for detecting active sites based on structural and electrostatic conformity - CataLytic Active Site Prediction (CLASP). In our pipelined model, physical 3D signature of any particular enzymatic function as defined by its active sites is used to obtain spatially congruent matches. While previous work has revealed that catalytic residues have large pKa deviations from standard values, we show that for a given enzymatic activity, electrostatic potential difference (PD) between analogous residue pairs in an active site taken from different proteins of the same family are similar. False positives in spatially congruent matches are further pruned by PD analysis where cognate pairs with large deviations are rejected. We first present the results of active site prediction by CLASP for two enzymatic activities - β-lactamases and serine proteases, two of the most extensively investigated enzymes. The results of CLASP analysis on motifs extracted from Catalytic Site Atlas (CSA) are also presented in order to demonstrate its ability to accurately classify any protein, putative or otherwise, with known structure. The source code and database is made available at www.sanchak.com/clasp/. Subsequently, we probed alkaline phosphatases (AP), one of the well known promiscuous enzymes, for additional activities. Such a search has led us to predict a hitherto unknown function of shrimp alkaline phosphatase (SAP), where the protein acts as a protease. Finally, we present experimental evidence of the prediction by CLASP by showing that SAP indeed has protease activity in vitro.

  13. Executive function deficits in congenital heart disease: why is intervention important?

    Science.gov (United States)

    Calderon, Johanna; Bellinger, David C

    2015-10-01

    It is widely recognised that children with congenital heart disease (CHD) are at high risk for neurodevelopmental impairments including attention deficit hyperactivity disorder and autism spectrum disorder symptoms. Executive function impairments are one of the most prominent neurodevelopmental features associated with CHD. These deficits can have widespread debilitating repercussions in children's neurocognitive, behavioural, and psycho-social development. There is a crucial gap in research regarding the efficacy of preventive or treatment strategies for these important cognitive morbidities. Executive functions are complex neurocognitive skills highly amenable to improvement. Evidence-based interventions have shown promising results in other paediatric populations, strongly suggesting that they might also benefit the growing population of children with CHD. In this review, we summarise the available data on executive function impairments in children and adolescents with CHD. We underline the important co-morbidity of executive dysfunction with other cognitive and psychiatric issues in CHD, which raises awareness of the crucial need to prevent or at least mitigate these deficits. Finally, we summarise future avenues for research in terms of interventions that may help reduce executive function impairments in youth with CHD.

  14. The Band-Importance Function for the Korean Standard Sentence Lists for Adults

    Science.gov (United States)

    Jin, In-Ki; Lee, Kyoungwon; Kim, Jinsook; Kim, Dongwook; Sohn, Junil; Lee, Kyung-Ju

    2016-01-01

    Background and Objectives The band-importance function (BIF) refers to a value characterizing the relative importance of different frequencies to speech intelligibility. The purpose of this study was to derive the BIF for the Korean standard sentence lists for adults (KS-SL-A). Subjects and Methods In this study, sentences from the KS-SL-A were used as the speech material. Twenty-six normal-hearing Korean listeners participated and intelligibility scores in 8 filters with 3 signal-to-noise ratio conditions were obtained. Based on the intelligibility score percentages, the BIF for the KS-SL-A was derived by using an established protocol. Results Band-importance weights varied across frequency bands. The most important frequency region was around 316 Hz (20.0%), and the importance of the frequency bands below the center frequency (CF) of 1,778 Hz was 59.6%. Therefore, low frequencies below the CF of 1,778 Hz were more important than high frequencies above the CF of 1,778 Hz. Conclusions The BIF for KS-SL-A could be applied towards developing a hearing aid fitting formulae for Korean listeners. PMID:27626080

  15. Mosquito distribution and West Nile virus infection in zoos and in important sites of migratory and resident birds, Thailand

    Directory of Open Access Journals (Sweden)

    Tanasak Changbunjong

    2012-08-01

    Full Text Available Objective: To investigate the distribution of mosquito species in the zoos and in important sites of migratory and resident birds and evaluate West Nile virus (WNV infection in mosquito species. Methods: Mosquitoes distribution investigation was carried out bimonthly from January 2009 to December 2010 in five areas of birds, Thailand by using Centers for Disease Control, light traps, and gravid traps. Mosquitoes were identified, pooled into groups of up to 50 mosquitoes by species, places and time of collection and tested for WNV infection by viral isolation and reverse transcriptase polymerase chain reaction. Results: A total of 66 597 mosquitoes comprising 26 species in 8 genera were collected. The five most abundant mosquito species collected were Culex tritaeniorhynchus (79.3%, Culex vishnui (8.2%, Culex sitiens (6%, Culex quinquefasciatus (3.3% and Anopheles peditaeniatus (1.1%. All 1 736 mosquito pools were negative for viral isolation and reverse transcriptase polymerase chain reaction. Conclusions: This study provides new information on number of mosquito species present and their relative abundance. Although our study found no evidence of WNV in the avifaunal sources of Thailand, mosquito active surveillance should be continuously conducted. The cooperation between related organizations is needed for early detection of WNV disease and development of effective veterinary and public health policies in this region.

  16. Residents' Attitudes Towards Tourism in a Globally Important Agricultural Heritage Systems Pilot Site:a Case Study in China

    Institute of Scientific and Technical Information of China (English)

    Sun Yehong; Min Qingwen; Cheng Shengkui

    2009-01-01

    Globally Important Agricultural Heritage Systems (GIAHS) is a wide program to promote the conservation and adaptive management of such systems and their associated landscapes,biodiversity,knowledge systems and cultures.Rice-Fish Systems (RFS) in Longxian village of China,as a traditional agricultural system,was selected as one of the five pilot sites of GIAHS in 2005.Researchers have paid more attention to the dynamic conservation and adaptive management of RFS because it is under severe threats from global development challenges.Tourism is suggested to be brought into the RFS conservation program as an alternative industry.This paper presents a comparative study of residents in three types of farm household in Longxian,seeking attitudes to the RFS conservation and tourism development and ways in which such information may guide future strategies.Results show residents,belonging to the household type in which most family members are abroad,have the most positive attitudes to RFS conservation and tourism development;while residents,as other household type in which less than 50% of family members are abroad,are the least sensitive group in these three household types,due to the motivation of moving abroad weakening their enthusiasm to participate in the local activities.Implications are discussed in the context of how resident attitudes will affect the future management of GIAHS conservation and tourism development,and then measures are put forward to foster tourism cooperation and multistakeholders process establishment.

  17. Functional diversity, soil features and community functioning: a test in a cerrado site.

    Science.gov (United States)

    Freitas, J R; Cianciaruso, M V; Batalha, M A

    2012-08-01

    Community functioning may be affected by functional diversity, which measures the extent of complementarity in resource use. We tested whether there was a relationship between functional diversity of woody species and community functioning on a fine scale, using FD as a measure of functional diversity and litter decomposition rate as a surrogate for community functioning. We measured eight functional traits from a woodland cerrado community in southeastern Brazil. Then, we tested the correlation between FD and the decomposition rate taking into account differences in soil features and between decomposition rate and each trait separately. The decomposition rate was related to the aluminium and phosphorus concentration in soil, but not to FD, pointing out that functional diversity was not a good predictor of community functioning. There was a non-significant relationship between FD and the decomposition rate even when we considered each trait separately. Most studies in the relationships between biodiversity and community functioning on fine scales were carried out by experimental manipulation of diversity and in temperate regions. We carried out this fine scale study as a mensurative experiment and in a tropical savanna. Our findings indicated that the relationship between biodiversity and community functioning is not as straightforward as usually assumed.

  18. Functional diversity, soil features and community functioning: a test in a cerrado site

    Directory of Open Access Journals (Sweden)

    JR. Freitas

    Full Text Available Community functioning may be affected by functional diversity, which measures the extent of complementarity in resource use. We tested whether there was a relationship between functional diversity of woody species and community functioning on a fine scale, using FD as a measure of functional diversity and litter decomposition rate as a surrogate for community functioning. We measured eight functional traits from a woodland cerrado community in southeastern Brazil. Then, we tested the correlation between FD and the decomposition rate taking into account differences in soil features and between decomposition rate and each trait separately. The decomposition rate was related to the aluminium and phosphorus concentration in soil, but not to FD, pointing out that functional diversity was not a good predictor of community functioning. There was a non-significant relationship between FD and the decomposition rate even when we considered each trait separately. Most studies in the relationships between biodiversity and community functioning on fine scales were carried out by experimental manipulation of diversity and in temperate regions. We carried out this fine scale study as a mensurative experiment and in a tropical savanna. Our findings indicated that the relationship between biodiversity and community functioning is not as straightforward as usually assumed.

  19. Importance of post-translational modifications on the function of key haemostatic proteins.

    Science.gov (United States)

    Karlaftis, Vasiliki; Perera, Sachin; Monagle, Paul; Ignjatovic, Vera

    2016-01-01

    Post-translational modifications (PTMs) such as glycosylation and phosphorylation play an important role on the function of haemostatic proteins and are critical in the setting of disease. Such secondary level changes to haemostatic proteins have wide ranging effects on their ability to interact with other proteins. This review aimed to summarize the knowledge of the common PTMs associated with haemostatic proteins and the implications of such modifications on protein function. Haemostatic proteins that represent the main focus for studies specific to PTMs are von Willebrand factor, tissue factor, factor VIII, antithrombin and fibrinogen. These proteins are susceptible to PTMs by glycosylation, phosphorylation, sulphation, citrullination and nitration, respectively, with a significant impact on their function. During synthesis, vWF must undergo extensive PTMs, with N-linked glycosylation being the most common. Increased phosphorylation of tissue factor results in increased affinity for platelets to the vessel endothelium. Citrullination of antithrombin leads to an increased anticoagulant function of this protein and therefore an anticoagulant state that inhibits clot formation. On the contrary, nitration of fibrinogen has been shown to result in a prothrombotic state, whilst sulphation is required for the normal function of Factor VIII. From this review, it is evident that PTMs of haemostatic proteins as a change in protein structure at a secondary level greatly influences the behaviour of the protein at a tertiary level.

  20. Improving ATLAS grid site reliability with functional tests using HammerCloud

    CERN Document Server

    Legger, F; The ATLAS collaboration; Medrano Llamas, R; Sciacca, G; Van der Ster, D C

    2012-01-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes more than 80 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short light-weight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate si...

  1. Investigation of the metal binding site in methionine aminopeptidase by density functional theory

    DEFF Research Database (Denmark)

    Jørgensen, Anne Techau; Norrby, Per-Ola; Liljefors, Tommy

    2002-01-01

    All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co2+ ions or Zn2+ ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions...... oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based...... on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion....

  2. Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori HtrA

    Science.gov (United States)

    Schmidt, Thomas P.; Perna, Anna M.; Fugmann, Tim; Böhm, Manja; Jan Hiss; Haller, Sarah; Götz, Camilla; Tegtmeyer, Nicole; Hoy, Benjamin; Rau, Tilman T.; Neri, Dario; Backert, Steffen; Schneider, Gisbert; Wessler, Silja

    2016-03-01

    The cell adhesion protein and tumour suppressor E-cadherin exhibits important functions in the prevention of gastric cancer. As a class-I carcinogen, Helicobacter pylori (H. pylori) has developed a unique strategy to interfere with E-cadherin functions. In previous studies, we have demonstrated that H. pylori secretes the protease high temperature requirement A (HtrA) which cleaves off the E-cadherin ectodomain (NTF) on epithelial cells. This opens cell-to-cell junctions, allowing bacterial transmigration across the polarised epithelium. Here, we investigated the molecular mechanism of the HtrA-E-cadherin interaction and identified E-cadherin cleavage sites for HtrA. Mass-spectrometry-based proteomics and Edman degradation revealed three signature motifs containing the [VITA]-[VITA]-x-x-D-[DN] sequence pattern, which were preferentially cleaved by HtrA. Based on these sites, we developed a substrate-derived peptide inhibitor that selectively bound and inhibited HtrA, thereby blocking transmigration of H. pylori. The discovery of HtrA-targeted signature sites might further explain why we detected a stable 90 kDa NTF fragment during H. pylori infection, but also additional E-cadherin fragments ranging from 105 kDa to 48 kDa in in vitro cleavage experiments. In conclusion, HtrA targets E-cadherin signature sites that are accessible in in vitro reactions, but might be partially masked on epithelial cells through functional homophilic E-cadherin interactions.

  3. The important role of stratum corneum lipids for the cutaneous barrier function.

    Science.gov (United States)

    van Smeden, J; Janssens, M; Gooris, G S; Bouwstra, J A

    2014-03-01

    The skin protects the body from unwanted influences from the environment as well as excessive water loss. The barrier function of the skin is located in the stratum corneum (SC). The SC consists of corneocytes embedded in a lipid matrix. This lipid matrix is crucial for the lipid skin barrier function. This paper provides an overview of the reported SC lipid composition and organization mainly focusing on healthy and diseased human skin. In addition, an overview is provided on the data describing the relation between lipid modulations and the impaired skin barrier function. Finally, the use of in vitro lipid models for a better understanding of the relation between the lipid composition, lipid organization and skin lipid barrier is discussed. This article is part of a Special Issue entitled The Important Role of Lipids in the Epidermis and their Role in the Formation and Maintenance of the Cutaneous Barrier. This article is part of a Special Issue entitled The Important Role of Lipids in the Epidermis and their Role in the Formation and Maintenance of the Cutaneous Barrier. Guest Editors: Kenneth R. Feingold and Peter Elias.

  4. The Human p73 Promoter: Characterization and Identification of Functional E2F Binding Sites

    Directory of Open Access Journals (Sweden)

    Ratnam S. Seelan

    2002-01-01

    Full Text Available p73, a member of the p53 family, is overexpressed in many cancers. To understand the mechanism(s underlying this overexpression, we have undertaken a detailed characterization of the human p73 promoter. The promoter is strongly activated in cells expressing exogenous E2F1 and suppressed by exogenous Rb. At least three functional E2F binding sites, located immediately upstream of exon 1 (at-284,-155 and-132 mediate this induction. 5' serially deleted promoter constructs and constructs harboring mutated E2F sites were analyzed for their response to exogenously expressed E2F1 or Rb to establish functionality of these sites. Authenticity of E2F sites was further confirmed by electrophoretic mobility shift assay (EMSA using E2F1 /DP1 heterodimers synthesized in vitro, followed by competition assays with unlabeled wild-type or mutant oligonucleotides and supershift analysis using anti-E2F1 antibodies. In vivo binding of E2F1 to the p73 promoter was demonstrated using nuclear extracts prepared from E2F1-inducible Saos2 cells. The region conferring the highest promoter activity was found to reside between-113 to-217 of the p73 gene. Two of the three functional E2F sites (at-155 and-132 reside within this region. Our results suggest that regulation of p73 expression is primarily mediated through binding of E2 F1 to target sites at-155 and-132.

  5. MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets

    Science.gov (United States)

    Bandyopadhyay, Sanghamitra; Ghosh, Dip; Mitra, Ramkrishna; Zhao, Zhongming

    2015-01-01

    MicroRNA (miRNA) regulates gene expression by binding to specific sites in the 3'untranslated regions of its target genes. Machine learning based miRNA target prediction algorithms first extract a set of features from potential binding sites (PBSs) in the mRNA and then train a classifier to distinguish targets from non-targets. However, they do not consider whether the PBSs are functional or not, and consequently result in high false positive rates. This substantially affects the follow up functional validation by experiments. We present a novel machine learning based approach, MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets), for accurate prediction of true or functional miRNA binding sites. Multiple instance learning framework is adopted to handle the lack of information about the actual binding sites in the target mRNAs. Biologically validated 9531 interacting and 973 non-interacting miRNA-mRNA pairs are identified from Tarbase 6.0 and confirmed with PAR-CLIP dataset. It is found that MBSTAR achieves the highest number of binding sites overlapping with PAR-CLIP with maximum F-Score of 0.337. Compared to the other methods, MBSTAR also predicts target mRNAs with highest accuracy. The tool and genome wide predictions are available at http://www.isical.ac.in/~bioinfo_miu/MBStar30.htm.

  6. Improving ATLAS grid site reliability with functional tests using HammerCloud

    Science.gov (United States)

    Elmsheuser, Johannes; Legger, Federica; Medrano Llamas, Ramon; Sciacca, Gianfranco; van der Ster, Dan

    2012-12-01

    With the exponential growth of LHC (Large Hadron Collider) data in 2011, and more coming in 2012, distributed computing has become the established way to analyse collider data. The ATLAS grid infrastructure includes almost 100 sites worldwide, ranging from large national computing centers to smaller university clusters. These facilities are used for data reconstruction and simulation, which are centrally managed by the ATLAS production system, and for distributed user analysis. To ensure the smooth operation of such a complex system, regular tests of all sites are necessary to validate the site capability of successfully executing user and production jobs. We report on the development, optimization and results of an automated functional testing suite using the HammerCloud framework. Functional tests are short lightweight applications covering typical user analysis and production schemes, which are periodically submitted to all ATLAS grid sites. Results from those tests are collected and used to evaluate site performances. Sites that fail or are unable to run the tests are automatically excluded from the PanDA brokerage system, therefore avoiding user or production jobs to be sent to problematic sites.

  7. Metal uptake by homegrown vegetables – The relative importance in human health risk assessments at contaminated sites

    Energy Technology Data Exchange (ETDEWEB)

    Augustsson, Anna L.M., E-mail: anna.augustsson@lnu.se [Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar (Sweden); Uddh-Söderberg, Terese E. [Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar (Sweden); Hogmalm, K. Johan [Department of Earth Sciences, University of Gothenburg, Gothenburg (Sweden); Filipsson, Monika E.M. [Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar (Sweden)

    2015-04-15

    Risk assessments of contaminated land often involve the use of generic bioconcentration factors (BCFs), which express contaminant concentrations in edible plant parts as a function of the concentration in soil, in order to assess the risks associated with consumption of homegrown vegetables. This study aimed to quantify variability in BCFs and evaluate the implications of this variability for human exposure assessments, focusing on cadmium (Cd) and lead (Pb) in lettuce and potatoes sampled around 22 contaminated glassworks sites. In addition, risks associated with measured Cd and Pb concentrations in soil and vegetable samples were characterized and a probabilistic exposure assessment was conducted to estimate the likelihood of local residents exceeding tolerable daily intakes. The results show that concentrations in vegetables were only moderately elevated despite high concentrations in soil, and most samples complied with applicable foodstuff legislation. Still, the daily intake of Cd (but not Pb) was assessed to exceed toxicological thresholds for about a fifth of the study population. Bioconcentration factors were found to vary more than indicated by previous studies, but decreasing BCFs with increasing metal concentrations in the soil can explain why the calculated exposure is only moderately affected by the choice of BCF value when generic soil guideline values are exceeded and the risk may be unacceptable. - Highlights: • Uptake of Cd and Pb by lettuce and potatoes increased with soil contamination. • Consumption of homegrown vegetables may lead to a daily Cd intake above TDIs. • The variability in the calculated BCFs is high when compared to previous studies. • Exposure assessments are most sensitive to the choice of BCFs at low contamination.

  8. Characteristics and distribution of trulli constructions in the area of the site of community importance Murgia of Trulli

    Directory of Open Access Journals (Sweden)

    Giuseppe Ruggiero

    2013-10-01

    Full Text Available The agro-forestry territory in the Region of Apulia, southern Italy, is characterised by a widespread and diversified presence of dry stone constructions, including trulli, rural buildings with a characteristic a conical shape. The trulli are mainly to be found in the central and eastern part of the region, called Murgia of Trulli. Trulli are perfectly integrated with the agro-environment specificity of the area, creating a unique landscape and establishing themselves as a testimony of tradition and rural culture. In fact, in this area, from the 17th until the mid-20th century, the trulli accompanied the development of agricultural activities. According to the number of cones they had, they were used as temporary shelters, places of support for primary production, or comfortable houses for the rural population. In recent decades, for several social and economic reasons, this heritage of rural buildings has been affected by abandonment and degradation phenomena. Interventions aimed at recovery and re-use have not always respected the origin of the buildings, their design characteristics or the landscape in which they had been built. In order to reduce the impact that this situation has had on environmental and territorial quality it is, therefore, necessary to develop initiatives to protect and valorise the trulli while respecting the identity of place, the architectural elements, and the agricultural and environmental characteristics of the territory. For this purpose, we need to analyse and characterise the heritage of the existing trulli and its relationship with the local reality. The present paper analyses the typology and distribution of the trulli located on the site of community importance Murgia of Trulli, a protected area with high environmental value in the central-eastern area of the Region of Apulia. Specifically, we analysed the relationship between the trulli buildings and the agro-environment context to acquire a basic

  9. Importance of Beta Cell Function for the Treatment of Type 2 Diabetes

    Directory of Open Access Journals (Sweden)

    Yoshifumi Saisho

    2014-08-01

    Full Text Available Type 2 diabetes (T2DM is characterized by insulin resistance and beta cell dysfunction. Recent evidence has emerged that beta cell dysfunction is a common pathogenetic feature of both type 1 and type 2 diabetes, and T2DM never develops without beta cell dysfunction. Therefore, treatment of T2DM should aim to restore beta cell function. Although the treatment of T2DM has greatly improved over the past few decades, remaining issues in the current treatment of T2DM include (1 hypoglycemia; (2 body weight gain; (3 peripheral hyperinsulinemia and (4 postprandial hyperglycemia, which are all associated with inappropriate insulin supplementation, again underpinning the important role of endogenous and physiological insulin secretion in the management of T2DM. This review summarizes the current knowledge on beta cell function in T2DM and discusses the treatment strategy for T2DM in relation to beta cell dysfunction.

  10. Green's functions for uniformly distributed loads acting on an inclined line in a poroelastic layered site

    Institute of Scientific and Technical Information of China (English)

    Liang Jianwen; You Hongbing

    2005-01-01

    Based on one type of practical Biot's equation and the dynamic-stiffness matrices ofa poroelastic soil layer and half-space, Green's functions were derived for uniformly distributed loads acting on an inclined line in a poroelastic layered site. This analysis overcomes significant problems in wave scattering due to local soil conditions and dynamic soil-structure interaction. The Green's functions can be reduced to the case of an elastic layered site developed by Wolf in 1985. Parametric studies are then carried out through two example problems.

  11. Determining importance weighting functions for Contributon theory eigenvalue sensitivity coefficient methodologies

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, C.; Martin, W. [Univ. of Michigan, Dept. of Nuclear Engineering and Radiological Sciences, 2355 Bonisteel Boulevard, Ann Arbor, MI 48109-2104 (United States); Rearden, B.; Williams, M. [Oak Ridge National Laboratory, Reactor and Nuclear Systems Div., Bldg. 5700, P.O. Box 2008, Oak Ridge, TN 37831-6170 (United States)

    2012-07-01

    This study introduced two new approaches for calculating the F*(r) importance weighting function for Contributon and CLUTCH eigenvalue sensitivity coefficient calculations, and compared them in terms of accuracy and applicability. The necessary levels of F*(r) mesh refinement and mesh convergence for obtaining accurate eigenvalue sensitivity coefficients were determined for two preliminary problems through two parametric studies, and the results of these studies suggest that a sufficiently accurate F*(r) mesh for calculating eigenvalue sensitivity coefficients can be obtained for these problems with only a small increase in problem runtime. (authors)

  12. Determining Importance Weighting Functions for Contributon Theory Eigenvalue Sensitivity Coefficient Methodologies

    Energy Technology Data Exchange (ETDEWEB)

    Perfetti, Christopher M [ORNL; Martin, William R [University of Michigan; Rearden, Bradley T [ORNL; Williams, Mark L [ORNL

    2012-01-01

    This study introduced three approaches for calculating the importance weighting function for Contributon and CLUTCH eigenvalue sensitivity coefficient calculations, and compared them in terms of accuracy and applicability. The necessary levels of mesh refinement and mesh convergence for obtaining accurate eigenvalue sensitivity coefficients were determined through two parametric studies, and the results of these studies suggest that a sufficiently-accurate mesh for calculating eigenvalue sensitivity coefficients can be obtained for the Contributon and CLUTCH methods with only a small increase in problem runtime.

  13. Site-specific differences in the association between plantar tactile perception and mobility function in older adults.

    Science.gov (United States)

    Cruz-Almeida, Yenisel; Black, Mieniecia L; Christou, Evangelos A; Clark, David J

    2014-01-01

    Impaired somatosensation is common in older adults and contributes to age-related loss of mobility function. However, little is known about whether somatosensation at different sites on the plantar surface of the foot are differentially related to mobility function. Such a finding may have important implications for clinical care of older adults and other at-risk populations, such as for optimizing interventions (e.g., footwear for augmenting somatosensory feedback) and for improving the efficiency of clinical assessment. Tactile perception was evaluated with a 10 g monofilament at four sites on the plantar surface of each foot: great toe (GT), first metatarsal head (MT1), heel (H) and fifth metatarsal head (MT5). Mobility function was assessed with the Berg Balance Scale and walking speed. Sixty-one older adults participated. Tactile perception was significantly positively associated with Berg Balance Score (adjusted r = 0.30 - 0.75; p = 0.03 - tactile perception found to be significantly associated with usual walking speed (adjusted r = 0.51; p tactile perception at MT1 is more closely linked to mobility function than is tactile perception at GT, MT5 or H. These findings warrant further research to examine whether interventions (e.g., textured insoles) and assessments that preferentially or exclusively focus on the site of MT1 may be more effective for optimizing clinical care.

  14. Site-specific differences in the association between plantar tactile perception and mobility function in older adults

    Directory of Open Access Journals (Sweden)

    Yenisel eCruz-Almeida

    2014-04-01

    Full Text Available Introduction Impaired somatosensation is common in older adults and contributes to age-related loss of mobility function. However, little is known about whether somatosensation at different sites on the plantar surface of the foot are differentially related to mobility function. Such a finding may have important implications for clinical care of older adults and other at-risk populations, such as for optimizing interventions (e.g., footwear for augmenting somatosensory feedback and for improving the efficiency of clinical assessment. Materials and Methods Tactile perception was evaluated with a 10g monofilament at four sites on the plantar surface of each foot: great toe (GT, first metatarsal head (MT1, heel (H and fifth metatarsal head (MT5. Mobility function was assessed with the Berg Balance Scale and walking speed. Results Sixty-one older adults participated. Tactile perception was significantly positively associated with Berg Balance Score (adjusted R2 = 0.30 - 0.75; p = 0.03 - Discussion The present findings indicate that tactile perception at MT1 is more closely linked to mobility function than is tactile perception at GT, MT5 or H. These findings warrant further research to examine whether interventions (e.g., textured insoles and assessments that preferentially or exclusively focus on the site of MT1 may be more effective for optimizing clinical care.

  15. Functional diversification of paralogous transcription factors via divergence in DNA binding site motif and in expression.

    Directory of Open Access Journals (Sweden)

    Larry N Singh

    Full Text Available BACKGROUND: Gene duplication is a major driver of evolutionary innovation as it allows for an organism to elaborate its existing biological functions via specialization or diversification of initially redundant gene paralogs. Gene function can diversify in several ways. Transcription factor gene paralogs in particular, can diversify either by changes in their tissue-specific expression pattern or by changes in the DNA binding site motif recognized by their protein product, which in turn alters their gene targets. The relationship between these two modes of functional diversification of transcription factor paralogs has not been previously investigated, and is essential for understanding adaptive evolution of transcription factor gene families. FINDINGS: Based on a large set of human paralogous transcription factor pairs, we show that when the DNA binding site motifs of transcription factor paralogs are similar, the expressions of the genes that encode the paralogs have diverged, so in general, at most one of the paralogs is highly expressed in a tissue. Moreover, paralogs with diverged DNA binding site motifs tend to be diverged in their function. Conversely, two paralogs that are highly expressed in a tissue tend to have dissimilar DNA binding site motifs. We have also found that in general, within a paralogous family, tissue-specific decrease in gene expression is more frequent than what is expected by chance. CONCLUSIONS: While previous investigations of paralogous gene diversification have only considered coding sequence divergence, by explicitly quantifying divergence in DNA binding site motif, our work presents a new paradigm for investigating functional diversification. Consistent with evolutionary expectation, our quantitative analysis suggests that paralogous transcription factors have survived extinction in part, either through diversification of their DNA binding site motifs or through alterations in their tissue-specific expression

  16. Cryptic biodiversity effects: importance of functional redundancy revealed through addition of food web complexity.

    Science.gov (United States)

    Philpott, Stacy M; Pardee, Gabriella L; Gonthier, David J

    2012-05-01

    Interactions between predators and the degree of functional redundancy among multiple predator species may determine whether herbivores experience increased or decreased predation risk. Specialist parasites can modify predator behavior, yet rarely have cascading effects on multiple predator species and prey been evaluated. We examined influences of specialist phorid parasites (Pseudacteon spp.) on three predatory ant species and herbivores in a coffee agroecosystem. Specifically, we examined whether changes in ant richness affected fruit damage by the coffee berry borer (Hypothenemus hampei) and whether phorids altered multi-predator effects. Each ant species reduced borer damage, and without phorids, increasing predator richness did not further decrease borer damage. However, with phorids, activity of one ant species was reduced, indicating that the presence of multiple ant species was necessary to limit borer damage. In addition, phorid presence revealed synergistic effects of multiple ant species, not observed without the presence of this parasite. Thus, a trait-mediated cascade resulting from a parasite-induced predator behavioral change revealed the importance of functional redundancy, predator diversity, and food web complexity for control of this important pest.

  17. Importance of NPA motifs in the expression and function of water channel aquaporin-1

    Institute of Scientific and Technical Information of China (English)

    JIANG Yong; MA TongHui

    2007-01-01

    The asparagine-proline-alanine sequences (NPA motifs) are highly conserved in aquaporin water channel family. Crystallographic studies of AQP1 structure demonstrated that the two NPA motifs are in the narrow central constriction of the channel, serving to bind water molecules for selective and efficient water passage. To investigate the importance of the two NPA motifs in the structure, function and biogenesis of aquaporin water channels, we generated AQP1 mutations with NPA1 deletion, NPA2 deletion and NPA1,2 double deletion. The coding sequences of the three mutated cDNAs were subcloned into the mammalian expression vector pcDNA3.1 to form expression plasmids. We established stably transfected CHO cell lines expressing these AQP1 mutants. Immunofluorescence indicated that all the three mutated AQP1 proteins are expressed normally on the plasma membrane of stably transfected CHO cells, suggesting that deletion of NPA motifs does not influence the expression and intracellular processing of AQP1. Functional analysis demonstrated that NPA1 or NPA2 deletion reduced AQP1 water permeability by 49.6% and 46.7%, respectively, while NPA1,2 double deletion had little effect on AQP1 water permeability. These results provide evidence that NPA motifs are important for water per-meation but not essential for the expression, intracellular processing and the basic structure of AQP1 water channel.

  18. Stone tool function at the paleolithic sites of Starosele and Buran Kaya III, Crimea: behavioral implications.

    Science.gov (United States)

    Hardy, B L; Kay, M; Marks, A E; Monigal, K

    2001-09-11

    Stone tools are often the most abundant type of cultural remains at Paleolithic sites, yet their function is often poorly understood. Investigations of stone tool function, including microscopic use-wear and residue analyses, were performed on a sample of artifacts from the Paleolithic sites of Starosele (40,000-80,000 years BP) and Buran Kaya III (32,000-37,000 years BP). The Middle Paleolithic levels at Starosele exhibit a typical variant of the local Micoquian Industry. The artifacts from Buran Kaya III most closely resemble an Early Streletskayan Industry associated with the early Upper Paleolithic. The results of the functional analyses suggest that hominids at both sites were exploiting woody and starchy plant material as well as birds and mammals. Both sites show evidence of hafting of a wide variety of tools and the possible use of projectile or thrusting spears. These analyses were performed by using two different techniques conducted by independent researchers. Combined residue and use-wear analyses suggest that both the Upper Paleolithic and Middle Paleolithic hominids at these sites were broad-based foragers capable of exploiting a wide range of resources.

  19. 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.

  20. Limits of Science and the Importance of Epistemological Functions of Religion

    Directory of Open Access Journals (Sweden)

    Qodratullah Qorbani

    2012-12-01

    Full Text Available Human is encountered by many metaphysical, scientific, religious and other fundamentalquestions which Science, and its potentials, can answer some of them, specially in the material realm.In fact, empirical science is limited to the material world, and it can’t answer human’s fundamentalquestions of his/her living. Then human can’t provide all his/her epistemological requirements byempirical science. In addition, contemporary human’s scientism caused many problems for him/her.Human tried to make empirical science as a worldview which caused some important andfundamental crisis. So he/she needs metaphysical, religious and other sources to know aboutsupernatural facts. Fulfilling this, he/she has to use religious teachings, because religions, in particulardivine ones, have many basic functions. They can make man aware about immaterial realms andexistents including God, origin and resurrection of man, the world system etc. They can give areasonable explanation of the origin and resurrection of human’s life and the meaning of human’sevolution in the mundane universe, and the philosophy of living by explaining the nature of Goodnessand Evil. Religions give some ethical and religious laws to manage and control his/her individual andsocial treatments. In fact, through religious teachings,man can take a suitable framework to managehis/her living, for example, by them man can determine functional results of his/her scientific andtechnological activities. In addition, religions can draw the spiritual future of human’s mundaneliving, and give a good motivation to get mundane and spiritual happiness. In the other word, man,only by the help of religious teachings, can take his/her fundamental requirements. Then, byconsidering the contemporary human epistemological crisis and important limits of human’sknowledge and science, there is the only way to refer to divine religions teachings. In this paper, it istried to explain religion functions in

  1. Cardiac Alpha1-Adrenergic Receptors: Novel Aspects of Expression, Signaling Mechanisms, Physiologic Function, and Clinical Importance

    Science.gov (United States)

    O’Connell, Timothy D.; Jensen, Brian C.; Baker, Anthony J.

    2014-01-01

    Adrenergic receptors (AR) are G-protein-coupled receptors (GPCRs) that have a crucial role in cardiac physiology in health and disease. Alpha1-ARs signal through Gαq, and signaling through Gq, for example, by endothelin and angiotensin receptors, is thought to be detrimental to the heart. In contrast, cardiac alpha1-ARs mediate important protective and adaptive functions in the heart, although alpha1-ARs are only a minor fraction of total cardiac ARs. Cardiac alpha1-ARs activate pleiotropic downstream signaling to prevent pathologic remodeling in heart failure. Mechanisms defined in animal and cell models include activation of adaptive hypertrophy, prevention of cardiac myocyte death, augmentation of contractility, and induction of ischemic preconditioning. Surprisingly, at the molecular level, alpha1-ARs localize to and signal at the nucleus in cardiac myocytes, and, unlike most GPCRs, activate “inside-out” signaling to cause cardioprotection. Contrary to past opinion, human cardiac alpha1-AR expression is similar to that in the mouse, where alpha1-AR effects are seen most convincingly in knockout models. Human clinical studies show that alpha1-blockade worsens heart failure in hypertension and does not improve outcomes in heart failure, implying a cardioprotective role for human alpha1-ARs. In summary, these findings identify novel functional and mechanistic aspects of cardiac alpha1-AR function and suggest that activation of cardiac alpha1-AR might be a viable therapeutic strategy in heart failure. PMID:24368739

  2. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues.

    Science.gov (United States)

    Spedaliere, C J; Hamilton, C S; Mueller, E G

    2000-08-01

    On the basis of sequence alignments, the pseudouridine synthases were grouped into four families that share no statistically significant global sequence similarity, though some common sequence motifs were discovered [Koonin, E. V. (1996) Nucleic Acids. Res. 24, 2411-2415; Gustafsson, C., Reid, R., Greene, P. J., and Santi, D. V. (1996) Nucleic Acids Res. 24, 3756-3762]. We have investigated the functional significance of these alignments by substituting the nearly invariant lysine and proline residues in Motif I of RluA and TruB, pseudouridine synthases belonging to different families. Contrary to our expectations, the altered enzymes display only very mild kinetic impairment. Substitution of the aligned lysine and proline residues does, however, reduce structural stability, consistent with a temperature sensitive phenotype that results from substitution of the cognate proline residue in Cbf5p, a yeast homologue of TruB [Zerbarjadian, Y., King, T., Fournier, M. J., Clarke, L., and Carbon, J. (1999) Mol. Cell. Biol. 19, 7461-7472]. Together, our data support a functional role for Motif I, as predicted by sequence alignments, though the effect of substituting the highly conserved residues was milder than we anticipated. By extrapolation, our findings also support the assignment of pseudouridine synthase function to certain physiologically important eukaryotic proteins that contain Motif I, including the human protein dyskerin, alteration of which leads to the disease dyskeratosis congenita.

  3. Perifoveal function in patients with North Carolina macular dystrophy: the importance of accounting for fixation locus.

    Science.gov (United States)

    Seiple, William; Szlyk, Janet P; Paliga, Jennifer; Rabb, Maurice F

    2006-04-01

    To quantify the extent of visual function losses in patients with North Carolina Macular Dystrophy (NCMD) and to demonstrate the importance of accounting for eccentric fixation when making comparisons with normal data. Five patients with NCMD who were from a single family were examined. Multifocal electroretinograms (mfERGs) and psychophysical assessments of acuity and luminance visual field sensitivities were measured throughout the central retina. Comparisons of responses from equivalent retinal areas were accomplished by shifting normal templates to be centered at the locus of fixation for each patient. Losses of psychophysically measured visual function in patients with NCMD extend to areas adjacent to the locations of visible lesions. The multifocal ERG amplitude was reduced only within the area of visible lesion. Multifocal ERG implicit times were delayed throughout the entire central retinal area assessed. ERG timing is a sensitive assay of retinal function, and our results indicate that NCMD has a widespread effect at the level of the mid and outer retina. The findings also demonstrated that it is necessary to account for fixation locus and to ensure that equivalent retinal areas are compared when testing patients with macular disease who have eccentric fixation.

  4. Formation and function of vacancies in Si/Ge Clathrates: The importance of broken symmetries

    Science.gov (United States)

    Bhattacharya, Amrita; Carbogno, Christian; Scheffler, Matthias; Dr. Matthias Scheffler Team, Prof.

    2015-03-01

    One promising material class for improved thermoelectrics are the clathrates, i.e., semiconducting host lattices encapsulating guest atom. Even in simple clathrates, such as, Si46 and Ge46, the introduction of guests can result in important but not yet understood effects: In Si hosts, the addition of K (or Ba) results in defect-free K8Si46 (Ba8Si46) phases. In spite of their structural and electronic similitude, Ge hosts behave fundamentally different upon filling, where, the spontaneously formed framework vacancies completely (or partially) balance the electron donated by K (or Ba) guests leading to K8Ge44(orBa8Ge43) clathrates. In this work, we use density-functional theory, carefully validating the exchange correlation functional, to compute the formation energies of vacancies and vacancy complexes in Si- and Ge-hosts as function of the filling of guests. By taking into account of the structural disorder, geometric relaxations, and vibrational entropies, we verify the experimentally found vacancy concentration and the thermodynamic stabilities of these compounds. We can trace back the contrasting behaviour of Si/Ge clathrates upon filling to a curious, charged vacancy induced break in symmetry that occurs in Si but not in Ge hosts.

  5. Identification of structures, systems, and components important to safety at the potential repository at Yucca Mountain; Yucca Mountain Site Characterization Project

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, D.J.; Miller, D.D. [Bechtel National, Inc., San Francisco, CA (United States); Klamerus, L.J. [Sandia National Labs., Albuquerque, NM (United States)

    1991-10-01

    This study recommends which structures, systems, and components of the potential repository at Yucca Mountain are important to safety. The assessment was completed in April 1990 and uses the reference repository configuration in the Site Characterization Plan Conceptual Design Report and follows the methodology required at that time by DOE Procedure AP6.10-Q. Failures of repository items during the preclosure period are evaluated to determine the potential offsite radiation doses and associated probabilities. Items are important to safety if, in the event they fail to perform their intended function, an accident could result which causes a dose commitment greater than 0.5 rem to the whole body or any organ of an individual in an unrestricted area. This study recommends that these repository items include the structures that house spent fuel and high-level waste, the associated filtered ventilation exhaust systems, certain waste- handling equipment, the waste containers, the waste treatment building structure, the underground waste transporters, and other items listed in this report. This work was completed April 1990. 27 refs., 7 figs., 9 tabs.

  6. Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis.

    Science.gov (United States)

    Uthup, T K; Rajamani, A; Ravindran, M; Saha, T

    2016-07-01

    Hydroxy-methylglutaryl coenzyme-A synthase (HMGS) is a rate-limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non-coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three-dimensional structural studies highlighting the structural positioning of non-synonymous SNPs from different HMGS haplotypes revealed that the ligand-binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants.

  7. LRR conservation mapping to predict functional sites within protein leucine-rich repeat domains.

    Directory of Open Access Journals (Sweden)

    Laura Helft

    Full Text Available Computational prediction of protein functional sites can be a critical first step for analysis of large or complex proteins. Contemporary methods often require several homologous sequences and/or a known protein structure, but these resources are not available for many proteins. Leucine-rich repeats (LRRs are ligand interaction domains found in numerous proteins across all taxonomic kingdoms, including immune system receptors in plants and animals. We devised Repeat Conservation Mapping (RCM, a computational method that predicts functional sites of LRR domains. RCM utilizes two or more homologous sequences and a generic representation of the LRR structure to identify conserved or diversified patches of amino acids on the predicted surface of the LRR. RCM was validated using solved LRR+ligand structures from multiple taxa, identifying ligand interaction sites. RCM was then used for de novo dissection of two plant microbe-associated molecular pattern (MAMP receptors, EF-TU RECEPTOR (EFR and FLAGELLIN-SENSING 2 (FLS2. In vivo testing of Arabidopsis thaliana EFR and FLS2 receptors mutagenized at sites identified by RCM demonstrated previously unknown functional sites. The RCM predictions for EFR, FLS2 and a third plant LRR protein, PGIP, compared favorably to predictions from ODA (optimal docking area, Consurf, and PAML (positive selection analyses, but RCM also made valid functional site predictions not available from these other bioinformatic approaches. RCM analyses can be conducted with any LRR-containing proteins at www.plantpath.wisc.edu/RCM, and the approach should be modifiable for use with other types of repeat protein domains.

  8. A Bioinformatics Approach to the Identification of Variants Associated with Type 1 and Type 2 Diabetes Mellitus that Reside in Functionally Validated miRNAs Binding Sites.

    Science.gov (United States)

    Ghaedi, Hamid; Bastami, Milad; Jahani, Mohammad Mehdi; Alipoor, Behnam; Tabasinezhad, Maryam; Ghaderi, Omar; Nariman-Saleh-Fam, Ziba; Mirfakhraie, Reza; Movafagh, Abolfazl; Omrani, Mir Davood; Masotti, Andrea

    2016-06-01

    The present work is aimed at finding variants associated with Type 1 and Type 2 diabetes mellitus (DM) that reside in functionally validated miRNAs binding sites and that can have a functional role in determining diabetes and related pathologies. Using bioinformatics analyses we obtained a database of validated polymorphic miRNA binding sites which has been intersected with genes related to DM or to variants associated and/or in linkage disequilibrium (LD) with it and is reported in genome-wide association studies (GWAS). The workflow we followed allowed us to find variants associated with DM that also reside in functional miRNA binding sites. These data have been demonstrated to have a functional role by impairing the functions of genes implicated in biological processes linked to DM. In conclusion, our work emphasized the importance of SNPs located in miRNA binding sites. The results discussed in this work may constitute the basis of further works aimed at finding functional candidates and variants affecting protein structure and function, transcription factor binding sites, and non-coding epigenetic variants, contributing to widen the knowledge about the pathogenesis of this important disease.

  9. The importance of geological data and derived information in seismic response assessment for urban sites. An example from the Island of Crete, Greece

    Science.gov (United States)

    Tsangaratos, Paraskevas; Loupasakis, Constantinos; Rozos, Dimitrios; Rondoyianni, Theodora; Vafidis, Antonios; Savvaidis, Alexandros; Soupios, Pantelis; Papadopoulos, Nikos; Sarris, Apostolos

    2015-04-01

    The magnitude, frequency content and duration of an earthquake ground motion depends mainly on the surrounding geological, tectonic and geomorphological conditions. Numerous reports have been contacted illustrating the necessity of providing accurate geological information in order to estimate the level of seismic hazard. In this context, geological information is the outcome of processing primary, raw field data and geotechnical investigation data that are non - organized and associated with the geological model of the study area. In most cases, the geological information is provided as an advance element, a key component of the "function" that solves any geo-environmental problem and is primarily reflected on analogue or digital maps. The main objective of the present study is to illustrate the importance of accurate geological information in the thirteen (13) selected sites of the Hellenic Accelerometric Network (HAN) in the area of Crete Island, in order to estimate the seismic action according to Eurocode (EC8). As an example the detailed geological-geotechnical map of the area around HAN site in Rethymno city, Crete is presented. The research area covers a 250m radius surrounding the RTHE HAN-station at a scale of 1: 2000 with detail description of the geological and geotechnical characteristics of the formations as well as the tectonic features (cracks, upthrust, thrust, etc) of the rock mass. The field survey showed that the RTHE station is founded over limestones and dolomites formations. The formations exhibit very good geomechanical behaviour; however they present extensive fragmentation and karstification. At this particular site the identification of a fault nearby the station proved to be significant information for the geophysical research as the location and orientation of the tectonic setting provided new perspective on the models of seismic wave prorogation. So, the geological data and the induced information along with the tectonic structure of

  10. Better estimation of protein-DNA interaction parameters improve prediction of functional sites

    Directory of Open Access Journals (Sweden)

    O'Flanagan Ruadhan A

    2008-12-01

    Full Text Available Abstract Background Characterizing transcription factor binding motifs is a common bioinformatics task. For transcription factors with variable binding sites, we need to get many suboptimal binding sites in our training dataset to get accurate estimates of free energy penalties for deviating from the consensus DNA sequence. One procedure to do that involves a modified SELEX (Systematic Evolution of Ligands by Exponential Enrichment method designed to produce many such sequences. Results We analyzed low stringency SELEX data for E. coli Catabolic Activator Protein (CAP, and we show here that appropriate quantitative analysis improves our ability to predict in vitro affinity. To obtain large number of sequences required for this analysis we used a SELEX SAGE protocol developed by Roulet et al. The sequences obtained from here were subjected to bioinformatic analysis. The resulting bioinformatic model characterizes the sequence specificity of the protein more accurately than those sequence specificities predicted from previous analysis just by using a few known binding sites available in the literature. The consequences of this increase in accuracy for prediction of in vivo binding sites (and especially functional ones in the E. coli genome are also discussed. We measured the dissociation constants of several putative CAP binding sites by EMSA (Electrophoretic Mobility Shift Assay and compared the affinities to the bioinformatics scores provided by methods like the weight matrix method and QPMEME (Quadratic Programming Method of Energy Matrix Estimation trained on known binding sites as well as on the new sites from SELEX SAGE data. We also checked predicted genome sites for conservation in the related species S. typhimurium. We found that bioinformatics scores based on SELEX SAGE data does better in terms of prediction of physical binding energies as well as in detecting functional sites. Conclusion We think that training binding site detection

  11. Performance evaluation of the short-time objective intelligibility measure with different band importance functions

    DEFF Research Database (Denmark)

    Heidemann Andersen, Asger; de Haan, Jan Mark; Tan, Zheng-Hua

    2017-01-01

    , is that all frequency bands are equally weighted in the final measure. This is in contrast to classical methods such as the speech intelligibility index (SII) which employs empirically determined band importance functions (BIFs), specifying the relative contribution of each frequency band to intelligibility....... In this study we investigated the use of BIFs in the STOI measure. BIFs were fitted to several datasets of measured intelligibility. This was done such as to minimize the root-mean-squared prediction error. We then performed a cross-evaluation of the obtained BIFs on all datasets, using three different...... performance measures: root-mean-squared-error, Pearson correlation, and Kendall rank correlation. The results show substantially improved performance when fitting and evaluating on the same dataset. However, this advantage does not necessarily subsist when fitting and evaluating on different datasets. When...

  12. Particle filter with importance density function generated by updated system equation

    Institute of Scientific and Technical Information of China (English)

    左军毅; 贾颖娜; 张炜; 高全学

    2013-01-01

    The current measurement was exploited in a more efficient way. Firstly, the system equation was updated by introducing a correction term, which depends on the current measurement and can be obtained by running a suboptimal filter. Then, a new importance density function(IDF) was defined by the updated system equation. Particles drawn from the new IDF are more likely to be in the significant region of state space and the estimation accuracy can be improved. By using different suboptimal filter, different particle filters(PFs) can be developed in this framework. Extensions of this idea were also proposed by iteratively updating the system equation using particle filter itself, resulting in the iterated particle filter. Simulation results demonstrate the effectiveness of the proposed IDF.

  13. Rapid high-resolution characterization of functionally important monoclonal antibody N-glycans by capillary electrophoresis.

    Science.gov (United States)

    Szabo, Zoltan; Guttman, András; Bones, Jonathan; Karger, Barry L

    2011-07-01

    Characterization of the N-glycosylation present in the Fc region of therapeutic monoclonal antibodies requires rapid, high-resolution separation methods to guarantee product safety and efficacy during all stages of process development. Determination of fucosylated oligosaccharides is particularly important during clone selection, product characterization, and lot release as fucose has been shown to adversely affect the ability of mAbs to induce antibody dependent cellular cytotoxicity (ADCC). Here, we apply a general capillary electrophoresis optimization strategy to separate functionally relevant fucosylated and afucosylated glycans on mononclonal antibody products in the presence of several high mannose oligosaccharides. The N-glycans chosen represent those most commonly reported on CHO cell derived therapeutic antibodies. A rapid (processing for automated 96 well plate-based glycosylation analyses of two nonproprietary therapeutic monoclonal antibodies, demonstrating ruggedness and suitability for high-throughput process and product monitoring applications.

  14. Long-term importance of right ventricular outflow tract patch function in patients with pulmonary regurgitation.

    Science.gov (United States)

    Puranik, Rajesh; Tsang, Victor; Lurz, Philip; Muthurangu, Vivek; Offen, Sophie; Frigiola, Alessandra; Norman, Wendy; Walker, Fiona; Bonhoeffer, Philip; Taylor, Andrew M

    2012-05-01

    Chronic pulmonary regurgitation (PR) has deleterious effects on right ventricular (RV) function in repaired tetralogy of Fallot (ToF). However, there are little data regarding right ventricular outflow tract (RVOT) contractile dysfunction in response to chronic PR and on both RV and LV volumes and function. We retrospectively identified consecutive patients with PR who were referred for magnetic resonance imaging quantification of "free PR" detected on echocardiography between 2003 and 2008. Patients had ToF and a transannular patch procedure (n = 30, 25.1 ± 1.2 years) or PR resulting from valvar pulmonary stenosis treated with surgical or percutaneous valvotomy (n = 30, 26.6 ± 1.8 years). The ToF and the PS groups were well matched for age at scan, age at repair surgery in ToF or initial valvotomy in PS, duration of exposure to PR, body surface area, heart rate, PR fraction, net forward pulmonary artery flow, and main and branch pulmonary artery dimensions. Severe PR fractions were identified in both groups (ToF: 40% ± 1% vs PS: 37% ± 2%, P = .2). Indexed RV and LV end-diastolic volumes were similar for both ToF and PS groups (RV end-diastolic volume index: 137 ± 6 mL/m(2) vs 128 ± 5 mL/m(2), P = .2, and LV end-diastolic volume index: 72 ± 2 mL/m(2) vs 67 ± 2 mL/m(2), P = .1, respectively). RV mass was also similar between groups (95 ± 5 g vs 81 ± 6 g, respectively, P = .08). However, indexed RV and LV end-systolic volumes were consistently higher in ToF when compared with PS (RV end-systolic volume index: 70 ± 5 mL/m(2) vs 54 ± 3 mL/m(2), P function in patients with ToF when compared with PS (RV ejection fraction: 52% ± 1.5% vs 59% ± 1%, P function were similar when only patients with contractile RV outflow tracts were compared. RV outflow tract patch dysfunction in repaired ToF is responsible for higher end-systolic volumes and thus lower global measures of ventricular systolic function. These findings were not evident in cases of PS treated with

  15. Site-selective Suzuki-Miyaura coupling of heteroaryl halides - understanding the trends for pharmaceutically important classes.

    Science.gov (United States)

    Almond-Thynne, Joshua; Blakemore, David C; Pryde, David C; Spivey, Alan C

    2017-01-01

    Suzuki-Miyaura cross-coupling reactions of heteroaryl polyhalides with aryl boronates are surveyed. Drawing on data from literature sources as well as bespoke searches of Pfizer's global chemistry RKB and CAS Scifinder® databases, the factors that determine the site-selectivity of these reactions are discussed with a view to rationalising the trends found.

  16. 5′ isomiR variation is of functional and evolutionary importance

    Science.gov (United States)

    Tan, Geok Chin; Chan, Elcie; Molnar, Attila; Sarkar, Rupa; Alexieva, Diana; Isa, Ihsan Mad; Robinson, Sophie; Zhang, Shuchen; Ellis, Peter; Langford, Cordelia F.; Guillot, Pascale V.; Chandrashekran, Anil; Fisk, Nick M.; Castellano, Leandro; Meister, Gunter; Winston, Robert M.; Cui, Wei; Baulcombe, David; Dibb, Nick J.

    2014-01-01

    We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3′ and/or 5′ end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5′ differences and in support of this we report that a 5′ isomiR-9–1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5′ isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes. PMID:25056318

  17. 5' isomiR variation is of functional and evolutionary importance.

    Science.gov (United States)

    Tan, Geok Chin; Chan, Elcie; Molnar, Attila; Sarkar, Rupa; Alexieva, Diana; Isa, Ihsan Mad; Robinson, Sophie; Zhang, Shuchen; Ellis, Peter; Langford, Cordelia F; Guillot, Pascale V; Chandrashekran, Anil; Fisk, Nick M; Castellano, Leandro; Meister, Gunter; Winston, Robert M; Cui, Wei; Baulcombe, David; Dibb, Nick J

    2014-08-01

    We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.

  18. Prognostic Importance of Pretransplant Functional Capacity After Allogeneic Hematopoietic Cell Transplantation

    Science.gov (United States)

    Devlin, Sean M.; Maloy, Molly A.; Wood, William A.; Tuohy, Sharlynn; Espiritu, Noel; Aquino, Jennifer; Kendig, Tiffany; Michalski, Meghan G.; Gyurkocza, Boglarka; Schaffer, Wendy L.; Ali, Benzar; Giralt, Sergio; Jakubowski, Ann A.

    2015-01-01

    Background. The purpose of this study was to investigate the prognostic importance of functional capacity in patients undergoing allogeneic hematopoietic cell transplantation (HCT) for hematological malignancies. Patients and Methods. Using a retrospective design, 407 patients completed a 6-minute walk distance (6MWD) test to assess functional capacity before HCT; 193 (47%) completed a 6MWD test after hospital discharge. Cox proportional hazards regression was used to estimate the risk of nonrelapse mortality (NRM) and overall survival (OS) according to the 6MWD category ( .05 for all). Patients presenting with a pre-HCT 6MWD of <400 m and experiencing a decline in 6MWD had the highest risk of NRM. Conclusion. The 6MWD is a significant univariate predictor of clinical outcomes but did not provide prognostic information beyond that of traditional prognostic markers in HCT. Implications for Practice: The pretransplant 6-minute walk test is a significant univariate predictor of clinical outcomes in hematological patients beyond age but not beyond that of performance status. On this basis, 6-minute walk distance testing should not be considered part of the standard battery of assessments for risk stratification before hematopoietic cell transplantation. PMID:26446235

  19. The Ironbridge Gorge Heritage Site and its local and regional functions

    National Research Council Canada - National Science Library

    Waldemar Cudny

    2017-01-01

    The article is devoted to the issue of heritage and its functions. Based on the existing literature, the author presents the definition of heritage, the classification of heritage resources, and its most important impacts...

  20. Asthma, respiratory symptoms and lung function in children living near a petrochemical site.

    Science.gov (United States)

    Rovira, Enric; Cuadras, Anna; Aguilar, Xavier; Esteban, Leonardo; Borràs-Santos, Alícia; Zock, Jan-Paul; Sunyer, Jordi

    2014-08-01

    Residential proximity to environmental hazards has been related to adverse health outcomes. Respiratory health and allergies in children living near petrochemical sites have not been extensively studied. We evaluated the association between residential proximity to the petrochemical site of Tarragona (Catalonia, Spain) and the prevalence of asthma, respiratory symptoms and lung function in children. Children aged 6-7 (n=2672) and adolescents aged 13-14 (n=2524) residing near two large petrochemical sites and those living in a city with medium vehicular traffic were cross-sectionally compared with children from an area with low vehicular traffic and without industry. The prevalence of symptoms was measured using the International Study of Asthma and Allergies in Childhood written and video questionnaires. Lung function measurements were done in a subsample of 959 adolescents in the four areas. Multivariable analyses were done to estimate the effects of the residential area on symptoms and lung function adjusted for potential confounders. Crude prevalence of symptoms was similar across the studied areas. After adjustment, children and adolescents living near a petrochemical site had a statistically significant higher prevalence of respiratory hospitalizations in the previous year (Prevalence Ratio (PR)=1.49; 95%CI, 1.06-2.09) and of nocturnal cough (PR=1.29; 95%CI 1.05-1.57), respectively. Reduced lung function values among adolescents residing near the petrochemical areas were not observed. Although a higher prevalence of asthma in children and adolescents living near the petrochemical sites could not be demonstrated, as described in other studies, respiratory hospitalizations and nocturnal cough could be related to short-term exposures to pollutants. Other clinical and sub-clinical respiratory health effects in the petrochemical industry areas should be investigated. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Differences in colorectal cancer survival between European and US populations: the importance of sub-site and morphology.

    Science.gov (United States)

    Gatta, G; Ciccolallo, L; Capocaccia, R; Coleman, M P; Hakulinen, T; Møller, H; Berrino, F

    2003-10-01

    A previous study has shown a lower survival for colorectal cancer in Europe than in the United States of America (USA). It is of interest to examine the extent to which anatomical location and morphological type influence this difference in colorectal cancer survival. We analysed survival for 151,244 European and 53,884 US patients diagnosed with colorectal cancer aged 15-99 years during the period of 1985-1989, obtained from 40 cancer registries that contribute to the EUROCARE study from 17 countries, and nine Surveillance, Epidemiology and End-Results (SEER) registries in the USA. Cases included in the analysis were first primary malignant tumours (ICD-O behaviour code 3 or higher). Relative survival was estimated to correct for competing causes of mortality. The Hakulinen-Tenkanen multiple regression approach was used to examine the prognostic impact of sub-site and ICD-O histology codes. Relative excess risks (RERs) derived from this approach estimate the extent to which the hazard of death differs from that in a reference region after adjustment for mortality in the general population. In order to explore geographical variation, we defined three groups of European registries within which survival rates were known to be broadly similar. The proportion of cases with unspecified sub-site was higher in Europe than the USA (10% versus 2%), but sub-site distributions were broadly similar in the two populations. With the exception of appendix, 5-year survival was 13-22% higher in the USA than in Europe for each anatomical sub-site. The proportion of non-microscopically-verified cases was higher in Europe than the USA (16 versus 3%). Adenocarcinomas arising in a polyp (ICD-O-2 8210, 8261, 8263) were more frequent in the USA than Europe (13 versus 2%). Five-year survival was higher in the USA than Europe for each morphological group, with the exception of non-microscopically-verified cases. When age, gender and sub-site were considered, RERs ranged from 1.52 to 2

  2. Synergistic effect between defect sites and functional groups on the hydrolysis of cellulose over activated carbon.

    Science.gov (United States)

    Foo, Guo Shiou; Sievers, Carsten

    2015-02-01

    The chemical oxidation of activated carbon by H2 O2 and H2 SO4 is investigated, structural and chemical modifications are characterized, and the materials are used as catalysts for the hydrolysis of cellulose. Treatment with H2 O2 enlarges the pore size and imparts functional groups such as phenols, lactones, and carboxylic acids. H2 SO4 treatment targets the edges of carbon sheets primarily, and this effect is more pronounced with a higher temperature. Adsorption isotherms demonstrate that the adsorption of oligomers on functionalized carbon is dominated by van der Waals forces. The materials treated chemically are active for the hydrolysis of cellulose despite the relative weakness of most of their acid sites. It is proposed that a synergistic effect between defect sites and functional groups enhances the activity by inducing a conformational change in the glucan chains if they are adsorbed at defect sites. This activates the glycosidic bonds for hydrolysis by in-plane functional groups. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  4. Complexation by natural heterogeneous compounds: Site occupation distribution functions, a normalized description of metal complexation

    Science.gov (United States)

    Buffle, J.; Altmann, R. S.; Filella, M.; Tessier, A.

    1990-06-01

    This paper presents a new conceptual approach to interpreting titration curves of metal complexation by physically and chemically heterogeneous natural complexants such as humic acids, clays, complete soils, or sediments. The physico-chemical and analytical difficulties encountered with such systems are reviewed by comparison with a system containing only a few simple ligands, followed by discussion of the new approach on the same basis. It is shown that interpretation of heterogeneous complexant properties necessitates a preliminary transformation of experimental raw data into a function sufficiently normalized so as to allow comparison of results obtained under different conditions. A normalized function called a Site Occupation Distribution Function (SODF) and its potential usefulness is described here. The SODF is a readily computable function which relates the complexation buffer intensity of the system to the differential free energy of the complexation sites present. Its major interest is that it enables one to obtain both a rigorous mathematical description of the complexant properties (even when highly heterogeneous) at the macroscopic level and, in certain cases, an estimation of the molecular-scale behavior of particular site types. The relationship of the SODF to other distribution functions proposed in the literature is discussed and applications are exemplified using simulated and real natural systems. In particular, its utility is discussed in detail for (1) discriminating between different site types (major, minor, dominant, background), (2) evaluating the degree of heterogeneity of an unknown complexant system, (3) estimating the nature and true thermodynamic constants of complexes, and (4) yielding a rigorous definition of "complexation capacity."

  5. HealthPaths: Using functional health trajectories to quantify the relative importance of selected health determinants

    Directory of Open Access Journals (Sweden)

    Michael Wolfson

    2014-10-01

    Full Text Available Background: It is widely known that that there is a significant dispersion in health status, as well as a strong correlation between health status and socio-economic status. But considerable uncertainty remains as to the quantitative importance of the various explanatory factors typically cited in this context. As health status is intrinsically a reflection of co-evolving dynamic processes, it is important to take a lifetime perspective when seeking to understand its determinants. The "bottom line" measure of overall population health is, though, health-adjusted life expectancy (HALE, which is an aggregation of individuals' health-adjusted life lengths (HALLs. Objective: In an exploratory mode, we intend to provide a realistic assessment of the relative importance of selected health determinants of HALE. Methods: This paper first draws on very detailed estimates of the covariates of vector-valued functional health trajectories, using the National Population Health Survey (Statistics Canada. We then use longitudinal microsimulation to draw out their implications by synthesising first a realistic base case -- specifically, a representative longitudinal population sample -- and then a series of exploratory counterfactual populations. Comparisons between and among counterfactuals and the base case are then used to estimate the quantitative importance of various factors in accounting for HALE. Results: Several surprising results emerged. Of the four risk factors explicitly examined, obesity had the smallest impacts on HALE: moving from the fifth to the 95th percentiles of BMI increased HALE 1.5 and 2.5 years for men and women, respectively. Eliminating smoking increased HALE by five and four years, while moving from the lowest to the highest levels of education had similar effects of about five years for both men and women. Perhaps surprisingly, moving from the fifth to the 95th percentiles of the psycho-social factor, Antonovsky's sense of coherence

  6. Neuroprotection by a novel NMDAR functional glycine site partial agonist, GLYX-13.

    Science.gov (United States)

    Stanton, Patric K; Potter, Pamela E; Aguilar, Jennifer; Decandia, Maria; Moskal, Joseph R

    2009-08-26

    GLYX-13 (threonine-proline-proline-threonine-amide) is an amidated di-pyrrolidine that acts as a functional partial agonist at the glycine site on N-methyl-D-aspartate glutamate receptors (NMDARs). GLYX-13 can both increase NMDAR conductance at NR2B-containing receptors, and reduce conductance of non-NR2B-containing receptors. Here, we report that GLYX-13 potently reduces delayed (24 h) death of CA1 pyramidal neurons produced by bilateral carotid occlusion in Mongolian gerbils, when administered up to 5 h post-ischemia. GLYX-13 also reduced delayed (24 h) neuronal death of CA1, CA3, and dentate gyrus principal neurons elicited by oxygen/glucose deprivation in in-vitro hippocampal organotypic slice cultures, when applied up to 2 h post-oxygen/glucose deprivation. The glycine site full agonist D-serine completely occluded neuroprotection, indicating that GLYX-13 acts by modulating activation of this site.

  7. Ground Truth and Application for the Anisotropic Receiver Functions Technique - Test site KTB: the installation campaign

    Science.gov (United States)

    Bianchi, Irene; Anselmi, Mario; Apoloner, Maria-Theresia; Qorbani, Ehsan; Gribovszki, Katalin; Bokelmann, Götz

    2015-04-01

    The project at hand is a field test around the KTB (Kontinentale Tiefbohrung) site in the Oberpfalz, Southeastern Germany, at the northwestern edge of the Bohemian Massif. The region has been extensively studied through the analysis of several seismic reflection lines deployed around the drilling site. The deep borehole had been placed into gneiss rocks of the Zone Erbendorf-Vohenstrauss. Drilling activity lasted since 1987 to 1994, and it descends down to a depth of 9101 meters. In our experiment, we aim to recover structural information as well as anisotropy of the upper crust using the receiver function technique. This retrieved information will form the base for a comparison between the resulting anisotropy amount and orientation with information of rock samples from up to 9 km depth, and with earlier high-frequency seismic experiments around the drill site. For that purpose, we installed 9 seismic stations, and recorded seismicity continuously for two years.

  8. Arthropod Diversity and Functional Importance in Old-Growth Forests of North America

    Directory of Open Access Journals (Sweden)

    Timothy Schowalter

    2017-03-01

    Full Text Available Old-growth forests have become rare in North America but provide habitat for unique assemblages of species that often are rare in younger forests. Insects and related arthropods reach their highest diversity in old-growth forests because of their stable moderate temperature and relative humidity and the rich variety of resources represented by high plant species richness and structural complexity. Old-growth arthropod assemblages typically are distinct from those in younger, managed forests. Major subcommunities include the arboreal community that is composed of a rich assemblage of herbivores, fungivores, and their associated predators and parasitoids that function to regulate primary production and nutrient fluxes, the stem zone community that includes bark- and wood-boring species and their associated predators and parasitoids that initiate the decomposition of coarse woody debris, and the forest floor community composed of a variety of detritivores, fungivores, burrowers, and their associated predators and parasitoids that are instrumental in litter decomposition. Insect outbreaks are relatively rare in old-growth forests, where the diversity of resources and predators limit population growth. In turn, insects contribute to plant diversity and limit primary production of host plant species, thereby promoting development of old-growth forest characteristics. Arthropods also provide important functions in decomposition and nutrient cycling that may be lost in younger, managed forests with limited provision of coarse woody debris and accumulated litter. Protection of remnant old-growth forests within the forest matrix may be particularly valuable for maintaining the diversity of plant and arthropod predators that can minimize outbreaks, thereby contributing to resilience to changing environmental conditions.

  9. Identification of a disulfide bridge important for transport function of SNAT4 neutral amino acid transporter.

    Directory of Open Access Journals (Sweden)

    Rugmani Padmanabhan Iyer

    Full Text Available SNAT4 is a member of system N/A amino acid transport family that primarily expresses in liver and muscles and mediates the transport of L-alanine. However, little is known about the structure and function of the SNAT family of transporters. In this study, we showed a dose-dependent inhibition in transporter activity of SNAT4 with the treatment of reducing agents, dithiothreitol (DTT and Tris(2-carboxyethylphosphine (TCEP, indicating the possible involvement of disulfide bridge(s. Mutation of residue Cys-232, and the two highly conserved residues Cys-249 and Cys-321, compromised the transport function of SNAT4. However, this reduction was not caused by the decrease of SNAT4 on the cell surface since the cysteine-null mutant generated by replacing all five cysteines with alanine was equally capable of being expressed on the cell surface as wild-type SNAT4. Interestingly, by retaining two cysteine residues, 249 and 321, a significant level of L-alanine uptake was restored, indicating the possible formation of disulfide bond between these two conserved residues. Biotinylation crosslinking of free thiol groups with MTSEA-biotin provided direct evidence for the existence of a disulfide bridge between Cys-249 and Cys-321. Moreover, in the presence of DTT or TCEP, transport activity of the mutant retaining Cys-249 and Cys-321 was reduced in a dose-dependent manner and this reduction is gradually recovered with increased concentration of H2O2. Disruption of the disulfide bridge also decreased the transport of L-arginine, but to a lesser degree than that of L-alanine. Together, these results suggest that cysteine residues 249 and 321 form a disulfide bridge, which plays an important role in substrate transport but has no effect on trafficking of SNAT4 to the cell surface.

  10. The importance of sexual self-disclosure to sexual satisfaction and functioning in committed relationships.

    Science.gov (United States)

    Rehman, Uzma S; Rellini, Alessandra H; Fallis, Erin

    2011-11-01

    Past research indicates that sexual self-disclosure, or the degree to which an individual is open with his or her partner about sexual preferences, is a key aspect of sexual satisfaction and that partner's lack of knowledge about one's sexual preferences is associated with persistent sexual dysfunction. To replicate and extend past research by examining (i) how one's own levels of sexual self-disclosure are related to one's own sexual health (after controlling for partner's levels of sexual self-disclosure); (ii) how one's partner's levels of sexual self-disclosure are associated with one's own sexual health (after controlling for one's own levels of sexual self-disclosure); and (iii) whether gender moderates the associations between sexual self-disclosure and sexual health. Scores from the Golombok Rust Inventory of Sexual Satisfaction and the Sexual Communication Satisfaction Scale. A cross-sectional dyadic study using a convenience sample of 91 heterosexual couples in long-term committed relationships. Data were analyzed using the Actor-Partner Interdependence Model. One's own level of sexual self-disclosure is positively associated with one's own sexual satisfaction, β = -0.24, t(172.85) = -3.50, P self-disclosure is associated with men's sexual satisfaction but not with women's sexual satisfaction, β = -0.45, t(86.81) = -4.06, P self-disclosure and sexual problems is stronger for women as compared with men, β = -0.72, t(87.00) = -6.31, P self-disclosure is significantly associated with sexual satisfaction and functioning for both men and women, albeit in different ways. Our findings underscore the importance of sexual self-disclosure and highlight the importance of the interpersonal level of analysis in understanding human sexuality. © 2011 International Society for Sexual Medicine.

  11. Identification of a karyopherin alpha 2 recognition site in PLAG1, which functions as a nuclear localization signal.

    Science.gov (United States)

    Braem, Caroline V; Kas, Koen; Meyen, Eva; Debiec-Rychter, Maria; Van De Ven, Wim J M; Voz, Marianne L

    2002-05-31

    The activation of the pleomorphic adenoma gene 1 (PLAG1) is the most frequent gain-of-function mutation found in pleomorphic adenomas of the salivary glands. To gain more insight into the regulation of PLAG1 function, we searched for PLAG1-interacting proteins. Using the yeast two-hybrid system, we identified karyopherin alpha2 as a PLAG1-interacting protein. Physical interaction between PLAG1 and karyopherin alpha2 was confirmed by an in vitro glutathione S-transferase pull-down assay. Karyopherin alpha2 escorts proteins into the nucleus via interaction with a nuclear localization sequence (NLS) composed of short stretches of basic amino acids. Two putative NLSs were identified in PLAG1. The predicted NLS1 (KRKR) was essential for physical interaction with karyopherin alpha2 in glutathione S-transferase pull-down assay, and its mutation resulted in decreased nuclear import of PLAG1. Moreover, NLS1 was able to drive the nuclear import of the cytoplasmic protein beta-galactosidase. In contrast, predicted NLS2 of PLAG1 (KPRK) was not involved in karyopherin alpha2 binding nor in its nuclear import. The residual nuclear import of PLAG1 after mutation of the NLS1 was assigned to the zinc finger domain of PLAG1. These observations indicate that the nuclear import of PLAG1 is governed by its zinc finger domain and by NLS1, a karyopherin alpha2 recognition site.

  12. Defining a similarity threshold for a functional proteinsequence pattern: The signal peptide cleavage site

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; von Heijne, Gunnar

    1996-01-01

    prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary...... threshold value for excluding redundant sequences. The impact of the choice of scoring matrix used in the alignments is examined. We demonstrate that the parameter determining the quality of the correlation is the relative entropy of the matrix, rather than the assumed(PAM or identity) substitution model....... Results are presented for the case of prediction of cleavage sites in signal peptides. By inspection of the false positives, several errors in the database were found. The procedure presented may be used as a general outline for finding a problem-specific similarity measure and threshold value...

  13. Effect of broadcast baiting on abundance patterns of red imported fire ants (Hymenoptera: Formicidae) and key local ant genera at long-term monitoring sites in Brisbane, Australia.

    Science.gov (United States)

    McNaught, Melinda K; Wylie, F Ross; Harris, Evan J; Alston, Clair L; Burwell, Chris J; Jennings, Craig

    2014-08-01

    In 2001, the red imported fire ant (Solenopsis invicta Buren) was identified in Brisbane, Australia. An eradication program involving broadcast bait treatment with two insect growth regulators and a metabolic inhibitor began in September of that year and is currently ongoing. To gauge the impacts of these treatments on local ant populations, we examined long-term monitoring data and quantified abundance patterns of S. invicta and common local ant genera using a linear mixed-effects model. For S. invicta, presence in pitfalls reduced over time to zero on every site. Significantly higher numbers of S. invicta workers were collected on high-density polygyne sites, which took longer to disinfest compared with monogyne and low-density polygyne sites. For local ants, nine genus groups of the 10 most common genera analyzed either increased in abundance or showed no significant trend. Five of these genus groups were significantly less abundant at the start of monitoring on high-density polygyne sites compared with monogyne and low-density polygyne sites. The genus Pheidole significantly reduced in abundance over time, suggesting that it was affected by treatment efforts. These results demonstrate that the treatment regime used at the time successfully removed S. invicta from these sites in Brisbane, and that most local ant genera were not seriously impacted by the treatment. These results have important implications for current and future prophylactic treatment efforts, and suggest that native ants remain in treated areas to provide some biological resistance to S. invicta.

  14. Dynamic stiffness matrix of a poroelastic multi-layered site and its Green's functions

    Institute of Scientific and Technical Information of China (English)

    梁建文; 尤红兵

    2004-01-01

    Few studies of wave propagation in layered saturated soils have been reported in the literature. In this paper, a general solution of the equation of wave motion in saturated soils, based on one kind of practical Biot's equation,was deduced by introducing wave potentials. Then exact dynamic-stiffness matrices for a poroelastic soil layer and halfspace were derived, which extended Wolf's theory for an elastic layered site to the case of poroelasticity, thus resolving a fundamental problem in the field of wave propagation and soil-structure interaction in a poroelastic layered soil site. By using the integral transform method, Green's functions of horizontal and vertical uniformly distributed loads in a poroelastic layered soil site were given. Finally, the theory was verified by numerical examples and dynamic responses by comparing three different soil sites. This study has the following advantages: all parameters in the dynamic-stiffness matrices have explicitly physical meanings and the thickness of the sub-layers does not affect the precision of the calculation which is very convenient for engineering applications. The present theory can degenerate into Wolf's theory and yields numerical results approaching those for an ideal elastic layered site when porosity tends to zero.

  15. Impact of the permanent ventricular pacing site on left ventricular function in children: a retrospective multicentre survey.

    Science.gov (United States)

    van Geldorp, Irene E; Delhaas, Tammo; Gebauer, Roman A; Frias, Patrick; Tomaske, Maren; Friedberg, Mark K; Tisma-Dupanovic, Svjetlana; Elders, Jan; Früh, Andreas; Gabbarini, Fulvio; Kubus, Petr; Illikova, Viera; Tsao, Sabrina; Blank, Andreas Christian; Hiippala, Anita; Sluysmans, Thierry; Karpawich, Peter; Clur, Sally-Ann; Ganame, Xavier; Collins, Kathryn K; Dann, Gisela; Thambo, Jean-Benoît; Trigo, Conceição; Nagel, Bert; Papagiannis, John; Rackowitz, Annette; Marek, Jan; Nürnberg, Jan-Hendrik; Vanagt, Ward Y; Prinzen, Frits W; Janousek, Jan

    2011-12-01

    Chronic right ventricular (RV) pacing is associated with deleterious effects on cardiac function. In an observational multicentre study in children with isolated atrioventricular (AV) block receiving chronic ventricular pacing, the importance of the ventricular pacing site on left ventricular (LV) function was investigated. Demographics, maternal autoantibody status and echocardiographic measurements on LV end-diastolic and end-systolic dimensions and volumes at age 1 year) for isolated AV block. LV fractional shortening (LVFS) and, if possible LV ejection fraction (LVEF) were calculated. Linear regression analyses were adjusted for patient characteristics. From 27 centres, 297 children were included, in whom pacing was applied at the RV epicardium (RVepi, n = 147), RV endocardium (RVendo, n = 113) or LV epicardium (LVepi, n = 37). LVFS was significantly affected by pacing site (p = 0.001), and not by maternal autoantibody status (p = 0.266). LVFS in LVepi (39 ± 5%) was significantly higher than in RVendo (33 ± 7%, p < 0.001) and RVepi (35 ± 8%, p = 0.001; no significant difference between RV-paced groups, p = 0.275). Subnormal LVFS (LVFS < 28%) was seen in 16/113 (14%) RVendo-paced and 21/147 (14%) RVepi-paced children, while LVFS was normal (LVFS ≥ 28%) in all LVepi-paced children (p = 0.049). These results are supported by the findings for LVEF (n = 122): LVEF was <50% in 17/69 (25%) RVendo- and in 10/35 (29%) RVepi-paced patients, while LVEF was ≥ 50% in 17/18 (94%) LVepi-paced patients. In children with isolated AV block, permanent ventricular pacing site is an important determinant of LV function, with LVFS being significantly higher with LV pacing than with RV pacing.

  16. Importance of Viral Sequence Length and Number of Variable and Informative Sites in Analysis of HIV Clustering.

    Science.gov (United States)

    Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor; Essex, M

    2015-05-01

    To improve the methodology of HIV cluster analysis, we addressed how analysis of HIV clustering is associated with parameters that can affect the outcome of viral clustering. The extent of HIV clustering and tree certainty was compared between 401 HIV-1C near full-length genome sequences and subgenomic regions retrieved from the LANL HIV Database. Sliding window analysis was based on 99 windows of 1,000 bp and 45 windows of 2,000 bp. Potential associations between the extent of HIV clustering and sequence length and the number of variable and informative sites were evaluated. The near full-length genome HIV sequences showed the highest extent of HIV clustering and the highest tree certainty. At the bootstrap threshold of 0.80 in maximum likelihood (ML) analysis, 58.9% of near full-length HIV-1C sequences but only 15.5% of partial pol sequences (ViroSeq) were found in clusters. Among HIV-1 structural genes, pol showed the highest extent of clustering (38.9% at a bootstrap threshold of 0.80), although it was significantly lower than in the near full-length genome sequences. The extent of HIV clustering was significantly higher for sliding windows of 2,000 bp than 1,000 bp. We found a strong association between the sequence length and proportion of HIV sequences in clusters, and a moderate association between the number of variable and informative sites and the proportion of HIV sequences in clusters. In HIV cluster analysis, the extent of detectable HIV clustering is directly associated with the length of viral sequences used, as well as the number of variable and informative sites. Near full-length genome sequences could provide the most informative HIV cluster analysis. Selected subgenomic regions with a high extent of HIV clustering and high tree certainty could also be considered as a second choice.

  17. Polar Behavior in a Magnetic Perovskite from A-Site Size Disorder: A Density Functional Study

    Science.gov (United States)

    Singh, D. J.; Park, Chul Hong

    2008-02-01

    We elucidate a mechanism for obtaining polar behavior in magnetic perovskites based on A-site disorder and demonstrate this mechanism by density functional calculations for the double perovskite (La,Lu)MnNiO6 with Lu concentrations at and below 50%. We show that this material combines polar behavior and ferromagnetism. The mechanism is quite general and may be applicable to a wide range of magnetic perovskites.

  18. On-Site Surface Functionalization for Titanium Dental Implant with Nanotopography: Review and Outlook

    OpenAIRE

    Byung Gyu Kim; Seog-Jin Seo; Jung-Hwan Lee; Hae-Won Kim

    2016-01-01

    Titanium (Ti) has been the first choice of material for dental implant due to bonding ability to natural bone and great biocompatibility. Various types of surface roughness modification in nanoscale have been made as promising strategy for accelerating osseointegration of Ti dental implant. To have synergetic effect with nanotopography oriented favors in cell attachment, on-site surface functionalization with reproducibility of nanotopography is introduced as next strategy to further enhance ...

  19. The Importance of Lower Mississippi River Alluvial Valley Reforestation and Wetland Restoration Sites to Wintering Migratory Birds: 2002 Annual Report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The annual report outlines the importance of conserving and restoring lands for migratory birds in the Lower Mississippi River Alluvial Valley.

  20. The Importance of Lower Mississippi River Alluvial Valley Reforestation and Wetland Restoration Sites to Wintering Migratory Birds: 2000 Annual Report

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The annual report outlines the importance of conserving and restoring lands for migratory birds in the Lower Mississippi River Alluvial Valley.

  1. Functional identification and characterization of sodium binding sites in Na symporters.

    Science.gov (United States)

    Loo, Donald D F; Jiang, Xuan; Gorraitz, Edurne; Hirayama, Bruce A; Wright, Ernest M

    2013-11-19

    Sodium cotransporters from several different gene families belong to the leucine transporter (LeuT) structural family. Although the identification of Na(+) in binding sites is beyond the resolution of the structures, two Na(+) binding sites (Na1 and Na2) have been proposed in LeuT. Na2 is conserved in the LeuT family but Na1 is not. A biophysical method has been used to measure sodium dissociation constants (Kd) of wild-type and mutant human sodium glucose cotransport (hSGLT1) proteins to identify the Na(+) binding sites in hSGLT1. The Na1 site is formed by residues in the sugar binding pocket, and their mutation influences sodium binding to Na1 but not to Na2. For the canonical Na2 site formed by two -OH side chains, S392 and S393, and three backbone carbonyls, mutation of S392 to cysteine increased the sodium Kd by sixfold. This was accompanied by a dramatic reduction in the apparent sugar and phlorizin affinities. We suggest that mutation of S392 in the Na2 site produces a structural rearrangement of the sugar binding pocket to disrupt both the binding of the second Na(+) and the binding of sugar. In contrast, the S393 mutations produce no significant changes in sodium, sugar, and phlorizin affinities. We conclude that the Na2 site is conserved in hSGLT1, the side chain of S392 and the backbone carbonyl of S393 are important in the first Na(+) binding, and that Na(+) binding to Na2 promotes binding to Na1 and also sugar binding.

  2. How the choice of safety performance function affects the identification of important crash prediction variables.

    Science.gov (United States)

    Wang, Ketong; Simandl, Jenna K; Porter, Michael D; Graettinger, Andrew J; Smith, Randy K

    2016-03-01

    Across the nation, researchers and transportation engineers are developing safety performance functions (SPFs) to predict crash rates and develop crash modification factors to improve traffic safety at roadway segments and intersections. Generalized linear models (GLMs), such as Poisson or negative binomial regression, are most commonly used to develop SPFs with annual average daily traffic as the primary roadway characteristic to predict crashes. However, while more complex to interpret, data mining models such as boosted regression trees have improved upon GLMs crash prediction performance due to their ability to handle more data characteristics, accommodate non-linearities, and include interaction effects between the characteristics. An intersection data inventory of 36 safety relevant parameters for three- and four-legged non-signalized intersections along state routes in Alabama was used to study the importance of intersection characteristics on crash rate and the interaction effects between key characteristics. Four different SPFs were investigated and compared: Poisson regression, negative binomial regression, regularized generalized linear model, and boosted regression trees. The models did not agree on which intersection characteristics were most related to the crash rate. The boosted regression tree model significantly outperformed the other models and identified several intersection characteristics as having strong interaction effects.

  3. Inulin and Oligofructosis: a review about functional properties, prebiotic effects and importance for food industry

    Directory of Open Access Journals (Sweden)

    Maria Celia de Oliveira Hauly

    2002-01-01

    Full Text Available Nowadays consumers are more conscious about the relation between food and health. Therefore food industry has been looking for food that has a lot of benefits besides good flavor and appearance. Inulin and oligofructose are fructose polimers, vastly found in plants as storage carbohydrates. They present important functional for the food industry. Both inulin and oligofructose have been used as fiber bulk in food products. Differently from other fibers, they do not add flavor, allowing the food to be improved without changing its viscosity. Inulin and oligofructose have similar nutritional properties. Inulin is more indicated for obtaining products with a low fat content such as ice cream, cake and soup, while oligofructose is indicated for yogurt with a low caloric value and in order to mask the residual flavor from high intensity sweeteners used in food preparation. Research has shown that inulin and oligofructose have prebiotic effects because they are not digestible and they can develop bifidogenic effects, improving the intestinal microflora. The simultaneous use of inulin and oligofructose with probiotic agents in food is recommended for symbiotic effects.

  4. Prognostic importance of weight change on short-term functional outcome in acute ischemic stroke.

    Science.gov (United States)

    Kim, Yerim; Kim, Chi Kyung; Jung, Seunguk; Ko, Sang-Bae; Lee, Seung-Hoon; Yoon, Byung-Woo

    2015-10-01

    Controversy exists regarding the question of whether weight change decreases or increases the risk of mortality. The aim of this study was to evaluate the prognostic importance of weight change on short-term outcomes in acute ischemic stroke patients. A total of 654 patients with acute ischemic stroke were enrolled in this study from March 2010 to May 2013. We assessed the weight change of each participant between admission and discharge from the Department of Neurology. Weight change was defined as change ≥0·05 kg/baseline body mass index unit. We evaluated the short-term outcomes using a modified Rankin Scale at three-months after the onset of a stroke. Among the 654 patients, 35·2% were included in the weight-change group. Weight loss occurred in 24·6% of the participants during the hospital stay following the stroke, which lasted an average of nine-days. Compared with the weight-stable group, the pronounced weight-loss group had a higher risk of unfavorable outcomes (odds ratio 2·43; 95% confidence interval 1·12-5·25). Short-term weight loss after stroke appears to be more common than we expected, and our results suggest that it is associated with unfavorable functional outcomes. Therefore, clinical nutrition should be considered as a component of medical treatment and weight loss should be monitored as an indicator of malnutrition. © 2015 World Stroke Organization.

  5. Particle filter based on iterated importance density function and parallel resampling

    Institute of Scientific and Technical Information of China (English)

    武勇; 王俊; 曹运合

    2015-01-01

    The design, analysis and parallel implementation of particle filter (PF) were investigated. Firstly, to tackle the particle degeneracy problem in the PF, an iterated importance density function (IIDF) was proposed, where a new term associating with the current measurement information (CMI) was introduced into the expression of the sampled particles. Through the repeated use of the least squares estimate, the CMI can be integrated into the sampling stage in an iterative manner, conducing to the greatly improved sampling quality. By running the IIDF, an iterated PF (IPF) can be obtained. Subsequently, a parallel resampling (PR) was proposed for the purpose of parallel implementation of IPF, whose main idea was the same as systematic resampling (SR) but performed differently. The PR directly used the integral part of the product of the particle weight and particle number as the number of times that a particle was replicated, and it simultaneously eliminated the particles with the smallest weights, which are the two key differences from the SR. The detailed implementation procedures on the graphics processing unit of IPF based on the PR were presented at last. The performance of the IPF, PR and their parallel implementations are illustrated via one-dimensional numerical simulation and practical application of passive radar target tracking.

  6. On the nature of Parr functions to predict the most reactive sites along organic polar reactions

    Science.gov (United States)

    Chamorro, Eduardo; Pérez, Patricia; Domingo, Luis R.

    2013-09-01

    Very recently, local electrophilic and nucleophilic “Parr functions” were empirically introduced (L.R. Domingo, P. Pérez, J.A. Saez RSC Adv. 3 (2013) 1486) in order to properly characterize the most reactive sites along polar chemical reactions. This Letter reports a theoretical advance to the new methodology by identifying these quantities with key Fukui descriptors of the spin-polarized density functional theory. Given such framework properly incorporates the treatment of both charge-transfer and spin-polarization, this finding provides a significant insight and substantial step forward within the field of a chemical reactivity theory based on the conceptual framework of density functional theory.

  7. Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs

    Directory of Open Access Journals (Sweden)

    Wang Zhouxi

    2013-02-01

    Full Text Available Abstract Background The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and to predict function from structure would add tremendous value to structural genomics data. We report on a new method, Structurally Aligned Local Sites of Activity (SALSA, for the prediction of biochemical function based on a local structural match at the predicted catalytic or binding site. Results Implementation of the SALSA method is described. For the structural genomics protein PY01515 (PDB ID 2aqw from Plasmodium yoelii, it is shown that the putative annotation, Orotidine 5'-monophosphate decarboxylase (OMPDC, is most likely correct. SALSA analysis of YP_001304206.1 (PDB ID 3h3l, a putative sugar hydrolase from Parabacteroides distasonis, shows that its active site does not bear close resemblance to any previously characterized member of its superfamily, the Concanavalin A-like lectins/glucanases. It is noted that three residues in the active site of the thermophilic beta-1,4-xylanase from Nonomuraea flexuosa (PDB ID 1m4w, Y78, E87, and E176, overlap with POOL-predicted residues of similar type, Y168, D153, and E232, in YP_001304206.1. The substrate recognition regions of the two proteins are rather different, suggesting that YP_001304206.1 is a new functional type within the superfamily. A structural genomics protein from Mycobacterium avium (PDB ID 3q1t has been reported to be an enoyl-CoA hydratase (ECH, but SALSA analysis shows a poor match between the predicted residues for the SG protein and those of known ECHs. A better local structural match is obtained with Anabaena beta-diketone hydrolase (ABDH, a known β-diketone hydrolase from Cyanobacterium anabaena (PDB ID 2j5s. This suggests that the reported ECH function of the SG protein is incorrect and that it is more likely a β-diketone hydrolase. Conclusions

  8. Homology modeling and functional sites prediction of azoreductase enzyme from the cyanobacterium Nostoc sp. PCC7120.

    Science.gov (United States)

    Devi, Philem Priyadarshini; Adhikari, Samrat

    2012-12-01

    Industrial dyes such as azodyes are potential environmental pollutants causing deleterious health hazards complications. These dyes are potentially degraded by azoreductase enzyme which is widely distributed in bacteria and also cyanobacteria. The azoreductase enzymes from cyanobacteria have not been explored in detail. Hence this enzyme from Nostoc sp. PCC 7120 has been addressed in detail in the present study considering to explore the physico-chemical properties, evolutionary relationships, functional sites and structural properties using various bioinformatics tools. Four conserved regions were obtained from the multiple sequence analysis. The multiple sequence alignment showed conserved regions at different stretches from 1-11, 40-57, 82-120 and 161-177 amino acid residues. These regions could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of azoreductase sequences from different source organisms. Domain analysis and functional site prediction showed the presence of functional sites and domain such as flavodoxin like fold responsible for enzyme activity. 3D model was constructed and the best model was selected and validated. Superimposition of the final structure and the template showed variations in certain regions which might be involved in the accommodation of various dyes. Our results may be helpful for further investigations like docking studies as well as in vivo and in vitro conditions although these predictions still need to be studied.

  9. N-Glycosylation Is Important for Proper Haloferax volcanii S-Layer Stability and Function.

    Science.gov (United States)

    Tamir, Adi; Eichler, Jerry

    2017-03-15

    N-Glycosylation, the covalent linkage of glycans to select Asn residues of target proteins, is an almost universal posttranslational modification in archaea. However, whereas roles for N-glycosylation have been defined in eukarya and bacteria, the function of archaeal N-glycosylation remains unclear. Here, the impact of perturbed N-glycosylation on the structure and physiology of the haloarchaeon Haloferax volcanii was considered. Cryo-electron microscopy was used to examine right-side-out membrane vesicles prepared from cells of a parent strain and from strains lacking genes encoding glycosyltransferases involved in assembling the N-linked pentasaccharide decorating the surface layer (S-layer) glycoprotein, the sole component of the S-layer surrounding H. volcanii cells. Whereas a regularly repeating S-layer covered the entire surface of vesicles prepared from parent strain cells, vesicles from the mutant cells were only partially covered. To determine whether such N-glycosylation-related effects on S-layer assembly also affected cell function, the secretion of a reporter protein was addressed in the parent and N-glycosylation mutant strains. Compromised S-layer glycoprotein N-glycosylation resulted in impaired transfer of the reporter past the S-layer and into the growth medium. Finally, an assessment of S-layer glycoprotein susceptibility to added proteases in the mutants revealed that in cells lacking AglD, which is involved in adding the final pentasaccharide sugar, a distinct S-layer glycoprotein conformation was assumed in which the N-terminal region was readily degraded. Perturbed N-glycosylation thus affects S-layer glycoprotein folding. These findings suggest that H. volcanii could adapt to changes in its surroundings by modulating N-glycosylation so as to affect S-layer architecture and function.IMPORTANCE Long held to be a process unique to eukaryotes, it is now accepted that bacteria and archaea also perform N-glycosylation, namely, the covalent

  10. Federal environmental standards of potential importance to operations and activities at US Department of Energy sites. Draft

    Energy Technology Data Exchange (ETDEWEB)

    Fowler, K.M.; Bilyard, G.R.; Davidson, S.A.; Jonas, R.J.; Joseph, J.

    1993-06-01

    The US Department of Energy (DOE) is now engaged in a program of environmental restoration nationwide across its 45 sites. It is also bringing its facilities into compliance with environmental regulations, decontaminating and decommissioning unwanted facilities, and constructing new waste management facilities. One of the most difficult questions that DOE must face in successfully remediating its inactive waste sites, decontaminating and decommissioning its inactive facilities, and operating its waste management facilities is: ``What criteria and standards should be met?`` Acceptable standards or procedures for determining standards will assist DOE in its conduct of ongoing waste management and pending cleanup activities by helping to ensure that those activities are conducted in compliance with applicable laws and regulations and are accepted by the regulatory community and the public. This document reports on the second of three baseline activities that are being conducted as prerequisites to either the development of quantitative standards that could be used by DOE, or consistent procedures for developing such standards. The first and third baseline activities are also briefly discussed in conjunction with the second of the three activities.

  11. 3D Information System of Historical Site – Proposal and Realisation of a Functional Prototype

    Directory of Open Access Journals (Sweden)

    J. Hodač

    2005-01-01

    Full Text Available The development of methods for 3D data acquisition, together with progress in information technologies raises the question of creating and using 3D models and 3D information systems (IS of historical sites and buildings. This paper presents the current state of the “Live Theatre” project. The theme of the project is the proposal and realisation of a 3D IS of the baroque theatre at Eeský Krumlov castle (UNESCO site.The project is divided into three main stages – creation of a 3D model, proposal of a conception for a 3D IS, and realisation of a functional prototype. 3D data was acquired by means of photogrammetric and surveying methods. An accurate 3D model (photo-realistic, textured was built up with MicroStation CAD system. The proposal of a conception of a 3D IS was the main outcome of the author’s dissertation. The essential feature of the proposed conception is the creation of subsystems targeted on three spheres – management, research and presentation of the site. The functionality of each subsystem is connected with its related sphere; however, each subsystem uses the same database. The present stage of the project involves making a functional prototype (with sample data. During this stage we are working on several basic technological topics. At present we are concerned with 3D data, its formats, format conversions (e.g. DGN _ VRML and its connection to other types of data. After that, we will be seeking a convenient technical solution based on network technologies (Internet and an appropriate layout for the data (database. The project is being carried out in close co-operation with the administration of the castle and some other partners. This stage of the project will be completed in December 2005.A functional prototype and the information acquired by testing it will form the basis for the final proposal of a complex IS of a historical site. The final proposal and appropriate technology will be the outcome of the project. The

  12. Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

    Science.gov (United States)

    Li, Yuan; Wang, Mingjun; Wang, Huilin; Tan, Hao; Zhang, Ziding; Webb, Geoffrey I.; Song, Jiangning

    2014-07-01

    Lysine acetylation is a reversible post-translational modification, playing an important role in cytokine signaling, transcriptional regulation, and apoptosis. To fully understand acetylation mechanisms, identification of substrates and specific acetylation sites is crucial. Experimental identification is often time-consuming and expensive. Alternative bioinformatics methods are cost-effective and can be used in a high-throughput manner to generate relatively precise predictions. Here we develop a method termed as SSPKA for species-specific lysine acetylation prediction, using random forest classifiers that combine sequence-derived and functional features with two-step feature selection. Feature importance analysis indicates functional features, applied for lysine acetylation site prediction for the first time, significantly improve the predictive performance. We apply the SSPKA model to screen the entire human proteome and identify many high-confidence putative substrates that are not previously identified. The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.

  13. Uncovering the Transmembrane Metal Binding Site of the Novel Bacterial Major Facilitator Superfamily-Type Copper Importer CcoA

    Directory of Open Access Journals (Sweden)

    Bahia Khalfaoui-Hassani

    2016-01-01

    Full Text Available Uptake and trafficking of metals and their delivery to their respective metalloproteins are important processes. Cells need precise control of each step to avoid exposure to excessive metal concentrations and their harmful consequences. Copper (Cu is a required micronutrient used as a cofactor in proteins. However, in large amounts, it can induce oxidative damage; hence, Cu homeostasis is indispensable for cell survival. Biogenesis of respiratory heme-Cu oxygen (HCO reductases includes insertion of Cu into their catalytic subunits to form heme-Cu binuclear centers. Previously, we had shown that CcoA is a major facilitator superfamily (MFS-type bacterial Cu importer required for biogenesis of cbb3-type cytochrome c oxidase (cbb3-Cox. Here, using Rhodobacter capsulatus, we focused on the import and delivery of Cu to cbb3-Cox. By comparing the CcoA amino acid sequence with its homologues from other bacterial species, we located several well-conserved Met, His, and Tyr residues that might be important for Cu transport. We determined the topology of the transmembrane helices that carry these residues to establish that they are membrane embedded, and substituted for them amino acids that do not ligand metal atoms. Characterization of these mutants for their uptake of radioactive 64Cu and cbb3-Cox activities demonstrated that Met233 and His261 of CcoA are essential and Met237 and Met265 are important, whereas Tyr230 has no role for Cu uptake or cbb3-Cox biogenesis. These findings show for the first time that CcoA-mediated Cu import relies on conserved Met and His residues that could act as metal ligands at the membrane-embedded Cu binding domain of this transporter.

  14. Linking functional traits and demographic rates in a subtropical tree community: the importance of size dependency

    National Research Council Canada - National Science Library

    Iida, Yoshiko; Kohyama, Takashi S; Swenson, Nathan G; Su, Sheng‐Hsin; Chen, Chien‐Teh; Chiang, Jyh‐Min; Sun, I‐Fang; Zuidema, Pieter

    2014-01-01

    .... Several functional traits have been shown to correlate with growth and mortality rates in trees, but less is known about how the relationships between functional traits and demographic rates change with tree size...

  15. Prognostic importance of systolic and diastolic function after acute myocardial infarction

    DEFF Research Database (Denmark)

    Møller, Jacob E; Egstrup, Kenneth; Køber, Lars

    2003-01-01

    BACKGROUND: Although risk stratification after acute myocardial infarction (AMI) often is focused on systolic left ventricular (LV) function, it appears that a more complete study of ventricular function including assessment of LV filling would be useful. Doppler echocardiography allows assessment...

  16. Automatic variance reduction for Monte Carlo simulations via the local importance function transform

    Energy Technology Data Exchange (ETDEWEB)

    Turner, S.A.

    1996-02-01

    The author derives a transformed transport problem that can be solved theoretically by analog Monte Carlo with zero variance. However, the Monte Carlo simulation of this transformed problem cannot be implemented in practice, so he develops a method for approximating it. The approximation to the zero variance method consists of replacing the continuous adjoint transport solution in the transformed transport problem by a piecewise continuous approximation containing local biasing parameters obtained from a deterministic calculation. He uses the transport and collision processes of the transformed problem to bias distance-to-collision and selection of post-collision energy groups and trajectories in a traditional Monte Carlo simulation of ``real`` particles. He refers to the resulting variance reduction method as the Local Importance Function Transform (LIFI) method. He demonstrates the efficiency of the LIFT method for several 3-D, linearly anisotropic scattering, one-group, and multigroup problems. In these problems the LIFT method is shown to be more efficient than the AVATAR scheme, which is one of the best variance reduction techniques currently available in a state-of-the-art Monte Carlo code. For most of the problems considered, the LIFT method produces higher figures of merit than AVATAR, even when the LIFT method is used as a ``black box``. There are some problems that cause trouble for most variance reduction techniques, and the LIFT method is no exception. For example, the author demonstrates that problems with voids, or low density regions, can cause a reduction in the efficiency of the LIFT method. However, the LIFT method still performs better than survival biasing and AVATAR in these difficult cases.

  17. Automatic variance reduction for Monte Carlo simulations via the local importance function transform

    Energy Technology Data Exchange (ETDEWEB)

    Turner, S.A.

    1996-02-01

    The author derives a transformed transport problem that can be solved theoretically by analog Monte Carlo with zero variance. However, the Monte Carlo simulation of this transformed problem cannot be implemented in practice, so he develops a method for approximating it. The approximation to the zero variance method consists of replacing the continuous adjoint transport solution in the transformed transport problem by a piecewise continuous approximation containing local biasing parameters obtained from a deterministic calculation. He uses the transport and collision processes of the transformed problem to bias distance-to-collision and selection of post-collision energy groups and trajectories in a traditional Monte Carlo simulation of ``real`` particles. He refers to the resulting variance reduction method as the Local Importance Function Transform (LIFI) method. He demonstrates the efficiency of the LIFT method for several 3-D, linearly anisotropic scattering, one-group, and multigroup problems. In these problems the LIFT method is shown to be more efficient than the AVATAR scheme, which is one of the best variance reduction techniques currently available in a state-of-the-art Monte Carlo code. For most of the problems considered, the LIFT method produces higher figures of merit than AVATAR, even when the LIFT method is used as a ``black box``. There are some problems that cause trouble for most variance reduction techniques, and the LIFT method is no exception. For example, the author demonstrates that problems with voids, or low density regions, can cause a reduction in the efficiency of the LIFT method. However, the LIFT method still performs better than survival biasing and AVATAR in these difficult cases.

  18. Ferritin has an important immune function in the ark shell Scapharca broughtonii.

    Science.gov (United States)

    Zheng, Libing; Liu, Zhihong; Wu, Biao; Dong, Yinghui; Zhou, Liqing; Tian, Jiteng; Sun, Xiujun; Yang, Aiguo

    2016-06-01

    Ferritin, the principle cytosolic iron storage protein in the majority of living organisms, has important roles during immune process in invertebrates. Detailed information about ferritin in the ark shell Scapharca broughtonii, however, has been very limited. In this study, full-length ferritin (termed SbFer) was cloned by the rapid amplication of cDNA ends (RACE) method based upon the sequence from the transcriptome library. The cDNA contained a 182 bp 5'-untranslated region, a 519 bp open reading frame encoding a polypeptide of 172 amino acids, a 229 bp 3'-untranslated region, and three introns (902, 373 and 402 bp) embedded in four exons. There was an iron response element (IRE) in the 5'-untranslated region. The deduced amino acid sequence of SbFer possessed many characteristics of vertebrate H type ferritin, shared 63%-91% identity with mollusks and greater identity with vertebrate H type ferritin compared to the L type. The SbFer gene expression pattern examined by quantitative real-time PCR showed ferritin mRNA was expressed in all ark shell tissues examined. The highest levels of expression were found in hemocytes with decreasing levels of expression in foot, mantle, gill, adductor muscle and hepatopancreas. A challenge with Vibrio anguillarum resulted in time-dependent significant upregulation of SbFer mRNA, indicating SbFer participated actively in the bacterial defense process. Further analysis of the antibacterial activity indicated recombinant SbFer could function as an immune antibacterial agent to both Gram-positive and Gram-negative bacteria. Taken together, these results suggested strongly that ferritin of the ark shell is involved in immune defense against microbial infection and it is a constitutive and inducible acute-phase protein.

  19. Intra-operative multi-site stimulation: Expanding methodology for cortical brain mapping of language functions.

    Science.gov (United States)

    Gonen, Tal; Gazit, Tomer; Korn, Akiva; Kirschner, Adi; Perry, Daniella; Hendler, Talma; Ram, Zvi

    2017-01-01

    Direct cortical stimulation (DCS) is considered the gold-standard for functional cortical mapping during awake surgery for brain tumor resection. DCS is performed by stimulating one local cortical area at a time. We present a feasibility study using an intra-operative technique aimed at improving our ability to map brain functions which rely on activity in distributed cortical regions. Following standard DCS, Multi-Site Stimulation (MSS) was performed in 15 patients by applying simultaneous cortical stimulations at multiple locations. Language functioning was chosen as a case-cognitive domain due to its relatively well-known cortical organization. MSS, performed at sites that did not produce disruption when applied in a single stimulation point, revealed additional language dysfunction in 73% of the patients. Functional regions identified by this technique were presumed to be significant to language circuitry and were spared during surgery. No new neurological deficits were observed in any of the patients following surgery. Though the neuro-electrical effects of MSS need further investigation, this feasibility study may provide a first step towards sophistication of intra-operative cortical mapping.

  20. The polyproline site in hinge 2 influences the functional capacity of truncated dystrophins.

    Directory of Open Access Journals (Sweden)

    Glen B Banks

    2010-05-01

    Full Text Available Mutations in dystrophin can lead to Duchenne muscular dystrophy or the more mild form of the disease, Becker muscular dystrophy. The hinge 3 region in the rod domain of dystrophin is particularly prone to deletion mutations. In-frame deletions of hinge 3 are predicted to lead to BMD, however the severity of disease can vary considerably. Here we performed extensive structure-function analyses of truncated dystrophins with modified hinges and spectrin-like repeats in mdx mice. We found that the polyproline site in hinge 2 profoundly influences the functional capacity of a microdystrophin(DeltaR4-R23/DeltaCT with a large deletion in the hinge 3 region. Inclusion of polyproline in microdystrophin(DeltaR4-R23/DeltaCT led to small myofibers (12% smaller than wild-type, Achilles myotendinous disruption, ringed fibers, and aberrant neuromuscular junctions in the mdx gastrocnemius muscles. Replacing hinge 2 of microdystrophin(DeltaR4-R23/DeltaCT with hinge 3 significantly improved the functional capacity to prevent muscle degeneration, increase muscle fiber area, and maintain the junctions. We conclude that the rigid alpha-helical structure of the polyproline site significantly impairs the functional capacity of truncated dystrophins to maintain appropriate connections between the cytoskeleton and extracellular matrix.

  1. Site-Specific Incorporation of Functional Components into RNA by an Unnatural Base Pair Transcription System

    Directory of Open Access Journals (Sweden)

    Rie Kawai

    2012-03-01

    Full Text Available Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienylimidazo[4,5-b]pyridine (Ds and pyrrole-2-carbaldehyde (Pa functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.

  2. The importance of code status discussions in the psychiatric hospital: results of a single site survey of psychiatrists.

    Science.gov (United States)

    McKean, Alastair J S; Lapid, Maria I; Geske, Jennifer R; Kung, Simon

    2015-04-01

    Documentation of code status is a requirement with hospital admission, yet this discussion may present unique challenges with psychiatric inpatients. Currently, no standards exist on conducting these discussions with psychiatric inpatients. The authors surveyed psychiatry trainees and faculty regarding their perceptions and practice to gain further insight into the types of approaches used. The authors conducted an IRB-approved, Web-based survey of psychiatry faculty and trainees using a 25-item questionnaire of demographics and opinions about code status among psychiatric inpatients. The response rate was 36.1 % (n = 30; 15 faculty and 15 trainees). Respondents felt that it was important to discuss code status with each admission. Faculty placed a higher emphasis on assessing patients with a recent suicide attempt (p = 0.024). Psychiatric faculty and trainees endorsed the importance of assessing code status with each admission. The authors suggest that educational programs are needed on strategies to conduct code status discussions properly and effectively in psychiatric populations.

  3. Dolomitic vegetation of the Sterkfontein Caves World Heritage Site and its importance in the conservation of Rocky Highveld Grassland

    Directory of Open Access Journals (Sweden)

    F. Siebert

    2005-06-01

    Full Text Available An analysis of the vegetation of the Sterkfontein Caves (i.e. the natural area surrounding the caves is presented. Releves were compiled in 24 stratified random sample plots. A TWINSPAN classification, refined by Braun-Blanquet procedures, revealed six plant communities, also referred to as vegetation units. For each of these vegetation units the species richness was determined. Plant communities of conservation importance were identified and new associations were formally described.

  4. The editing sites in transcripts of functional genes of rice mitochondria

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    RNA editing exists extensively in the higher plant mitochondria, and is a required step for forming functional proteins. There may be some relationship between RNA editing and cytoplasmic male sterility (CMS), a kind of phenomenon that is attributed to mitochondrial genome mutations. The research materials used are the gametophytic male sterility line (A), maintainer line (B) and F1 hybrid (F1) of HL-type CMS rice. cDNAs and DNAs of atp6 and coxII have been obtained from A, B and F1 by PCR and RT-PCR. Comparing sequences of cDNAs and DNAs, 18 and 15 editing sites were found respectively in the transcripts of atp6 and coxII. A, B and F1 shared the same editing sites. RNA editing improves hydrophobicity and conservation of the predicted protein as compared with other organisms.

  5. Identifying faecal impaction is important for ensuring the timely diagnosis of childhood functional constipation

    DEFF Research Database (Denmark)

    Modin, Line; Walsted, Anne-Mette; Jakobsen, Marianne Skytte

    2015-01-01

    AIM: Most research on functional constipation has been carried out at a tertiary level. We focused this study on a secondary-level hospital outpatients' department, assessing the distribution of diagnostic criteria for childhood functional constipation and evaluating the consequences of current...... diagnostic practice based on current guidelines. METHODS: We enrolled 235 children, aged two to 16 years of age, with functional constipation according to the Rome III criteria and assessed them using medical histories and physical examinations, including rectal examinations and ultrasound measurements...... the timely diagnosis of childhood functional constipation at the secondary care level. Ultrasound examination proved a reliable alternative to rectal examination or abdominal radiography when identifying faecal impaction....

  6. The importance of biodiversity and dominance for multiple ecosystem functions in a human-modified tropical landscape.

    Science.gov (United States)

    Lohbeck, Madelon; Bongers, Frans; Martinez-Ramos, Miguel; Poorter, Lourens

    2016-10-01

    Many studies suggest that biodiversity may be particularly important for ecosystem multifunctionality, because different species with different traits can contribute to different functions. Support, however, comes mostly from experimental studies conducted at small spatial scales in low-diversity systems. Here, we test whether different species contribute to different ecosystem functions that are important for carbon cycling in a high-diversity human-modified tropical forest landscape in Southern Mexico. We quantified aboveground standing biomass, primary productivity, litter production, and wood decomposition at the landscape level, and evaluated the extent to which tree species contribute to these ecosystem functions. We used simulations to tease apart the effects of species richness, species dominance and species functional traits on ecosystem functions. We found that dominance was more important than species traits in determining a species' contribution to ecosystem functions. As a consequence of the high dominance in human-modified landscapes, the same small subset of species mattered across different functions. In human-modified landscapes in the tropics, biodiversity may play a limited role for ecosystem multifunctionality due to the potentially large effect of species dominance on biogeochemical functions. However, given the spatial and temporal turnover in species dominance, biodiversity may be critically important for the maintenance and resilience of ecosystem functions.

  7. Functional outcomes of child and adolescent mental disorders. Current disorder most important but psychiatric history matters as well

    NARCIS (Netherlands)

    Ormel, J; Oerlemans, A M; Raven, D; Laceulle, O M; Hartman, C A; Veenstra, R.; Verhulst, F C; Vollebergh, W; Rosmalen, J G M; Reijneveld, S A; Oldehinkel, A J

    Background. Various sources indicate that mental disorders are the leading contributor to the burden of disease among youth. An important determinant of functioning is current mental health status. This study investigated whether psychiatric history has additional predictive power when predicting

  8. The 101st Canton Fair,Import Functions Added, Eyes New Market,New Trade Partners

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ The 101st Session of Canton Fair will be held in Canton city,Guangdong province from April 15 to 30, 2007. The fair, used to be named as China Export Commodities Fair for 100 sessions, is to be rebranded as China Import and Export Fair. By changing the name, a new service as import will be added, so as to encourage more import to meet the capacious market demand in China market, pursuing a more balanced and healthier international trade development.

  9. Functionalization of Defect Sites in Graphene with RuO2 for High Capacitive Performance.

    Science.gov (United States)

    Yang, Fan; Zhang, Lianbing; Zuzuarregui, Ana; Gregorczyk, Keith; Li, Le; Beltrán, Mikel; Tollan, Christopher; Brede, Jens; Rogero, Celia; Chuvilin, Andrey; Knez, Mato

    2015-09-23

    Graphene is an attractive material for its physicochemical properties, but for many applications only chemically synthesized forms such as graphene oxide (GO) and reduced graphene oxide (rGO) can be produced in sufficient amounts. If considered as electrode material, the intrinsic defects of GO or rGO may have negative influence on the conductivity and electrochemical properties. Such defects are commonly oxidized sites that offer the possibility to be functionalized with other materials in order to improve performance. In this work, we demonstrate how such ultimately efficient functionalization can be achieved: namely, through controlled binding of very small amount of materials such as RuO2 to rGO by atomic layer deposition (ALD), in this way substituting the native defect sites with RuO2 defects. For the example of a supercapacitor, we show that defect functionalization results in significantly enhanced specific capacitance of the electrode and that its energy density can be stabilized even at high consumption rates.

  10. The importance of current contributions to shielding constants in density-functional theory.

    Science.gov (United States)

    Reimann, Sarah; Ekström, Ulf; Stopkowicz, Stella; Teale, Andrew M; Borgoo, Alex; Helgaker, Trygve

    2015-07-28

    The sources of error in the calculation of nuclear-magnetic-resonance shielding constants determined by density-functional theory are examined. Highly accurate Kohn-Sham wave functions are obtained from coupled-cluster electron density functions and used to define accurate-but current independent-density-functional shielding constants. These new reference values, in tandem with high-accuracy coupled-cluster shielding constants, provide a benchmark for the assessment of errors in common density-functional approximations. In particular the role of errors arising in the diamagnetic and paramagnetic terms is investigated, with particular emphasis on the role of current-dependence in the latter. For carbon and nitrogen the current correction is found to be, in some cases, larger than 10 ppm. This indicates that the absence of this correction in general purpose exchange-correlation functionals is one of the main sources of error in shielding calculations using density functional theory. It is shown that the current correction improves the shielding performance of many popular approximate DFT functionals.

  11. Insights from Cognitive Neuroscience: The Importance of Executive Function for Early Reading Development and Education

    Science.gov (United States)

    Cartwright, Kelly B.

    2012-01-01

    Research Findings: Executive function begins to develop in infancy and involves an array of processes, such as attention, inhibition, working memory, and cognitive flexibility, which provide the means by which individuals control their own behavior, work toward goals, and manage complex cognitive processes. Thus, executive function plays a…

  12. Importance of Microbial Activity On Groundwater Iodate and Organo-Iodine Speciation and Mobility At Two DOE Sites

    Energy Technology Data Exchange (ETDEWEB)

    Santschi, Peter H. [Texas A & M Univ., College Station, TX (United States); Xu, Chen [Texas A & M Univ., College Station, TX (United States); Schwehr, Kathleen A. [Texas A & M Univ., College Station, TX (United States); Kaplan, Daniel I. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Yeager, Chris M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-03-01

    Iodine (I) occurs in multiple oxidation states in aquatic systems in the form of organic and inorganic species (iodide and iodate). This fact leads to complex biogeochemical cycling of Iodine and its long-lived isotope, 129I, a major by-product of nuclear fission. Results from our newly developed, sensitive and rapid method for speciated isotopic ratios (129I/127I) via GC-MS, which compare favorably with Accelerator Mass Spectroscopy, demonstrate that the mobility of 129I species greatly depends on the type of I species and its concentration, pH, and sediment redox state. At ambient concentrations (~107 M), I- and IO-3 are significantly retarded by sorption to mineral surfaces and covalent binding to aromatic moieties in natural organic matter (NOM), even when NOM is present at low concentrations such as occur at Hanford. At concentrations traditionally examined in sorption studies (≥ 10-4 M), I- travels along with the water. Iodate removal can also occur through incorporation into CaCO3 crystal lattice, e.g., at the Hanford Site. Removal of iodine from the groundwater through interaction with NOM is complicated by the release of mobile organo-I species, as was observed at SRS and Hanford. A small fraction of NOM that is bound to iodine can behave as a mobile organo-I source, a process that we were able to numerically simulate. Field and laboratory studies evaluating the cause for steady increases in 129I concentrations (up to 1000 pCi L-1) emanating from radiological basins at SRS indicate that an increase of 0.7 pH units in groundwater over 17 years can account for the observed increased groundwater 129I concentrations. Bacteria from a 129I-contaminated aerobic aquifer at the F-area of SRS can accumulate I- at environmentally relevant concentrations (10-7 M), and enzymatically oxidize I-, which together with microbially produced Mn

  13. Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids

    Science.gov (United States)

    Pan, Yang; Yan, Cheng; Hu, Yu; Fan, Yu; Pan, Qing; Wan, Quan; Torcivia-Rodriguez, John; Mazumder, Raja

    2017-01-01

    Single nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types. By leveraging patient information for somatic pfsSNVs, we identified 17 loss of functional site SNVs and 60 gain of functional site SNVs which are significantly enriched in patients with specific cancer types. Of the key pfsSNVs identified in our analysis above, we highlight 132 key pfsSNVs within 17 genes that are found in well-established cancer associated gene lists. For illustrating how key pfsSNVs can be prioritized further, we provide a use case where we performed survival analysis showing that a loss of phosphorylation site pfsSNV at position 105 in MEF2A is significantly associated with decreased pancreatic cancer patient survival rate. These 132 pfsSNVs can be used in developing genetic testing pipelines. PMID:28176830

  14. Interpersonal Attraction Toward a Black Person as a Function of Value Importance.

    Science.gov (United States)

    Penner, Louis A.

    The purpose of this study was to test two hypotheses derived from Rokeach's (1968) theory of values and value change. These were: (1) that interpersonal attraction toward a black person will be correlated with the importance of the value, "equality," and (2) that changes in the importance of the value, "equality," will be…

  15. DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

    Science.gov (United States)

    Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

    2013-01-01

    Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

  16. Type 2 diabetes mellitus: phylogenetic motifs for predicting protein functional sites

    Indian Academy of Sciences (India)

    Ashok Sharma; Tanuja Rastogi; Meenakshi Bhartiya; A K Shasany; S P S Khanuja

    2007-08-01

    Diabetes mellitus, commonly referred to as diabetes, is a medical condition associated with abnormally high levels of glucose (or sugar) in the blood. Keeping this view, we demonstrate the phylogenetic motifs (PMs) identification in type 2 diabetes mellitus very likely corresponding to protein functional sites. In this article, we have identified PMs for all the candidate genes for type 2 diabetes mellitus. Glycine 310 remains conserved for glucokinase and potassium channel KCNJ11. Isoleucine 137 was conserved for insulin receptor and regulatory subunit of a phosphorylating enzyme. Whereas residues valine, leucine, methionine were highly conserved for insulin receptor. Occurrence of proline was very high for calpain 10 gene and glucose transporter

  17. Cortisol secretion and functional disabilities in old age: importance of using adaptive control strategies.

    Science.gov (United States)

    Wrosch, Carsten; Miller, Gregory E; Schulz, Richard

    2009-11-01

    To examine whether the use of health-related control strategies moderates the association between elevated diurnal cortisol secretion and increases in older adults' functional disabilities. Functional disabilities of 164 older adults were assessed over 4 years by measuring participants' problems with performing activities of daily living. The main predictors included baseline levels of diurnal cortisol secretion and control strategies used to manage physical health threats. A large increase in functional disabilities was observed among participants who secreted elevated baseline levels of cortisol and did not use health-related control strategies. By contrast, high cortisol level was not associated with increases in functional disabilities among participants who reported using these control strategies. Among participants with low cortisol level, there was a relatively smaller increase in functional disabilities over time, and the use of control strategies was not significantly associated with changes in functional disabilities. The findings suggest that high cortisol level is associated with an increase in older adults' functional disabilities, but only if older adults do not engage in adaptive control strategies.

  18. Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues

    Directory of Open Access Journals (Sweden)

    Liu Tianyun

    2010-02-01

    Full Text Available Abstract Background The emergence of structural genomics presents significant challenges in the annotation of biologically uncharacterized proteins. Unfortunately, our ability to analyze these proteins is restricted by the limited catalog of known molecular functions and their associated 3D motifs. Results In order to identify novel 3D motifs that may be associated with molecular functions, we employ an unsupervised, two-phase clustering approach that combines k-means and hierarchical clustering with knowledge-informed cluster selection and annotation methods. We applied the approach to approximately 20,000 cysteine-based protein microenvironments (3D regions 7.5 Å in radius and identified 70 interesting clusters, some of which represent known motifs (e.g. metal binding and phosphatase activity, and some of which are novel, including several zinc binding sites. Detailed annotation results are available online for all 70 clusters at http://feature.stanford.edu/clustering/cys. Conclusions The use of microenvironments instead of backbone geometric criteria enables flexible exploration of protein function space, and detection of recurring motifs that are discontinuous in sequence and diverse in structure. Clustering microenvironments may thus help to functionally characterize novel proteins and better understand the protein structure-function relationship.

  19. A density functional theory for colloids with two multiple bonding associating sites.

    Science.gov (United States)

    Haghmoradi, Amin; Wang, Le; Chapman, Walter G

    2016-06-22

    Wertheim's multi-density formalism is extended for patchy colloidal fluids with two multiple bonding patches. The theory is developed as a density functional theory to predict the properties of an associating inhomogeneous fluid. The equation of state developed for this fluid depends on the size of the patch, and includes formation of cyclic, branched and linear clusters of associated species. The theory predicts the density profile and the fractions of colloids in different bonding states versus the distance from one wall as a function of bulk density and temperature. The predictions from our theory are compared with previous results for a confined fluid with four single bonding association sites. Also, comparison between the present theory and Monte Carlo simulation indicates a good agreement.

  20. PKA regulates calcineurin function through the phosphorylation of RCAN1: Identification of a novel phosphorylation site

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seon Sook; Lee, Eun Hye [Department of Molecular Bioscience, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Lee, Kooyeon [Department of Bio-Health Technology, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Jo, Su-Hyun, E-mail: suhyunjo@kangwon.ac.kr [Department of Physiology, BK21 Plus Graduate Program, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of); Seo, Su Ryeon, E-mail: suryeonseo@kangwon.ac.kr [Department of Molecular Bioscience, College of Biomedical Science, Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon 200-701 (Korea, Republic of)

    2015-04-17

    Calcineurin is a calcium/calmodulin-dependent phosphatase that has been implicated in T cell activation through the induction of nuclear factors of activated T cells (NFAT). We have previously suggested that endogenous regulator of calcineurin (RCAN1, also known as DSCR1) is targeted by protein kinase A (PKA) for the control of calcineurin activity. In the present study, we characterized the PKA-mediated phosphorylation site in RCAN1 by mass spectrometric analysis and revealed that PKA directly phosphorylated RCAN1 at the Ser 93. PKA-induced phosphorylation and the increase in the half-life of the RCAN1 protein were prevented by the substitution of Ser 93 with Ala (S93A). Furthermore, the PKA-mediated phosphorylation of RCAN1 at Ser 93 potentiated the inhibition of calcineurin-dependent pro-inflammatory cytokine gene expression by RCAN1. Our results suggest the presence of a novel phosphorylation site in RCAN1 and that its phosphorylation influences calcineurin-dependent inflammatory target gene expression. - Highlights: • We identify novel phosphorylation sites in RCAN1 by LC-MS/MS analysis. • PKA-dependent phosphorylation of RCAN1 at Ser 93 inhibits calcineurin-mediated intracellular signaling. • We show the immunosuppressive function of RCAN1 phosphorylation at Ser 93 in suppressing cytokine expression.

  1. Stable isotope probing reveals the importance of Comamonas and Pseudomonadaceae in RDX degradation in samples from a Navy detonation site.

    Science.gov (United States)

    Jayamani, Indumathy; Cupples, Alison M

    2015-07-01

    This study investigated the microorganisms involved in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) degradation from a detonation area at a Navy base. Using Illumina sequencing, microbial communities were compared between the initial sample, samples following RDX degradation, and controls not amended with RDX to determine which phylotypes increased in abundance following RDX degradation. The effect of glucose on these communities was also examined. In addition, stable isotope probing (SIP) using labeled ((13)C3, (15)N3-ring) RDX was performed. Illumina sequencing revealed that several phylotypes were more abundant following RDX degradation compared to the initial soil and the no-RDX controls. For the glucose-amended samples, this trend was strong for an unclassified Pseudomonadaceae phylotype and for Comamonas. Without glucose, Acinetobacter exhibited the greatest increase following RDX degradation compared to the initial soil and no-RDX controls. Rhodococcus, a known RDX degrader, also increased in abundance following RDX degradation. For the SIP study, unclassified Pseudomonadaceae was the most abundant phylotype in the heavy fractions in both the presence and absence of glucose. In the glucose-amended heavy fractions, the 16S ribosomal RNA (rRNA) genes of Comamonas and Anaeromxyobacter were also present. Without glucose, the heavy fractions also contained the 16S rRNA genes of Azohydromonas and Rhodococcus. However, all four phylotypes were present at a much lower level compared to unclassified Pseudomonadaceae. Overall, these data indicate that unclassified Pseudomonadaceae was primarily responsible for label uptake in both treatments. This study indicates, for the first time, the importance of Comamonas for RDX removal.

  2. Evaluating the Importance of Plant Functional Traits: the Subalpine and Alpine

    Science.gov (United States)

    Sanchez, A.; Smith, W. K.

    2011-12-01

    Over the past several decades, researchers have attempted to characterize plant groups according to traits that are considered functional, i.e. contributing significantly to fitness. Due to the complexity of measuring fitness, the capability for photosynthetic carbon gain is often used as a proxy. Thus, this approach correlates structural differences to photosynthetic performance, especially those differences that are known to be associated with photosynthesis, are easily measured and inexpensive. At the often sharp boundary between the subalpine forest and alpine community (treeline ecotone), plant structural traits change dramatically, i.e. tall evergreen trees give way abruptly to low-stature shrubs, grasses, forbs, and herbs. Yet, the differences in functional traits, so abundant in the literature for a variety of species and communities, have not been compared contiguous communities such as the subalpine forest and alpine. Can differences in functional traits already identified in the literature also be used to characterize species of these two contrasting communities? Or are there other traits that are most functional and/or, possibly, unique to each community and not the most popular traits reported so far in the literature. Also, does the community structure itself help determine functional traits? For example, the top ten most frequently studied traits (145 total papers from approximately 63 different refereed journals) considered functional include the following (% of the 145 publications): specific leaf area or mass (SLA or SLM 39%), plant height (36%), leaf nitrogen content (34%), leaf size (19%), leaf area (16%), leaf photosynthetic performance (15%), leaf dry matter content (LDMC 15%), leaf mass per unit leaf area (LMA 15%), leaf thickness (15%), and seed mass (14%). In addition, another 120 traits were mentioned as functional, although all fell below a 14% citation rate. Particular focus was placed on this group due to the possibility that they might

  3. Variable importance of macrofaunal functional biodiversity for biogeochemical cycling in temperate coastal sediments

    OpenAIRE

    Braeckman, U.; Yazdani Foshtomi, M.; Van Gansbeke, D.; Meysman, F.; Soetaert, K.; Vincx, M.; Vanaverbeke, J.

    2014-01-01

    Coastal marine systems are currently subject to a variety of anthropogenic and climate-change-induced pressures. An important challenge is to predict how marine sediment communities and benthic biogeochemical cycling will be affected by these ongoing changes. To this end, it is of paramount importance to first better understand the natural variability in coastal benthic biogeochemical cycling and how this is influenced by local environmental conditions and faunal biodiversity. Here, we studie...

  4. The functional asymmetry of cosN, the nicking site for bacteriophage lambda DNA packaging, is dependent on the terminase binding site, cosB.

    Science.gov (United States)

    Hang, J Q; Catalano, C E; Feiss, M

    2001-11-06

    cosN is the site at which terminase, the DNA packaging enzyme of phage lambda, introduces staggered nicks into viral concatemeric DNA to initiate genome packaging. Although the nick positions and many of the base pairs of cosN show 2-fold rotational symmetry, cosN is functionally asymmetric. That is, the cosN G2C mutation in the left half-site (cosNL) causes a strong virus growth defect whereas the symmetrically disposed cosN C11G mutation in the right half-site (cosNR) does not affect virus growth. The experiments reported here test the proposal that the genetic asymmetry of cosN results from terminase interactions with cosB, a binding site to the right of cosN. In the presence of cosB, the left half-site mutation, cosN G2C, strongly affected the cos cleavage reaction, while the symmetric right half-site mutation, cosN C11G, had little effect. In the absence of cosB, the two mutations moderately reduced the rate of cos cleavage by the same amount. The results indicated that the functional asymmetry of cosNdepends on the presence of cosB. A model is discussed in which terminase-cosN interactions in the nicking complex are assisted by anchoring of terminase to cosB.

  5. Importance of the Kinetic Energy Density for Band Gap Calculations in Solids with Density Functional Theory.

    Science.gov (United States)

    Tran, Fabien; Blaha, Peter

    2017-05-04

    Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.

  6. Importance of local exact exchange potential in hybrid functionals for accurate excited states

    CERN Document Server

    Kim, Jaewook; Hwang, Sang-Yeon; Ryu, Seongok; Choi, Sunghwan; Kim, Woo Youn

    2016-01-01

    Density functional theory has been an essential analysis tool for both theoretical and experimental chemists since accurate hybrid functionals were developed. Here we propose a local hybrid method derived from the optimized effective potential (OEP) method and compare its distinct features with conventional nonlocal ones from the Hartree-Fock (HF) exchange operator. Both are formally exact for ground states and thus show similar accuracy for atomization energies and reaction barrier heights. For excited states, the local version yields virtual orbitals with N-electron character, while those of the nonlocal version have mixed characters between N- and (N+1)-electron orbitals. As a result, the orbital energy gaps from the former well approximate excitation energies with a small mean absolute error (MAE = 0.40 eV) for the Caricato benchmark set. The correction from time-dependent density functional theory with a simple local density approximation kernel further improves its accuracy by incorporating multi-config...

  7. The structure, function, and importance of ceramides in skin and their use as therapeutic agents in skin-care products.

    Science.gov (United States)

    Meckfessel, Matthew H; Brandt, Staci

    2014-07-01

    Ceramides (CERs) are epidermal lipids that are important for skin barrier function. Much research has been devoted to identifying the numerous CERs found in human skin and their function. Alterations in CER content are associated with a number of skin diseases such as atopic dermatitis. Newer formulations of skin-care products have incorporated CERs into their formulations with the goal of exogenously applying CERs to help skin barrier function. CERs are a complex class of molecules and because of their growing ubiquity in skin-care products, a clear understanding of their role in skin and use in skin-care products is essential for clinicians treating patients with skin diseases. This review provides an overview of the structure, function, and importance of skin CERs in diseased skin and how CERs are being used in skin-care products to improve or restore skin barrier function. Copyright © 2014 American Academy of Dermatology, Inc. Published by Mosby, Inc. All rights reserved.

  8. Single-site Green function of the Dirac equation for full-potential electron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kordt, Pascal

    2012-05-30

    I present an elaborated analytical examination of the Green function of an electron scattered at a single-site potential, for both the Schroedinger and the Dirac equation, followed by an efficient numerical solution, in both cases for potentials of arbitrary shape without an atomic sphere approximation. A numerically stable way to calculate the corresponding regular and irregular wave functions and the Green function is via the angular Lippmann-Schwinger integral equations. These are solved based on an expansion in Chebyshev polynomials and their recursion relations, allowing to rewrite the Lippmann-Schwinger equations into a system of algebraic linear equations. Gonzales et al. developed this method for the Schroedinger equation, where it gives a much higher accuracy compared to previous perturbation methods, with only modest increase in computational effort. In order to apply it to the Dirac equation, I developed relativistic Lippmann-Schwinger equations, based on a decomposition of the potential matrix into spin spherical harmonics, exploiting certain properties of this matrix. The resulting method was embedded into a Korringa-Kohn-Rostoker code for density functional calculations. As an example, the method is applied by calculating phase shifts and the Mott scattering of a tungsten impurity. (orig.)

  9. The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

    Directory of Open Access Journals (Sweden)

    Widaningrum Dyah Lestari

    2014-03-01

    Full Text Available This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package’s impact. The results of House of Quality development described that Conjoint Analysis – QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers’ requirements in the early stages of HOQ process

  10. The Importance of Take-Out Food Packaging Attributes: Conjoint Analysis and Quality Function Deployment Approach

    Science.gov (United States)

    Lestari Widaningrum, Dyah

    2014-03-01

    This research aims to investigate the importance of take-out food packaging attributes, using conjoint analysis and QFD approach among consumers of take-out food products in Jakarta, Indonesia. The conjoint results indicate that perception about packaging material (such as paper, plastic, and polystyrene foam) plays the most important role overall in consumer perception. The clustering results that there is strong segmentation in which take-out food packaging material consumer consider most important. Some consumers are mostly oriented toward the colour of packaging, while another segment of customers concerns on packaging shape and packaging information. Segmentation variables based on packaging response can provide very useful information to maximize image of products through the package's impact. The results of House of Quality development described that Conjoint Analysis - QFD is a useful combination of the two methodologies in product development, market segmentation, and the trade off between customers' requirements in the early stages of HOQ process

  11. How Language Learners Can Improve Their Emotional Functioning: Important Psychological and Psychospiritual Theories

    Science.gov (United States)

    Oxford, Rebecca L.

    2015-01-01

    Emotion is "the primary human motive" (MacIntyre, 2002, p. 61). The human brain is an emotional brain, creating relationships among thought, emotion, and motivation in a complex dynamic system (Dörnyei, 2009). Emotion "functions as an amplifier, providing the intensity, urgency, and energy to propel our behavior" in…

  12. How Language Learners Can Improve Their Emotional Functioning: Important Psychological and Psychospiritual Theories

    Science.gov (United States)

    Oxford, Rebecca L.

    2015-01-01

    Emotion is "the primary human motive" (MacIntyre, 2002, p. 61). The human brain is an emotional brain, creating relationships among thought, emotion, and motivation in a complex dynamic system (Dörnyei, 2009). Emotion "functions as an amplifier, providing the intensity, urgency, and energy to propel our behavior" in…

  13. IMPORTANCE OF ACTIVATED CARBON'S OXYGEN SURFACE FUNCTIONAL GROUPS ON ELEMENTAL MERCURY ADSORPTION

    Science.gov (United States)

    The effect of varying physical and chemical properties of activated carbons on adsorption of elemental mercury [Hg(0)] was studied by treating two activated carbons to modify their surface functional groups and pore structures. Heat treatment (1200 K) in nitrogen (N2), air oxidat...

  14. Self-Monitoring Interventions for At-Risk Middle School Students: The Importance of Considering Function

    Science.gov (United States)

    Briere, Donald E., III; Simonsen, Brandi

    2011-01-01

    Self-monitoring is a popular, efficient, and effective intervention that is associated with improved academic and social behavior for students across age and ability levels. To date, this is the first study to directly compare the outcomes of self-monitoring functionally relevant and non-relevant replacement behaviors. Specifically, we used an…

  15. Small molecule functional analogs of peptides that inhibit lambda site-specific recombination and bind Holliday junctions.

    Science.gov (United States)

    Ranjit, Dev K; Rideout, Marc C; Nefzi, Adel; Ostresh, John M; Pinilla, Clemencia; Segall, Anca M

    2010-08-01

    Our lab has isolated hexameric peptides that are structure-selective ligands of Holliday junctions (HJ), central intermediates of several DNA recombination reactions. One of the most potent of these inhibitors, WRWYCR, has shown antibacterial activity in part due to its inhibition of DNA repair proteins. To increase the therapeutic potential of these inhibitors, we searched for small molecule inhibitors with similar activities. We screened 11 small molecule libraries comprising over nine million individual compounds and identified a potent N-methyl aminocyclic thiourea inhibitor that also traps HJs formed during site-specific recombination reactions in vitro. This inhibitor binds specifically to protein-free HJs and can inhibit HJ resolution by RecG helicase, but only showed modest growth inhibition of bacterial with a hyperpermeable outer membrane; nonetheless, this is an important step in developing a functional analog of the peptide inhibitors. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. A comprehensive software suite for protein family construction and functional site prediction

    Science.gov (United States)

    Haft, David Renfrew; Haft, Daniel H.

    2017-01-01

    In functionally diverse protein families, conservation in short signature regions may outperform full-length sequence comparisons for identifying proteins that belong to a subgroup within which one specific aspect of their function is conserved. The SIMBAL workflow (Sites Inferred by Metabolic Background Assertion Labeling) is a data-mining procedure for finding such signature regions. It begins by using clues from genomic context, such as co-occurrence or conserved gene neighborhoods, to build a useful training set from a large number of uncharacterized but mutually homologous proteins. When training set construction is successful, the YES partition is enriched in proteins that share function with the user’s query sequence, while the NO partition is depleted. A selected query sequence is then mined for short signature regions whose closest matches overwhelmingly favor proteins from the YES partition. High-scoring signature regions typically contain key residues critical to functional specificity, so proteins with the highest sequence similarity across these regions tend to share the same function. The SIMBAL algorithm was described previously, but significant manual effort, expertise, and a supporting software infrastructure were required to prepare the requisite training sets. Here, we describe a new, distributable software suite that speeds up and simplifies the process for using SIMBAL, most notably by providing tools that automate training set construction. These tools have broad utility for comparative genomics, allowing for flexible collection of proteins or protein domains based on genomic context as well as homology, a capability that can greatly assist in protein family construction. Armed with this new software suite, SIMBAL can serve as a fast and powerful in silico alternative to direct experimentation for characterizing proteins and their functional interactions. PMID:28182651

  17. New functions of the chloroplast Preprotein and Amino acid Transporter (PRAT) family members in protein import.

    Science.gov (United States)

    Rossig, Claudia; Reinbothe, Christiane; Gray, John; Valdes, Oscar; von Wettstein, Diter; Reinbothe, Steffen

    2014-01-01

    Plant cells contain distinct compartments such as the nucleus, the endomembrane system comprising the endoplasmic reticulum and Golgi apparatus, peroxisomes, vacuoles, as well as mitochondria and chloroplasts. All of these compartments are surrounded by 1 or 2 limiting membranes and need to import proteins from the cytosol. Previous work led to the conclusion that mitochondria and chloroplasts use structurally different protein import machineries in their outer and inner membranes for the uptake of cytosolic precursor proteins. Our most recent data show that there is some unexpected overlap. Three members of the family of preprotein and amino acid transporters, PRAT, were identified in chloroplasts that mediate the uptake of transit sequence-less proteins into the inner plastid envelope membrane. By analogy, mitochondria contain with TIM22 a related PRAT protein that is involved in the import of transit sequence-less proteins into the inner mitochondrial membrane. Both mitochondria and chloroplasts thus make use of similar import mechanisms to deliver some of their proteins to their final place. Because single homologs of HP20- and HP30-like proteins are present in algae such as Chlamydomonas, Ostreococcus, and Volvox, which diverged from land plants approximately 1 billion years ago, it is likely that the discovered PRAT-mediated mechanism of protein translocation evolved concomitantly with the secondary endosymbiotic event that gave rise to green plants.

  18. Heterologous expression of a membrane-spanning auxin importer: implications for functional analyses of auxin transporters.

    Science.gov (United States)

    Carrier, David John; Abu Bakar, Norliza Tendot; Lawler, Karen; Dorrian, James Matthew; Haider, Ameena; Bennett, Malcolm John; Kerr, Ian Derek

    2009-01-01

    Biochemical studies of plant auxin transporters in vivo are made difficult by the presence of multiple auxin transporters and auxin-interacting proteins. Furthermore, the expression level of most such transporters in plants is likely to be too low for purification and downstream functional analysis. Heterologous expression systems should address both of these issues. We have examined a number of such systems for their efficiency in expressing AUX1 from Arabidopsis thaliana. We find that a eukaryotic system based upon infection of insect cells with recombinant baculovirus provides a high level, easily scalable expression system capable of delivering a functional assay for AUX1. Furthermore, a transient transfection system in mammalian cells enables localization of AUX1 and AUX1-mediated transport of auxin to be investigated. In contrast, we were unable to utilise P. pastoris or L. lactis expression systems to reliably express AUX1.

  19. Importance of N-Glycosylation on CD147 for Its Biological Functions

    Directory of Open Access Journals (Sweden)

    Yang Bai

    2014-04-01

    Full Text Available Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

  20. Emotion perception and functional outcome in schizophrenia: the importance of negative valence and fear.

    Science.gov (United States)

    Brittain, Philip J; Ffytche, Dominic H; Surguladze, Simon A

    2012-12-30

    A substantial body of work has demonstrated that persons with schizophrenia have a deficit in the perception of emotional stimuli. More recently this deficit has been linked to poor functional outcomes (FO) in this group. The current research investigated the perception of emotional stimuli in a group of 64 schizophrenia patients and 65 matched healthy controls. In the patient group, across two different emotion perception tasks and a social perception task, small deficits were found in the perception of negative, positive and neutrally valenced stimuli. Only the ability to perceive negative and neutrally valenced stimuli significantly correlated with a set of FO measures in the patients, with one task indicating these associations were strongest for the perception of fear. Subsequent regression modelling, controlling for the effects of symptomatology, demonstrated that for each of the three tasks, the measure of negative valence perception accounted for a similar but small amount (4%) of the variance seen in the functional status of the patients.

  1. Importance of N-glycosylation on CD147 for its biological functions.

    Science.gov (United States)

    Bai, Yang; Huang, Wan; Ma, Li-Tian; Jiang, Jian-Li; Chen, Zhi-Nan

    2014-04-15

    Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

  2. Cherubism Gene Sh3bp2 is Important for Optimal Bone Formation, Osteoblast Differentiation and Function

    Science.gov (United States)

    Mukherjee, Padma M.; Wang, Chiachien J.; Chen, I-Ping; Jafarov, Toghrul; Olsen, Bjorn R.; Ueki, Yasuyoshi; Reichenberger, Ernst J.

    2012-01-01

    Introduction Cherubism is a human genetic disorder that causes bilateral symmetrical enlargement of the maxilla and mandible in children. It is caused by mutations in SH3BP2. The exact pathogenesis of the disorder is an area of active research. Sh3bp2 knock-in mice were developed by introducing a Pro416Arg mutation (Pro418Arg in humans) in the mouse genome. The osteoclast phenotype of this mouse model was recently described. Methods We examined the bone phenotype of the cherubism mouse model, the role of Sh3bp2 during bone formation, osteoblast differentiation and osteoblast function. Results We observed delays in early postnatal development of homozygous Sh3bp2KI/KI mice. Sh3bp2KI/KI mice exhibit increased growth plate thickness and significantly decreased trabecular bone thickness and reduced bone mineral density. Histomorphometric and μ-CT analyses reveal bone loss in cranial and appendicular skeleton. Sh3bp2KI/KI mice also exhibit a significant decrease in osteoid formation that indicates a defect in osteoblast function. Calvarial osteoblast cell cultures exhibit a decrease in alkaline phosphatase expression and mineralization suggesting reduced differentiation potential. Gene expression of osteoblast differentiation markers like collagen type-I, alkaline phosphatase and osteocalcin are decreased in osteoblast cultures from Sh3bp2KI/KI mice. Conclusions These data suggest that Sh3bp2 function regulates bone homeostasis not only through osteoclast-specific effects but also through effects on osteoblast differentiation and function. PMID:20691350

  3. Hippocampal volumes are important predictors for memory function in elderly women

    Directory of Open Access Journals (Sweden)

    Adolfsdottir Steinunn

    2009-08-01

    Full Text Available Abstract Background Normal aging involves a decline in cognitive function that has been shown to correlate with volumetric change in the hippocampus, and with genetic variability in the APOE-gene. In the present study we utilize 3D MR imaging, genetic analysis and assessment of verbal memory function to investigate relationships between these factors in a sample of 170 healthy volunteers (age range 46–77 years. Methods Brain morphometric analysis was performed with the automated segmentation work-flow implemented in FreeSurfer. Genetic analysis of the APOE genotype was determined with polymerase chain reaction (PCR on DNA from whole-blood. All individuals were subjected to extensive neuropsychological testing, including the California Verbal Learning Test-II (CVLT. To obtain robust and easily interpretable relationships between explanatory variables and verbal memory function we applied the recent method of conditional inference trees in addition to scatterplot matrices and simple pairwise linear least-squares regression analysis. Results APOE genotype had no significant impact on the CVLT results (scores on long delay free recall, CVLT-LD or the ICV-normalized hippocampal volumes. Hippocampal volumes were found to decrease with age and a right-larger-than-left hippocampal asymmetry was also found. These findings are in accordance with previous studies. CVLT-LD score was shown to correlate with hippocampal volume. Multivariate conditional inference analysis showed that gender and left hippocampal volume largely dominated predictive values for CVLT-LD scores in our sample. Left hippocampal volume dominated predictive values for females but not for males. APOE genotype did not alter the model significantly, and age was only partly influencing the results. Conclusion Gender and left hippocampal volumes are main predictors for verbal memory function in normal aging. APOE genotype did not affect the results in any part of our analysis.

  4. Importance of Being Nernst: Synaptic Activity and Functional Relevance in Stem Cell-derived Neurons

    Science.gov (United States)

    2015-07-26

    derived from totipotent cells collected from the inner cell mass of embryos at the blastocyst stage[115]. Mouse ESC are frequently differentiated to...neurons derived from fetal NSCs have also found that long- term integration and transplanted neurons conferred resistance to PD in mouse models[208... Transplantation increases regeneration and functional recovery after ischemic stroke in neonatal rats. Stem Cells 2014; 32: 3075-3087 [PMID: 25132189 DOI

  5. IMPORTANCE OF ILIOPSOAS AND ERECTOR SPINAE MUSCLES IN PREDICTING THE FUNCTIONAL COMPETENCE OF TRANSFEMORAL AMPUTEES

    Directory of Open Access Journals (Sweden)

    Lajja K Rishi

    2014-10-01

    Full Text Available Purpose: Muscle imbalance in transfemoral amputees impair physical mobility and activities of daily living. Aim of this study was to correlate the muscle imbalance with functional competence in transfemoral amputees. Methods: Thirty amputees were evaluated under inclusion criteria and randomly allocated into 2 groups. Group A received stretching(1 week followed by strengthening(3 weeks and in group B strengthening(3 weeks were followed by stretching(1 week . Phase I includes values after 1 week stretching program in group A and 3 weeks strengthening program in group B. Data were recorded at baseline, after phase I completion and end of treatment. Physical mobility was assessed by “Timed up and go” test. Results: Muscle imbalance and physical mobility improved significantly in both groups at the end of treatment. The correlation values of “Timed up and go” test with Iliopsoas and Erector spinae muscle showed significant improvement in both groups. Conclusion: Baseline measurements showed that Iliopsoas and Erector spinae muscles were tight whereas Gluteus maximus and Abdominal muscles were weak in transfemoral amputees. Functional mobility improved after correction of muscle imbalance. Stretching followed by strengthening gave more significant results than vice versa. Good posture in transfemoral amputee prevents muscle dysfunction and improves functional mobility.

  6. [Obesity in old age and its importance for functionality and frailty].

    Science.gov (United States)

    Wojzischke, Julia; Diekmann, Rebecca; Bauer, Jürgen M

    2016-10-01

    In later life a high body mass index (BMI) is associated with the lowest age-related mortality rate. The BMI range used by the World Health Organization (WHO) to classify overweight, a BMI of 25-30 kg/m(2), can be regarded as normal weight in old age; nevertheless, obesity is associated with an increased risk of disability and of a deterioration in physical functionality, particularly among older age groups. This relationship to obesity has also been established for frailty. For this reason, a reduction in weight may be appropriate under functional aspects if BMI values exceed 30 kg/m(2); however, such a decision cannot be made on the basis of an individual BMI alone. The functional status, body composition, comorbidities and, in particular the life perspectives of the patient should also be taken into consideration. If weight loss is intended, it must always be performed under strict medical supervision involving optimized protein intake, a carefully calculated moderate reduction in calories and adequate physical training. In the case of chronically ill elderly patients, weight reduction is not usually appropriate. Restrictive diets of any kind should principally be critically viewed in old age because even temporary inadequate energy intake may lead to accelerated deterioration of muscle and bone structure.

  7. Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

    Science.gov (United States)

    Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

    2013-12-15

    The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.

  8. On the function and importance of research design in existential-phenomenological qualitative research

    DEFF Research Database (Denmark)

    Feilberg, Casper

    inquiry. This is very different from the research traditions within the social sciences, which traditionally emphasizes the importance of research design and a controlled inquiry, even with respect to qualitative research. Social research is traditionally divided into three phases: planning, execution...... and reporting. Both De Vaus (2001, Research Design in Social Research) and Blaikie (2009, Designing Social Research) highlight the preparatory phase stressing the importance of designing an inquiry in a way, that brings empirical material forth that makes it possible to answer the research question...... the argument that there would be a fruitful contribution to much phenomenological research from a greater emphasis on research design and controlled inquiry. But is it possible to combine these social science research principles with a phenomenological and hermeneutical approach to qualitative research...

  9. The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

    Science.gov (United States)

    Webb, Matthew H; Terauds, Aleks; Tulloch, Ayesha; Bell, Phil; Stojanovic, Dejan; Heinsohn, Robert

    2017-10-01

    The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence-background (i.e., presence-only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine-resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine-resolution data). The occupancy models produced significantly (P < 0.001) smaller (up to an order of magnitude) and more spatially discrete estimates of the total occupied area than climate-based models. The spatial location and extent of the total area occupied with the occupancy models was highly variable between years (131 and 1498 km(2) ). Estimates accounting for the area of functional habitats were significantly smaller (2-58% [SD 16]) than estimates based only on the total area occupied. An increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the

  10. Overuse wrist injuries in young athletes: What do sports physicians consider important signals and functional limitations?

    Science.gov (United States)

    Kox, Laura S; Kuijer, P Paul F M; Opperman, Jip; Kerkhoffs, Gino M M J; Maas, Mario; Frings-Dresen, Monique H W

    2017-02-21

    This study's objective was to collect items from experienced sports physicians, relating to the presence and severity of overuse wrist injuries in young athletes, for developing a measurement instrument for signals of overuse wrist injury. Seven Dutch elite sports physicians involved in guidance and treatment of young athletes in wrist-loading sports (gymnastics, tennis, judo, field hockey, volleyball and rowing) participated in a focus group. They discussed signals and limitations related to overuse wrist injuries in young athletes. Data were coded and categorised into signals and limitations with subcategories, using an inductive approach. Of the resulting 61 signals and limitations in nineteen (sub)categories, 20 were considered important, forming a comprehensive item set for identifying overuse wrist injury in young athletes. Signals such as pain, "click", crepitations, swelling and limited range of motion were marked useful for early identification of overuse wrist injury. Limitations in movement and performance were considered indicative of severe overuse injury but less relevant for initial injury identification. The focus group provided 17 important signals and 3 important limitations indicative of overuse wrist injury. These provide the basis for a valid measurement instrument for identifying overuse wrist injury in young athletes, with equal emphasis on pain and on other symptoms.

  11. Schistosome elastases: biological importance, structure, function and stage-specific expression.

    Science.gov (United States)

    Newport, G; McKerrow, J; Hedstrom, R; Culpepper, J; McGarrigle, L; Agabian, N

    1987-01-01

    Larval schistosomes (Digenea: Trematoda) invade their definitive host by directly penetrating the skin. During the process they secrete a number of macromolecules, ostensibly to facilitate their entry. Among these we have identified and characterized a dominant proteolytic species: a serine protease capable of fragmenting keratin, types IV and VIII collagen, proteoglycan, fibronectin, laminin, and elastin. The enzyme exhibits the specificity characteristic of elastases, has a molecular mass of 30,000 Da and pI of 7.8, and is potently immunogenic in its native form. Specificity of the active site has been analysed, tetrapeptides having large hydrophobic or aromatic amino acids at size P1 serving as best substrates. The amino terminal 20 amino acids of the mature enzyme have been sequenced and the information derived has been used to construct an oligonucleotide (22-mer) complement of its corresponding mRNA. The latter has been used to establish, by Northern analysis, that expression of the enzyme is stage specific (differing in this respect from most schistosome immunogens), and under transcriptional control. Transcripts are encoded by a multigene family. Several cDNAs hybridizing to the oligonucleotide have been isolated, subcloned into bacteriophage M-13, and sequenced by the di-deoxy method. It is our expectation that this line of investigation will lead towards: (i) an anti-infection vaccine; (ii) a means for chemically preventing infection (using enzyme inhibitors), and/or (iii) a rapid diagnostic assay of prepatent infection.

  12. The importance of rare species: a trait-based assessment of rare species contributions to functional diversity and possible ecosystem function in tall-grass prairies.

    Science.gov (United States)

    Jain, Meha; Flynn, Dan Fb; Prager, Case M; Hart, Georgia M; Devan, Caroline M; Ahrestani, Farshid S; Palmer, Matthew I; Bunker, Daniel E; Knops, Johannes Mh; Jouseau, Claire F; Naeem, Shahid

    2014-01-01

    The majority of species in ecosystems are rare, but the ecosystem consequences of losing rare species are poorly known. To understand how rare species may influence ecosystem functioning, this study quantifies the contribution of species based on their relative level of rarity to community functional diversity using a trait-based approach. Given that rarity can be defined in several different ways, we use four different definitions of rarity: abundance (mean and maximum), geographic range, and habitat specificity. We find that rarer species contribute to functional diversity when rarity is defined by maximum abundance, geographic range, and habitat specificity. However, rarer species are functionally redundant when rarity is defined by mean abundance. Furthermore, when using abundance-weighted analyses, we find that rare species typically contribute significantly less to functional diversity than common species due to their low abundances. These results suggest that rare species have the potential to play an important role in ecosystem functioning, either by offering novel contributions to functional diversity or via functional redundancy depending on how rare species are defined. Yet, these contributions are likely to be greatest if the abundance of rare species increases due to environmental change. We argue that given the paucity of data on rare species, understanding the contribution of rare species to community functional diversity is an important first step to understanding the potential role of rare species in ecosystem functioning.

  13. N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Reveals an Intronic Residue Critical for Caenorhabditis elegans 3′ Splice Site Function in Vivo

    Science.gov (United States)

    Itani, Omar A.; Flibotte, Stephane; Dumas, Kathleen J.; Guo, Chunfang; Blumenthal, Thomas; Hu, Patrick J.

    2016-01-01

    Metazoan introns contain a polypyrimidine tract immediately upstream of the AG dinucleotide that defines the 3′ splice site. In the nematode Caenorhabditis elegans, 3′ splice sites are characterized by a highly conserved UUUUCAG/R octamer motif. While the conservation of pyrimidines in this motif is strongly suggestive of their importance in pre-mRNA splicing, in vivo evidence in support of this is lacking. In an N-ethyl-N-nitrosourea (ENU) mutagenesis screen in Caenorhabditis elegans, we have isolated a strain containing a point mutation in the octamer motif of a 3′ splice site in the daf-12 gene. This mutation, a single base T-to-G transversion at the -5 position relative to the splice site, causes a strong daf-12 loss-of-function phenotype by abrogating splicing. The resulting transcript is predicted to encode a truncated DAF-12 protein generated by translation into the retained intron, which contains an in-frame stop codon. Other than the perfectly conserved AG dinucleotide at the site of splicing, G at the –5 position of the octamer motif is the most uncommon base in C. elegans 3′ splice sites, occurring at closely paired sites where the better match to the splicing consensus is a few bases downstream. Our results highlight both the biological importance of the highly conserved –5 uridine residue in the C. elegans 3′ splice site octamer motif as well as the utility of using ENU as a mutagen to study the function of polypyrimidine tracts and other AU- or AT-rich motifs in vivo. PMID:27172199

  14. Importance of Highly Conserved Peptide Sites of Human Cytomegalovirus gO for Formation of the gH/gL/gO Complex.

    Science.gov (United States)

    Stegmann, Cora; Abdellatif, Mohamed E A; Laib Sampaio, Kerstin; Walther, Paul; Sinzger, Christian

    2017-01-01

    The glycoprotein O (gO) is betaherpesvirus specific. Together with the viral glycoproteins H and L, gO forms a covalent trimeric complex that is part of the viral envelope. This trimer is crucial for cell-free infectivity of human cytomegalovirus (HCMV) but dispensable for cell-associated spread. We hypothesized that the amino acids that are conserved among gOs of different cytomegaloviruses are important for the formation of the trimeric complex and hence for efficient virus spread. In a mutational approach, nine peptide sites, containing all 13 highly conserved amino acids, were analyzed in the context of HCMV strain TB40-BAC4 with regard to infection efficiency and formation of the gH/gL/gO complex. Mutation of amino acids (aa) 181 to 186 or aa 193 to 198 resulted in the loss of the trimer and a complete small-plaque phenotype, whereas mutation of aa 108 or aa 249 to 254 caused an intermediate phenotype. While individual mutations of the five conserved cysteines had little impact, their relevance was revealed in a combined mutation, which abrogated both complex formation and cell-free infectivity. C343 was unique, as it was sufficient and necessary for covalent binding of gO to gH/gL. Remarkably, however, C218 together with C167 rescued infectivity in the absence of detectable covalent complex formation. We conclude that all highly conserved amino acids contribute to the function of gO to some extent but that aa 181 to 198 and cysteines 343, 218, and 167 are particularly relevant. Surprisingly, covalent binding of gO to gH/gL is required neither for its incorporation into virions nor for proper function in cell-free infection. Like all herpesviruses, the widespread human pathogen HCMV depends on glycoproteins gB, gH, and gL for entry into target cells. Additionally, gH and gL have to bind gO in a trimeric complex for efficient cell-free infection. Homologs of gO are shared by all cytomegaloviruses, with 13 amino acids being highly conserved. In a mutational

  15. Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics

    Directory of Open Access Journals (Sweden)

    Antonio Rosato

    2016-05-01

    Full Text Available Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands. The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS. MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB. They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity.

  16. Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics

    Science.gov (United States)

    Rosato, Antonio; Valasatava, Yana; Andreini, Claudia

    2016-01-01

    Metal ions play a functional role in numerous biochemical processes and cellular pathways. Indeed, about 40% of all enzymes of known 3D structure require a metal ion to be able to perform catalysis. The interactions of the metals with the macromolecular framework determine their chemical properties and reactivity. The relevant interactions involve both the coordination sphere of the metal ion and the more distant interactions of the so-called second sphere, i.e., the non-bonded interactions between the macromolecule and the residues coordinating the metal (metal ligands). The metal ligands and the residues in their close spatial proximity define what we call a minimal functional site (MFS). MFSs can be automatically extracted from the 3D structures of metal-binding biological macromolecules deposited in the Protein Data Bank (PDB). They are 3D templates that describe the local environment around a metal ion or metal cofactor and do not depend on the overall macromolecular structure. MFSs provide a different view on metal-binding proteins and nucleic acids, completely focused on the metal. Here we present different protocols and tools based upon the concept of MFS to obtain deeper insight into the structural and functional properties of metal-binding macromolecules. We also show that structure conservation of MFSs in metalloproteins relates to local sequence similarity more strongly than to overall protein similarity. PMID:27153067

  17. The importance of the on-site electron-electron interaction for the magnetic coupling in the zigzag spin-chain compound In2VO5

    KAUST Repository

    Wang, Hao

    2010-09-27

    We present first-principles electronic structure calculations for the zigzag spin-chain compound In2VO5 using the generalized gradient approximation both with and without inclusion of an on-site Coulomb interaction. It has been proposed that In2VO5 is characterized by itinerant V 3d electrons at high temperature and localized electrons at low temperature. Consequently, it is to be expected that electronic correlations play an important role for the magnetic transition from ferromagnetic to antiferromagnetic exchange around 120 K. In this context, we study the electronic and magnetic properties of a set of possible spin configurations. Our calculations show that inclusion of an on-site Coulomb interaction in fact changes the ground state from ferromagnetic to antiferromagnetic. © 2010 IOP Publishing Ltd.

  18. Importance of orthodontic movement in interdisciplinary treatment for restoring esthetics and functional occlusion

    Directory of Open Access Journals (Sweden)

    Carlos Henrique Guimarães

    2015-01-01

    Full Text Available This article describes interdisciplinary treatment conducted in adult patients, 49-year-old, with periodontal problems, losses and dental inclination, occlusal trauma, localized bone loss, and necessity of rehabilitation with dental implants. Alignment and leveling of the teeth, the molars uprighting with cantilever, and space closure were performed the treatment was facilitated by periodic periodontal control. The resultant occlusion was stable throughout a 5-year retention period. In conclusion, interdisciplinary treatment combined with periodontics, orthodontics, implantodontist, and restorative dentistry was useful for improving the patient′s oral health, function, and esthetics.

  19. TECHNOLOGICAL AND FUNCTIONAL PROPERTIES OF LACTIC ACID BACTERIA: THE IMPORTANCE OF THESE MICROORGANISMS FOR FOOD

    Directory of Open Access Journals (Sweden)

    Amanda de Souza Motta

    2015-12-01

    Full Text Available Eacters of coccus or rods Gram-positive, catalase negative, non-sporulating, which produce lactic acid as the major end product during the fermentation of carbohydrates. When applied on food, provides beneficial effects to consumers through its functional and technological properties. With this the present review article, explore the potential application of lactic acid bacteria in food. The following genera are considered the principal lactic acid bacteria: Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Oenococcus, Pediococcus, Streptococcus, Tetragenococcus, Vagococcus and Weissella. These cultures have been used as starter or adjunct cultures for the fermentation of foods and beverages due to their contributions to the sensorial characteristics of these products and by microbiological stability. Their probiotic properties have also been investigated. More recent studies by indigenous cultures have received increased attention in light of the search for isolated cultures of a given raw material and a certain region. These microorganisms are being investigated for its functional and technological potential that may be applied in product development with its own characteristics and designation of origin. Those properties will be discussed in the present review in order to highlight the performance of these bacteria and the high degree of control over the fermentation process and standardization of the final product. The use of autochthonous cultures will be considered due the increase of studies of new cultures of lactic acid bacteria isolated of milk and meat of distinct products.

  20. Importance of oestrogen receptors to preserve functional β-cell mass in diabetes.

    Science.gov (United States)

    Tiano, Joseph P; Mauvais-Jarvis, Franck

    2012-02-14

    Protecting the functional mass of insulin-producing β cells of the pancreas is a major therapeutic challenge in patients with type 1 (T1DM) or type 2 diabetes mellitus (T2DM). The gonadal hormone 17β-oestradiol (E2) is involved in reproductive, bone, cardiovascular and neuronal physiology. In rodent models of T1DM and T2DM, treatment with E2 protects pancreatic β cells against oxidative stress, amyloid polypeptide toxicity, lipotoxicity and apoptosis. Three oestrogen receptors (ERs)--ERα, ERβ and the G protein-coupled ER (GPER)--have been identified in rodent and human β cells. Whereas activation of ERα enhances glucose-stimulated insulin biosynthesis, reduces islet toxic lipid accumulation and promotes β-cell survival from proapoptotic stimuli, activation of ERβ increases glucose-stimulated insulin secretion. However, activation of GPER protects β cells from apoptosis, raises glucose-stimulated insulin secretion and lipid homeostasis without affecting insulin biosynthesis. Oestrogens are also improving islet engraftment in rodent models of pancreatic islet transplantation. This Review describes developments in the role of ERs in islet insulin biosynthesis and secretion, lipid homeostasis and survival. Moreover, we discuss why and how enhancing ER action in β cells without the undesirable effect of general oestrogen therapy is a therapeutic avenue to preserve functional β-cell mass in patients with diabetes mellitus.

  1. A function of DivIVA in Listeria monocytogenes division site selection.

    Science.gov (United States)

    Kaval, Karan Gautam; Rismondo, Jeanine; Halbedel, Sven

    2014-11-01

    The cell division protein DivIVA influences protein transport via the accessory SecA2 secretion route in Listeria monocytogenes. In contrast, DivIVA from the closely related bacterium Bacillus subtilis contributes to division site selection via the MinCDJ system. However, no classical min phenotype, i.e. filamentation and minicell production was observed with a listerial ΔdivIVA mutant. This has prompted the speculation that division site selection is DivIVA-independent in L. monocytogenes. We addressed this question with genetic, cytological and bacterial two-hybrid experiments and the data obtained correct this view. DivIVA not only binds to MinJ but also directly interacts with MinD. Experiments with fluorescently tagged proteins showed that localization of MinC and MinD was clearly DivIVA-dependent, whereas localization of MinJ was not. An impact of DivIVA on cell division was confirmed by careful comparisons of cell size distributions of divIVA and secA2 mutants. Gene deletion studies and epistasis experiments consistently reinforced these findings, and also revealed that MinJ must have a DivIVA-independent function. The frequency of minicell formation is low in L. monocytogenes min mutants. However, since listerial minicells might be useful as carriers for the introduction of therapeutic compounds into eukaryotic cells, we present a strategy how minicell frequency can be increased.

  2. An Insertion Mutation That Distorts Antibody Binding Site Architecture Enhances Function of a Human Antibody

    Energy Technology Data Exchange (ETDEWEB)

    Krause, Jens C.; Ekiert, Damian C.; Tumpey, Terrence M.; Smith, Patricia B.; Wilson, Ian A.; Crowe, Jr., James E. (Vanderbilt); (Scripps); (CDC)

    2011-09-02

    The structural and functional significance of somatic insertions and deletions in antibody chains is unclear. Here, we demonstrate that a naturally occurring three-amino-acid insertion within the influenza virus-specific human monoclonal antibody 2D1 heavy-chain variable region reconfigures the antibody-combining site and contributes to its high potency against the 1918 and 2009 pandemic H1N1 influenza viruses. The insertion arose through a series of events, including a somatic point mutation in a predicted hot-spot motif, introduction of a new hot-spot motif, a molecular duplication due to polymerase slippage, a deletion due to misalignment, and additional somatic point mutations. Atomic resolution structures of the wild-type antibody and a variant in which the insertion was removed revealed that the three-amino-acid insertion near the base of heavy-chain complementarity-determining region (CDR) H2 resulted in a bulge in that loop. This enlarged CDR H2 loop impinges on adjacent regions, causing distortion of the CDR H1 architecture and its displacement away from the antigen-combining site. Removal of the insertion restores the canonical structure of CDR H1 and CDR H2, but binding, neutralization activity, and in vivo activity were reduced markedly because of steric conflict of CDR H1 with the hemagglutinin antigen.

  3. "Importin" signaling roles for import proteins: the function of Drosophila importin-7 (DIM-7) in muscle-tendon signaling.

    Science.gov (United States)

    Liu, Ze Cindy; Geisbrecht, Erika R

    2012-01-01

    The formation of a mature myotendinous junction (MTJ) between a muscle and its site of attachment is a highly regulated process that involves myofiber migration, cell-cell signaling, and culminates with the stable adhesion between the adjacent muscle-tendon cells. Improper establishment or maintenance of muscle-tendon attachment sites results in a decrease in force generation during muscle contraction and progressive muscular dystrophies in vertebrate models. Many studies have demonstrated the important role of the integrins and integrin-associated proteins in the formation and maintenance of the MTJ. We recently demonstrated that moleskin (msk), the gene that encodes for Drosophila importin-7 (DIM-7), is required for the proper formation of muscle-tendon adhesion sites in the developing embryo. Further studies demonstrated an enrichment of DIM-7 to the ends of muscles where the muscles attach to their target tendon cells. Genetic analysis supports a model whereby msk is required in the muscle and signals via the secreted epidermal growth factor receptor (Egfr) ligand Vein to regulate tendon cell maturation. These data demonstrate a novel role for the canonical nuclear import protein DIM-7 in establishment of the MTJ.

  4. Site-specific functionalization of anisotropic nanoparticles: from colloidal atoms to colloidal molecules

    DEFF Research Database (Denmark)

    Li, Fan; Yoo, Won Cheol; Beernink, Molly B

    2009-01-01

    Multipodal nanoparticles (NPs) with controlled tethers are promising principal building blocks, useful for constructing more complex materials, much like atoms are connected into more complex molecules. Here we report colloidal sphere templating as a viable means to create tetrapodal NPs with site......-specific tethers. Amorphous sol-gel materials were molded by the template into shaped NPs that mimic tetravalent atoms but on the length scale of colloids. Synthetic methods were developed to modify only the tips of the tetrapods with a range of possible functional groups to generate anisotropic NPs capable...... of directional bonding to other NPs. We also illustrate that sets of tethered "colloidal atoms" can assemble themselves into "colloidal molecules" with precise placement of the modifying colloids. The templating and tethering approaches to these anisotropic colloidal building blocks and the assembly methods...

  5. On the binding mode of urease active site inhibitors: A density functional study

    Science.gov (United States)

    Leopoldini, M.; Marino, T.; Russo, N.; Toscano, M.

    The way with which boric acid, a rapid reversible competitive inhibitor, binds the urease active site was explored at density functional B3LYP level of theory. The catalytic core of the enzyme was simulated by two models of different size. In both cases, amino acid residues belonging to the inner and to the outer coordination spheres of nickel ions were replaced by smaller molecular species. Contrary to the experimental indication that attributes the inhibitory ability of this acid to the lack of a nucleophilic attack by the enzyme to the boron atom, we instead found that another possibility exists based on the presence of a strong covalent sigma bond between boron and urease that we think can be hardly broken to allow any course of the reaction.

  6. Delineation of Polypharmacology across the Human Structural Kinome Using a Functional Site Interaction Fingerprint Approach.

    Science.gov (United States)

    Zhao, Zheng; Xie, Li; Xie, Lei; Bourne, Philip E

    2016-05-12

    Targeted polypharmacology of kinases has emerged as a promising strategy to design efficient and safe therapeutics. Here, we perform a systematic study of kinase-ligand binding modes for the human structural kinome at scale (208 kinases, 1777 unique ligands, and their complexes) by integrating chemical genomics and structural genomics data and by introducing a functional site interaction fingerprint (Fs-IFP) method. New insights into kinase-ligand binding modes were obtained. We establish relationships between the features of binding modes, the ligands, and the binding pockets, respectively. We also drive the intrinsic binding specificity and which correlation with amino acid conservation. Third, we explore the landscape of the binding modes and highlight the regions of "selectivity pocket" and "selectivity entrance". Finally, we demonstrate that Fs-IFP similarity is directly correlated to the experimentally determined profile. These improve our understanding of kinase-ligand interactions and contribute to the design of novel polypharmacological therapies targeting kinases.

  7. Improving the functional expression of a Bacillus licheniformis laccase by random and site-directed mutagenesis

    Directory of Open Access Journals (Sweden)

    Schmid Rolf D

    2009-02-01

    Full Text Available Abstract Background Laccases have huge potential for biotechnological applications due to their broad substrate spectrum and wide range of reactions they are able to catalyze. These include, for example, the formation and degradation of dimers, oligomers, polymers, and ring cleavage as well as oxidation of aromatic compounds. Potential applications of laccases include detoxification of industrial effluents, decolorization of textile dyes and the synthesis of natural products by, for instance, dimerization of phenolic acids. We have recently published a report on the cloning and characterization of a CotA Bacillus licheniformis laccase, an enzyme that catalyzes dimerization of phenolic acids. However, the broad application of this laccase is limited by its low expression level of 26 mg l-1 that was achieved in Escherichia coli. To counteract this shortcoming, random and site-directed mutagenesis have been combined in order to improve functional expression and activity of CotA. Results A CotA double mutant, K316N/D500G, was constructed by combining random and site-directed mutagenesis. It can be functionally expressed at an 11.4-fold higher level than the wild-type enzyme. In addition, it is able to convert ferulic acid much faster than the wild-type enzyme (21% vs. 14% and is far more efficient in decolorizing a range of industrial dyes. The investigation of the effects of the mutations K316N and D500G showed that amino acid at position 316 had a major influence on enzyme activity and position 500 had a major influence on the expression of the laccase. Conclusion The constructed double mutant K316N/D500G of the Bacillus licheniformis CotA laccase is an appropriate candidate for biotechnological applications due to its high expression level and high activity in dimerization of phenolic acids and decolorization of industrial dyes.

  8. The Importance of REST for Development and Function of Beta Cells

    DEFF Research Database (Denmark)

    Martin, David; Grapin-Botton, Anne

    2017-01-01

    these, the transcriptional repressor RE-1 Silencing Transcription factor (REST) is expressed in most cells of the body, excluding most populations of neurons, as well as pancreatic beta and alpha cells. In the cell types where it is expressed, REST represses the expression of hundreds of genes...... that are crucial for both neuronal and pancreatic endocrine function, through the recruitment of multiple transcriptional and epigenetic co-regulators. REST targets include genes encoding transcription factors, proteins involved in exocytosis, synaptic transmission or ion channeling, and non-coding RNAs. REST...... is expressed in the progenitors of both neurons and beta cells during development, but it is down-regulated as the cells differentiate. Although REST mutations and deregulation have yet to be connected to diabetes in humans, REST activation during both development and in adult beta cells leads to diabetes...

  9. Recovery of important physiological functions in 3D culture of immortal hepatocytes

    DEFF Research Database (Denmark)

    Wrzesinski, Krzysztof; Fey, S. J.

    2011-01-01

    hepatocytes using the classical approaches (in “2D”) and using a system which leads to the generation of spheroids of cells held in suspension (“3D”). Both approaches gave rise to cultures where the large majority of cells were viable, produced similar amounts of ATP, incorporated similar amounts......It is widely expected that cells grown in 3D environments (in suspension, on scaffolds etc.) will be superior to growing cells in classical 2D culture flasks. These expectations include the belief that cells grown in 3D culture will possess physiological characteristics that resemble more closely...... to grow human liver cells in ‘3 dimensional’ cultures so that they behave very similar to the liver in our bodies. By growing the immortal hepatocytes in specially designed bioreactors they form small pieces of ‘pseudotissue’ which exhibit several of the functions seen in the adult liver. We have grown...

  10. The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world

    DEFF Research Database (Denmark)

    Griffiths, Jennifer R.; Kadin, Martina; Nascimento, Francisco J. A.

    2017-01-01

    and function is strongly affected by anthropogenic pressures, however there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling...... processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study, and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic......-pelagic coupling processes (e.g. nutrient exchange and sedimentation of organic material) are to some extent quantifiable but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects...

  11. Function and importance of p63 in normal oral mucosa and squamous cell carcinoma of the head and neck

    DEFF Research Database (Denmark)

    Thurfjell, Niklas; Coates, Philip J; Boldrup, Linda

    2005-01-01

    53, whilst others have functions that oppose p53. METHODS: To understand the function and importance of p63 in oral mucosa and tumour development we have studied protein as well as mRNA expression in normal oral mucosa and tumours. RESULTS/CONCLUSION: Expression of p63 proteins differs between...... and amplification of chromosome 3q21-29, where the p63 gene is located. This gene encodes 6 proteins and is crucial for formation of the oral mucosa, teeth, salivary glands and skin. Each of the 6 different p63 proteins has different characteristics and functions, where some resemble the tumour suppressor protein p...

  12. Function and importance of p63 in normal oral mucosa and squamous cell carcinoma of the head and neck

    DEFF Research Database (Denmark)

    Thurfjell, Niklas; Coates, Philip J; Boldrup, Linda

    2005-01-01

    and amplification of chromosome 3q21-29, where the p63 gene is located. This gene encodes 6 proteins and is crucial for formation of the oral mucosa, teeth, salivary glands and skin. Each of the 6 different p63 proteins has different characteristics and functions, where some resemble the tumour suppressor protein p......53, whilst others have functions that oppose p53. METHODS: To understand the function and importance of p63 in oral mucosa and tumour development we have studied protein as well as mRNA expression in normal oral mucosa and tumours. RESULTS/CONCLUSION: Expression of p63 proteins differs between...

  13. Expression and functional importance of collagen-binding integrins, alpha 1 beta 1 and alpha 2 beta 1, on virus-activated T cells

    DEFF Research Database (Denmark)

    Andreasen, Susanne Ø; Thomsen, Allan R; Koteliansky, Victor E

    2003-01-01

    Adhesive interactions are crucial to cell migration into inflammatory sites. Using murine lymphocytic choriomeningitis virus as an Ag model system, we have investigated expression and function of collagen-binding integrins, alpha(1)beta(1) and alpha(2)beta(1), on activated and memory T cells. Using...... this system and MHC tetramers to define Ag-specific T cells, we demonstrate that contrary to being VLAs, expression of alpha(1)beta(1) and alpha(2)beta(1) can be rapidly induced on acutely activated T cells, that expression of alpha(1)beta(1) remains elevated on memory T cells, and that expression of alpha(1...... decreased responses were seen upon transfer of alpha(1)-deficient activated/memory T cells. Thus, expression of alpha(1)beta(1) and alpha(2)beta(1) integrins on activated T cells is directly functionally important for generation of inflammatory responses within tissues. Finally, the inhibitory effect...

  14. Functional analysis of the BRI1 receptor kinase by Thr-for-Ser substitution in a regulatory autophosphorylation site

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    Man-Ho eOh

    2015-07-01

    Full Text Available BRI1 becomes highly phosphorylated in vivo upon perception of the ligand, brassinolide, as a result of autophosphorylation and transphosphorylation by its co-receptor kinase, BAK1. Important autophosphorylation sites include those involved in activation of kinase activity and those that are inhibitory, such as Ser-891. The inhibitory sites are autophosphorylated after kinase activation has been achieved and are postulated to contribute to deactivation of the kinase. The function of phosphosites is usually tested by substituting a non-phosphorylatable residue or an acidic residue that can act as a phosphomimetic. What has typically not been examined is substitution of a Thr for a Ser phosphosite (or vice versa but given that Thr and Ser are not equivalent amino acids this type of substitution may represent a new approach to engineer regulatory phosphorylation. In the present study with BRI1, we substituted Thr at the Ser-891 phosphosite to generate the S891T directed mutant. The recombinant Flag-BRI1 (S891T cytoplasmic domain protein (the S891T protein was catalytically active and phosphorylation occurred at the engineered Thr-891 site. However, the S891T recombinant protein autophosphorylated more slowly than the wild type protein during expression in E. coli. As a result, activation of peptide kinase activity (measured in vitro was delayed as was transphosphorylation of bacterial proteins in situ. Stable transgenic expression of BRI1 (S891T-Flag in Arabidopsis bri1-5 plants did not fully rescue the brassinosteroid (BR phenotype indicating that BR signaling was constrained. Our working model is that restricted signaling in the S891T plants occurs as a result of the reduced rate of activation of the mutant BRI1 kinase by autophosphorylation. These results provide the platform for future studies to critically test this new model in vivo and establish Ser-Thr substitutions at phosphosites as an interesting approach to consider with other protein

  15. RSC Chromatin-Remodeling Complex Is Important for Mitochondrial Function in Saccharomyces cerevisiae.

    Science.gov (United States)

    Imamura, Yuko; Yu, Feifei; Nakamura, Misaki; Chihara, Yuhki; Okane, Kyo; Sato, Masahiro; Kanai, Muneyoshi; Hamada, Ryoko; Ueno, Masaru; Yukawa, Masashi; Tsuchiya, Eiko

    2015-01-01

    RSC (Remodel the Structure of Chromatin) is an ATP-dependent chromatin remodeling complex essential for the growth of Saccharomyces cerevisiae. RSC exists as two distinct isoforms that share core subunits including the ATPase subunit Nps1/Sth1 but contain either Rsc1or Rsc2. Using the synthetic genetic array (SGA) of the non-essential null mutation method, we screened for mutations exhibiting synthetic growth defects in combination with the temperature-sensitive mutant, nps1-105, and found connections between mitochondrial function and RSC. rsc mutants, including rsc1Δ, rsc2Δ, and nps1-13, another temperature-sensitive nps1 mutant, exhibited defective respiratory growth; in addition, rsc2Δ and nps1-13 contained aggregated mitochondria. The rsc2Δ phenotypes were relieved by RSC1 overexpression, indicating that the isoforms play a redundant role in respiratory growth. Genome-wide expression analysis in nps1-13 under respiratory conditions suggested that RSC regulates the transcription of some target genes of the HAP complex, a transcriptional activator of respiratory gene expression. Nps1 physically interacted with Hap4, the transcriptional activator moiety of the HAP complex, and overexpression of HAP4 alleviated respiratory defects in nps1-13, suggesting that RSC plays pivotal roles in mitochondrial gene expression and shares a set of target genes with the HAP complex.

  16. The Importance of Saccular Function to Motor Development in Children with Hearing Impairments

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    Mary S. Shall

    2009-01-01

    Full Text Available Children with hearing deficits frequently have delayed motor development. The purpose of this study was to evaluate saccular function in children with hearing impairments using the Vestibular Evoked Myogenic Potential (VEMP. The impact of the saccular hypofunction on the timely maturation of normal balance strategies was examined using the Movement Assessment Battery for Children (Movement ABC. Thirty-three children with bilateral severe/profound hearing impairment between 4 and 7 years of age were recruited from a three-state area. Approximately half of the sample had one or bilateral cochlear implants, one used bilateral hearing aids, and the rest used no amplification. Parents reported whether the hearing impairment was diagnosed within the first year or after 2 years of age. No VEMP was evoked in two thirds of the hearing impaired (HI children in response to the bone-conducted stimulus. Children who were reportedly hearing impaired since birth had significantly poorer scores when tested with the Movement ABC.

  17. Graphene Oxide Catalyzed C-H Bond Activation: The Importance Oxygen Functional Groups for Biaryl Construction

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Yongjun; Tang, Pei; Zhou, Hu; Zhang, Wei; Yang, Hanjun; Yan, Ning; Hu, Gang; Mei, Donghai; Wang, Jianguo; Ma, Ding

    2016-02-24

    A heterogeneous, inexpensive and environment-friendly carbon catalytic system was developed for the C-H bond arylation of benzene resulting in the subsequent formation of biaryl compounds. The oxygen-containing groups on these graphene oxide sheets play an essential role in the observed catalytic activity. The catalytic results of model compounds and DFT calculations show that these functional groups promote this reaction by stabilization and activation of K ions at the same time of facilitating the leaving of I. And further mechanisms studies show that it is the charge induced capabilities of oxygen groups connected to specific carbon skeleton together with the giant π-reaction platform provided by the π-domain of graphene that played the vital roles in the observed excellent catalytic activity. D. Mei acknowledges the support from the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle. Computing time was granted by the grand challenge of computational catalysis of the William R. Wiley Environmental Molecular Sciences Laboratory.

  18. Dual Sensory Loss and Depressive Symptoms: The Importance of Hearing, Daily Functioning and Activity Engagement

    Directory of Open Access Journals (Sweden)

    Kim Matthew Kiely

    2013-12-01

    Full Text Available Background: The association between dual sensory loss (DSL and mental health has been well established. However, most studies have relied on self-report data and lacked measures that would enable researchers to examine causal pathways between DSL and depression. This study seeks to extend this research by examining the effects of DSL on mental health, and identify factors that explain the longitudinal associations between sensory loss and depressive symptoms. Methods: Piecewise linear-mixed models were used to analyse 16-years of longitudinal data collected on up to five occasions from 1611 adults (51% men aged between 65 and 103 years. Depressive symptoms were assessed by the Centre for Epidemiological Studies Depression (CES-D. Vision loss (VL was defined by corrected visual acuity greater than 0.3 logMAR in the better eye, blindness or glaucoma. Hearing loss (HL was defined by pure tone average (PTA greater than 25 dB in the better hearing ear. Analyses were adjusted for socio-demographics, medical conditions, lifestyle behaviours, Activities of Daily Living (ADLs, cognitive function, and social engagement. Results: Unadjusted models indicated that higher levels of depressive symptoms were associated with HL (B=1.16, SE=0.33 and DSL (B=2.15, SE=0.39 but not VL. Greater rates of change in depressive symptoms were also evident after the onset of HL (B=0.16, SE=0.06, p

  19. Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery.

    Science.gov (United States)

    Chu, Derrick M; Ma, Jun; Prince, Amanda L; Antony, Kathleen M; Seferovic, Maxim D; Aagaard, Kjersti M

    2017-03-01

    Human microbial communities are characterized by their taxonomic, metagenomic and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to determine the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites and assess the effect of the mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early third trimester (n = 81) were prospectively enrolled for longitudinal sampling through 6 weeks after delivery, and a second matched cross-sectional cohort (n = 81) was additionally recruited for sampling once at the time of delivery. Samples across multiple body sites, including stool, oral gingiva, nares, skin and vagina were collected for each maternal-infant dyad. Whole-genome shotgun sequencing and sequencing analysis of the gene encoding the 16S rRNA were performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogeneous across all body sites at delivery, with the notable exception of the neonatal meconium. However, by 6 weeks after delivery, the infant microbiota structure and function had substantially expanded and diversified, with the body site serving as the primary determinant of the composition of the bacterial community and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with the cesarean mode of delivery in some body sites (oral gingiva, nares and skin; R(2) = 0.038), this was not true for neonatal stool (meconium; Mann-Whitney P > 0.05), and there was no observable difference in community function regardless of delivery mode

  20. Relative importance of energy dependent diffuseness parameter and barrier position in the analysis of fusion excitation function data

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    Kharab Rajesh

    2014-03-01

    Full Text Available We have investigated the relative importance of the energy dependence of diffuseness parameter and barrier position in the description of the fusion excitation function data of some heavy ion systems in near barrier energy region. The effects of the energy dependent diffuseness parameter are found to be much more prominent in comparison to those of barrier position.

  1. A whole-path importance-sampling scheme for Feynman path integral calculations of absolute partition functions and free energies.

    Science.gov (United States)

    Mielke, Steven L; Truhlar, Donald G

    2016-01-21

    Using Feynman path integrals, a molecular partition function can be written as a double integral with the inner integral involving all closed paths centered at a given molecular configuration, and the outer integral involving all possible molecular configurations. In previous work employing Monte Carlo methods to evaluate such partition functions, we presented schemes for importance sampling and stratification in the molecular configurations that constitute the path centroids, but we relied on free-particle paths for sampling the path integrals. At low temperatures, the path sampling is expensive because the paths can travel far from the centroid configuration. We now present a scheme for importance sampling of whole Feynman paths based on harmonic information from an instantaneous normal mode calculation at the centroid configuration, which we refer to as harmonically guided whole-path importance sampling (WPIS). We obtain paths conforming to our chosen importance function by rejection sampling from a distribution of free-particle paths. Sample calculations on CH4 demonstrate that at a temperature of 200 K, about 99.9% of the free-particle paths can be rejected without integration, and at 300 K, about 98% can be rejected. We also show that it is typically possible to reduce the overhead associated with the WPIS scheme by sampling the paths using a significantly lower-order path discretization than that which is needed to converge the partition function.

  2. Optimization of Functioning of the Klintsovsky State Nature Reserve of Regional Importance in the Bryansk Region

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    Moskalenko Igor Vladimirovich

    2015-09-01

    Full Text Available The paper provides information on the current status of specially protected natural territories of the Bryansk region – namely, the Klintsovsky state nature reserve of regional importance located on the territory of the Bryansk region. The authors touch upon the problems of global biodiversity and conservation of rare and endangered plant species. The species composition is specified, and the habitats of rare plant species are revealed. The purpose of the research is to develop policies and programs aimed at the conservation of biodiversity and restoration of rare and endangered species of plants growing in the region, including in the Klintsovsky reserve of the Bryansk region. The authors have developed the methods on preservation and restorations of rare and endangered plants species populations growing in the reserve. For successful implementation of a number of issues on environmental trends, the authors identified the feasibility of establishing an interregional introduction center. The task of introduction center for issues related to the identification and involvement of economically valuable species of plants, including rare and endangered species in the center. The article also deals with the organization of research on their biology and ecology, modeling optimal conditions for mass breeding and cultivation of planting material and the development of programs for the implementation of these species in natural habitats in order to restore the size and population density.

  3. Site-specific function and regulation of Osterix in tooth root formation

    Science.gov (United States)

    He, Y. D.; Sui, B. D.; Li, M.; Huang, J.; Chen, S.; Wu, L. A.

    2016-01-01

    Congenital diseases of tooth roots, in terms of developmental abnormalities of short and thin root phenotypes, can lead to loss of teeth. A more complete understanding of the genetic molecular pathways and biological processes controlling tooth root formation is required. Recent studies have revealed that Osterix (Osx), a key mesenchymal transcriptional factor participating in both the processes of osteogenesis and odontogenesis, plays a vital role underlying the mechanisms of developmental differences between root and crown. During tooth development, Osx expression has been identified from late embryonic to postnatal stages when the tooth root develops, particularly in odontoblasts and cementoblasts to promote their differentiation and mineralization. Furthermore, the site-specific function of Osx in tooth root formation has been confirmed, because odontoblastic Osx-conditional knockout mice demonstrate primarily short and thin root phenotypes with no apparent abnormalities in the crown (Journal of Bone and Mineral Research 30, 2014 and 742, Journal of Dental Research 94, 2015 and 430). These findings suggest that Osx functions to promote odontoblast and cementoblast differentiation and root elongation only in root, but not in crown formation. Mechanistic research shows regulatory networks of Osx expression, which can be controlled through manipulating the epithelial BMP signalling, mesenchymal Runx2 expression and cellular phosphorylation levels, indicating feasible routes of promoting Osx expression postnatally (Journal of Cellular Biochemistry 114, 2013 and 975). In this regard, a promising approach might be available to regenerate the congenitally diseased root and that regenerative therapy would be the best choice for patients with developmental tooth diseases. PMID:26599722

  4. Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data.

    Science.gov (United States)

    Wang, Hongyang; Li, Rui; Zhou, Xiang; Xue, Liyao; Xu, Xuewen; Liu, Bang

    2016-11-04

    Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3' end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3'UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.

  5. Understanding Rubredoxin Redox Sites by Density Functional Theory Studies of Analogues

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Yan; Niu, Shuqiang; Ichiye, Toshiko

    2012-09-06

    Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH3)4]0/1-/2-, [Fe(S2-o-xyl)2]0/1-/2-, and Na+[Fe(S2-oxyl) 2]1-/2- in different conformations. In particular, the study of Na+[Fe(S2-o-xyl)2]1-/2- is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ~0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.

  6. Extreme evolutionary conservation of functionally important regions in H1N1 influenza proteome.

    Directory of Open Access Journals (Sweden)

    Samantha Warren

    Full Text Available The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1 do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2 in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80's, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights

  7. Effect of halloysite nanotubes on the structure and function of important multiple blood components.

    Science.gov (United States)

    Wu, Keke; Feng, Ru; Jiao, Yanpeng; Zhou, Changren

    2017-06-01

    Many researchers have investigated the application of halloysite nanotubes (HNTs) in biomedicine, because of their special nanoscale hollow tubular structure. Although the cytocompatibility of HNTs has been studied, their blood compatibility has not been systematically investigated. In this work, the effect of HNTs on the structure and function of different blood components has been studied, including the morphology and hemolysis of red blood cells (RBCs). Based on scanning electron microscopy (SEM) observations, optical density test and flow cytometry analysis, we found that HNTs can affect the morphology and membrane integrity of RBCs in phosphate buffered saline (PBS) in a content-dependent way. In particular, based on UV-vis absorption spectra, fluorescence spectra and circular dichroism (CD) spectra, HNTs can alter the secondary structure and conformation of human fibrinogen and γ-globulins. In addition, the detection of biomarker molecules C3a and C5a in plasma suggests that HNTs can trigger complement activation. In the blood clotting assay, HNTs were found to significantly prolong the activated partial thromboplastin time (APTT), shorten the prothrombin time (PT) of platelet-poor plasma (PPP), and change the thromboelastography (TEG) parameters of whole blood coagulation. Furthermore, confocal laser scanning microscopy and flow cytometry analysis were used to test intracellular uptake by macrophages, and the cellular uptake of HNTs in the RAW 264.7 was found to be content-dependent, but not time-dependent. These findings provide insight for the potential use of HNTs as biofriendly nanocontainers for biomaterials in vivo. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Myosin VIIA, important for human auditory function, is necessary for Drosophila auditory organ development.

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    Sokol V Todi

    Full Text Available BACKGROUND: Myosin VIIA (MyoVIIA is an unconventional myosin necessary for vertebrate audition [1]-[5]. Human auditory transduction occurs in sensory hair cells with a staircase-like arrangement of apical protrusions called stereocilia. In these hair cells, MyoVIIA maintains stereocilia organization [6]. Severe mutations in the Drosophila MyoVIIA orthologue, crinkled (ck, are semi-lethal [7] and lead to deafness by disrupting antennal auditory organ (Johnston's Organ, JO organization [8]. ck/MyoVIIA mutations result in apical detachment of auditory transduction units (scolopidia from the cuticle that transmits antennal vibrations as mechanical stimuli to JO. PRINCIPAL FINDINGS: Using flies expressing GFP-tagged NompA, a protein required for auditory organ organization in Drosophila, we examined the role of ck/MyoVIIA in JO development and maintenance through confocal microscopy and extracellular electrophysiology. Here we show that ck/MyoVIIA is necessary early in the developing antenna for initial apical attachment of the scolopidia to the articulating joint. ck/MyoVIIA is also necessary to maintain scolopidial attachment throughout adulthood. Moreover, in the adult JO, ck/MyoVIIA genetically interacts with the non-muscle myosin II (through its regulatory light chain protein and the myosin binding subunit of myosin II phosphatase. Such genetic interactions have not previously been observed in scolopidia. These factors are therefore candidates for modulating MyoVIIA activity in vertebrates. CONCLUSIONS: Our findings indicate that MyoVIIA plays evolutionarily conserved roles in auditory organ development and maintenance in invertebrates and vertebrates, enhancing our understanding of auditory organ development and function, as well as providing significant clues for future research.

  9. Salt effects on functional traits in model and in economically important Lotus species.

    Science.gov (United States)

    Uchiya, P; Escaray, F J; Bilenca, D; Pieckenstain, F; Ruiz, O A; Menéndez, A B

    2016-07-01

    A common stress on plants is NaCl-derived soil salinity. Genus Lotus comprises model and economically important species, which have been studied regarding physiological responses to salinity. Leaf area ratio (LAR), root length ratio (RLR) and their components, specific leaf area (SLA) and leaf mass fraction (LMF) and specific root length (SRL) and root mass fraction (RMF) might be affected by high soil salinity. We characterised L. tenuis, L. corniculatus, L. filicaulis, L. creticus, L. burtii and L. japonicus grown under different salt concentrations (0, 50, 100 and 150 mm NaCl) on the basis of SLA, LMF, SRL and RMF using PCA. We also assessed effects of different salt concentrations on LAR and RLR in each species, and explored whether changes in these traits provide fitness benefit. Salinity (150 mm NaCl) increased LAR in L. burtii and L. corniculatus, but not in the remaining species. The highest salt concentration caused a decrease of RLR in L. japonicus Gifu, but not in the remaining species. Changes in LAR and RLR would not be adaptive, according to adaptiveness analysis, with the exception of SLA changes in L. corniculatus. PCA revealed that under favourable conditions plants optimise surfaces for light and nutrient acquisition (SLA and SRL), whereas at higher salt concentrations they favour carbon allocation to leaves and roots (LMF and RMF) in detriment to their surfaces. PCA also showed that L. creticus subjected to saline treatment was distinguished from the remaining Lotus species. We suggest that augmented carbon partitioning to leaves and roots could constitute a salt-alleviating mechanism through toxic ion dilution.

  10. Functional Importance of Deletion Mutant Genotypes in an Insect Nucleopolyhedrovirus Population

    Science.gov (United States)

    Simón, Oihane; Williams, Trevor; López-Ferber, Miguel; Caballero, Primitivo

    2005-01-01

    A Nicaraguan isolate of a nucleopolyhedrovirus (SfNIC) that attacks the fall armyworm, Spodoptera frugiperda, survives as a mixture of nine genotypes (SfNIC A to I) that all present genomic deletions, except variant B (complete genotype). Sequencing of cloned restriction fragments revealed that genotypic variants lack between 5 and 16 of the open reading frames present in a contiguous sequence of 18 kb of the SfNIC genome. The absence of oral infectivity of SfNIC-C and -D variants is related to the deletion of the pif and/or pif-2 gene, while that of SfNIC-G remains unexplained. The presence of open reading frame 10, homolog of Se030, also appeared to influence pathogenicity in certain variants. Previous studies demonstrated a significant positive interaction between genotypes B and C. We compared the median lethal concentration of single genotypes (A, B, C, D, and F) and co-occluded genotype mixtures (B+A, B+D, B+F, A+C, and F+C in a 3:1 ratio). Mixtures B+A and B+D showed increased pathogenicity, although only B+D restored the activity of the mixture to that of the natural population. Mixtures of two deletion variants (A+C and F+C) did not show interactions in pathogenicity. We conclude that minority genotypes have an important influence on the overall pathogenicity of the population. These results clearly demonstrate the value of retaining genotypic diversity in virus-based bioinsecticides. PMID:16085811

  11. SIZE AND FIELD OF ACTIVITY INFLUENCE ON WEB SITES FUNCTIONALITY FOR ROMANIAN COMPANIES

    Directory of Open Access Journals (Sweden)

    Tarca Ioan

    2008-05-01

    Full Text Available The internet became an important part of the company’s informational system. In order to take advantage on the Internet’s interactive nature, a lot of companies have created their own websites. Companies use the website for numerous applications: to promote themselves, online shopping, and communication with targeted clients. This study reveals the fact that the company’s size and field of activity have influence on website’s functionality and interactivity. Small companies use the website to successfully compete corporations which do not have yet necessary stimulants to fully exploit the internet capacities.

  12. A novel functional site in the PB2 subunit of influenza A virus essential for acetyl-CoA interaction, RNA polymerase activity, and viral replication.

    Science.gov (United States)

    Hatakeyama, Dai; Shoji, Masaki; Yamayoshi, Seiya; Hirota, Takenori; Nagae, Monami; Yanagisawa, Shin; Nakano, Masahiro; Ohmi, Naho; Noda, Takeshi; Kawaoka, Yoshihiro; Kuzuhara, Takashi

    2014-09-05

    The PA, PB1, and PB2 subunits, components of the RNA-dependent RNA polymerase of influenza A virus, are essential for viral transcription and replication. The PB2 subunit binds to the host RNA cap (7-methylguanosine triphosphate (m(7)GTP)) and supports the endonuclease activity of PA to "snatch" the cap from host pre-mRNAs. However, the structure of PB2 is not fully understood, and the functional sites remain unknown. In this study, we describe a novel Val/Arg/Gly (VRG) site in the PB2 cap-binding domain, which is involved in interaction with acetyl-CoA found in eukaryotic histone acetyltransferases (HATs). In vitro experiments revealed that the recombinant PB2 cap-binding domain that includes the VRG site interacts with acetyl-CoA; moreover, it was found that this interaction could be blocked by CoA and various HAT inhibitors. Interestingly, m(7)GTP also inhibited this interaction, suggesting that the same active pocket is capable of interacting with acetyl-CoA and m(7)GTP. To elucidate the importance of the VRG site on PB2 function and viral replication, we constructed a PB2 recombinant protein and recombinant viruses including several patterns of amino acid mutations in the VRG site. Substitutions of the valine and arginine residues or of all 3 residues of the VRG site to alanine significantly reduced the binding ability of PB2 to acetyl-CoA and its RNA polymerase activity. Recombinant viruses containing the same mutations could not be replicated in cultured cells. These results indicate that the PB2 VRG sequence is a functional site that is essential for acetyl-CoA interaction, RNA polymerase activity, and viral replication. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Patients with autosomal dominant spinocerebellar ataxia have more risk of falls, important balance impairment, and decreased ability to function

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    Carolina Yuri P. Aizawa

    2013-08-01

    Full Text Available OBJECTIVES: To assess balance and ability to function in patients with spinocerebellar ataxia. METHODS: A total of 44 patients with different spinocerebellar ataxia types 1, 2, 3, and 6 were evaluated using the Tinetti balance and gait assessment and the functional independence measure. The scale for the assessment and rating of ataxia and the international cooperative ataxia rating scale were used to evaluate disease severity. RESULTS: Most patients showed significant risk of falls. The balance scores were significantly different in spinocerebellar ataxia types. A significant positive correlation between balance and disease severity was found. CONCLUSION: Patients with spinocerebellar ataxia have important balance impairment and risk of falls that influence the ability to function such as self-care, transfers, and locomotion. Furthermore, the more severe ataxia is, the more compromised are postural balance, risk of falls, and ability to function.

  14. Proposed criteria and indicators of ecosystem function for reclaimed oil sands sites : final report

    Energy Technology Data Exchange (ETDEWEB)

    Welham, C.; Robinson, N. [FOR rx Consulting Inc., Belcarra, BC (Canada)

    2006-10-13

    Sustainable forest management programs develop criteria and indicator (C and I) methodologies in order to demonstrate sustainability as well as to identify problems so that remedial actions can be employed. A critical feature of forestry-based C and I is the assumption that most of the basic ecosystem functions and services are in place at the time management activities are implemented. Application of the C and I approach to open-pit mining is often problematic, as the basic attributes of an ecosystem have been largely removed during mining operations. This report described a comprehensive list of indicators of forest ecosystem function along with a description of how they might be used to assess reclamation success in the oil sands region. Indicators were compiled from a workshop conducted at the University of British Columbia. The list was constrained by the fact that reclaimed oil sands sites are large and spatially heterogenous. The spatial and temporal nature of the data meant that sampling protocols were also necessary. Robust indicators that were economically expensive were favoured. Indicators were grouped under the following 3 criteria: (1) that the physical, chemical and biological properties of the soil are restored to target levels; (2) that the structure, composition and vigor of vegetation cover are restored to target levels; and (3) that critical ecosystem processes are restored to target levels. Criteria were selected to reflect the core attributes necessary for assessing development of a reclaimed ecosystem. Indicators included nitrogen-fixing symbionts; soil fauna; soil nutrients; mycorrhizae; snags; invasive species; wetland input water chemistry; foliar nutrition; nutrient budgets; and plant carbon allocation. It was noted that reference sites should be equivalent ecologically to their reclaimed analogue and located close to the restoration project, so that success in oil sands remediation projects can be evaluated by the rate at which a given

  15. The action sites of propofol in the normal human brain revealed by functional magnetic resonance imaging.

    Science.gov (United States)

    Zhang, Hui; Wang, Wei; Zhao, Zhijing; Ge, Yali; Zhang, Jinsong; Yu, Daihua; Chai, Wei; Wu, Shengxi; Xu, Lixian

    2010-12-01

    Propofol has been used for many years but its functional target in the intact brain remains unclear. In the present study, we used functional magnetic resonance imaging to demonstrate blood oxygen level dependence signal changes in the normal human brain during propofol anesthesia and explored the possible action targets of propofol. Ten healthy subjects were enrolled in two experimental sessions. In session 1, the Observer's Assessment of Alertness/Sedation Scale was performed to evaluate asleep to awake/alert status. In session 2, images with blood oxygen level dependence contrast were obtained with echo-planar imaging on a 1.5-T Philips Gyroscan Magnetic Resonance System and analyzed. In both sessions, subjects were intravenously administered with saline (for 3 min) and then propofol (for 1.5 min) and saline again (for 10.5 min) with a constant speed infusion pump. Observer's Assessment of Alertness/Sedation Scale scoring showed that the subjects experienced conscious–sedative–unconscious–analepsia, which correlated well with the signal decreases in the anesthesia states. Propofol induced significant signal decreases in hypothalamus (18.2%±3.6%), frontal lobe (68.5%±11.2%), and temporal lobe (34.7%±6.1%). Additionally, the signals at these three sites were fulminant and changed synchronously. While in the thalamus, the signal decrease was observed in 5 of 10 of the subjects and the magnitude of decrease was 3.9%±1.6%. These results suggest that there is most significant inhibition in hypothalamus, frontal lobe, and temporal in propofol anesthesia and moderate inhibition in thalamus. These brain regions might be the targets of propofol anesthesia in human brain.

  16. A comparative structure-function analysis of active-site inhibitors of Vibrio cholerae cholix toxin.

    Science.gov (United States)

    Lugo, Miguel R; Merrill, A Rod

    2015-09-01

    Cholix toxin from Vibrio cholerae is a novel mono-ADP-ribosyltransferase (mART) toxin that shares structural and functional properties with Pseudomonas aeruginosa exotoxin A and Corynebacterium diphtheriae diphtheria toxin. Herein, we have used the high-resolution X-ray structure of full-length cholix toxin in the apo form, NAD(+) bound, and 10 structures of the cholix catalytic domain (C-domain) complexed with several strong inhibitors of toxin enzyme activity (NAP, PJ34, and the P-series) to study the binding mode of the ligands. A pharmacophore model based on the active pose of NAD(+) was compared with the active conformation of the inhibitors, which revealed a cationic feature in the side chain of the inhibitors that may determine the active pose. Moreover, a conformational search was conducted for the missing coordinates of one of the main active-site loops (R-loop). The resulting structural models were used to evaluate the interaction energies and for 3D-QSAR modeling. Implications for a rational drug design approach for mART toxins were derived.

  17. Design of Hanford Site 4th Generation Multi Function Corrosion Monitoring System

    Energy Technology Data Exchange (ETDEWEB)

    NORMAN, E.C.

    2000-08-30

    This document describes the design of the fourth-generation corrosion monitoring system scheduled to be installed in DST 241-AN-104 early in fiscal year 2001. A fourth-generation multi-function corrosion monitoring system has been designed for installation into a DST in the 241-AN farm at the Hanford Site in FY 2001. Improvements and upgrades from the third-generation system (installed in 241-AN-105) that have been incorporated into the fourth-generation system include: Addition of a built-in water lance to assist installation of probe into tanks with a hard crust layer at the surface of the waste; and Improvement of the electrode mounting apparatus used to attach the corrosion monitoring electrodes to the stainless steel probe body (new design simplifies probe assembly/wiring). These new features improve on the third-generation design and yield a system that is easier to fabricate and install, provides for a better understanding of the relationship between corrosion and other tank operating parameters, and optimizes the use of the riser that houses the probe in the tank.

  18. When the shifting agriculture is gone: functionality of Atlantic Coastal Forest in abandoned farming sites

    Directory of Open Access Journals (Sweden)

    Rogério Ribeiro de Oliveira

    Full Text Available Slash-and-burn agriculture has been practiced for a very long time by the traditional populations (caiçaras on Ilha Grande, Rio de Janeiro State, Brazil. After a few years of use the plots are abandoned to fallow. We examined the processes of litter production and decomposition and the relationships between forest lands used by caiçara populations and landscape functionality. Five and 25-year-old forests growing on areas once used for subsistence agriculture were compared to a near-climax forest site. No significant differences between the three areas were noted in terms of litter production over a 2-yr period; the average litter productions were 9,927, 8,707 and 10,031 kg/ha/yr for the 5-year, 25-year and climax forests respectively. N and K nutrient input through litter was greatest in the climax forest; P and Mg input was greatest in the 5-yr forest; and Na greatest in the 25-yr forest. Ground litter accumulation (3,040-3,730 kg/ha/yr was not significantly different in the three areas. Litter turnover times (1/K were 0.33, 0.42 and 0.38 for the 5-yr, 25-yr and climax forests respectively. These secondary forests cover almost all of Ilha Grande and demonstrate low species diversity, but they have production and decomposition systems similar to those of mature forests.

  19. Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context.

    Science.gov (United States)

    Kel, Alexander E; Niehof, Monika; Matys, Volker; Zemlin, Rüdiger; Borlak, Jürgen

    2008-01-01

    We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4alpha binding sites and significantly improved an overall recognition of faithful HNF4alpha targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

  20. Differential methylation status of IGF2-H19 locus does not affect the fertility of crossbred bulls but some of the CTCF binding sites could be potentially important.

    Science.gov (United States)

    Jena, Subas C; Kumar, Sandeep; Rajput, Sandeep; Roy, Bhaskar; Verma, Arpana; Kumaresan, Arumugam; Mohanty, Tushar K; De, Sachinandan; Kumar, Rakesh; Datta, Tirtha K

    2014-04-01

    Associations between abnormal methylation of spermatozoan DNA with male infertility have been sought in recent years to identify a molecular explanation of differential spermatozoan function. The present work was undertaken to investigate the methylation profile of differentially methylated regions (DMRs) in the IGF2-H19 locus of Bos taurus X Bos indicus crossbred bull spermatozoa. Bulls having more than at least 100 insemination records over a period of 12 years were classified into two groups of five bulls each belonging to low- and high-fertility groups. The IGF2 and H19 DMR sequences in B. indicus cattle were observed to be in absolute homology with B. taurus cattle. The DNA of crossbred bull spermatozoa was isolated, bisulfite treated, and amplified for specific DMR regions using methylation-change-specific primers. The overall degree of methylation at IGF2-H19 DMRs was not found to be significantly different among two groups of bulls. The sixth CTCF binding site (CCCTC) identified in H19 DMR, however, had a significant methylation difference between the high- and low-fertility bulls. It was concluded that alteration of the methylation levels at IGF2-H19 DMRs might not be responsible for the fertility difference of crossbred bulls, although the role played by the specific CTCF binding sites at this locus, which could influence IGF2 expression during spermatogenesis and early embryonic development, deserves further attention.

  1. Identification of the Mycobacterium marinum Apa antigen O-mannosylation sites reveals important glycosylation variability with the M. tuberculosis Apa homologue.

    Science.gov (United States)

    Coddeville, Bernadette; Wu, Sz-Wei; Fabre, Emeline; Brassart, Colette; Rombouts, Yoann; Burguière, Adeline; Kremer, Laurent; Khoo, Kay-Hooi; Elass-Rochard, Elisabeth; Guérardel, Yann

    2012-10-22

    The 45/47 kDa Apa, an immuno-dominant antigen secreted by Mycobacterium tuberculosis is O-mannosylated at multiple sites. Glycosylation of Apa plays a key role in colonization and invasion of the host cells by M. tuberculosis through interactions of Apa with the host immune system C-type lectins. Mycobacterium marinum (M.ma) a fish pathogen, phylogenetically close to M. tuberculosis, induces a granulomatous response with features similar to those described for M. tuberculosis in human. Although M.ma possesses an Apa homologue, its glycosylation status is unknown, and whether this represents a crucial element in the pathophysiology induced by M.ma remains to be addressed. To this aim, we have identified two concanavalin A-reactive 45/47 kDa proteins from M.ma, which have been further purified by a two-step anion exchange chromatography process. Advanced liquid chromatography-nanoESI mass spectrometry-based proteomic analyses of peptides, derived from either tryptic digestion alone or in combination with the Asp-N endoproteinase, established that M.ma Apa possesses up to seven distinct O-mannosylated sites with mainly single mannose substitutions, which can be further extended at the Ser/Thr/Pro rich region near the N-terminus. This opens the way to further studies focussing on the involvement and biological functions of Apa O-mannosylation using the M.ma/zebrafish model. Copyright © 2012 Elsevier B.V. All rights reserved.

  2. Starch grain analysis reveals function of grinding stone tools at Shangzhai site, Beijing

    Institute of Scientific and Technical Information of China (English)

    YANG XiaoYan; YU JinCheng; LI HouYuan; CUI TianXing; GUO JingNing; GE QuanSheng

    2009-01-01

    Prehistoric groundstone tools including slabs (metate, mo-pan) and mullers (mano, mo-bang) are often considered to be tools that were used to process cereals in ancient China. Most archaeologists believe that groundstone tools are indicators of an agrarian economy. This study employed starch grain analysis to examine a slab and a muller excavated from the Shangzhai Site (7500--7000 cal a BP), Beijing. Identifiable starch grains recovered from the stone tools were classified into 9 genera and 12 species, most of which were from acorns and foxtail millets. Remains from the oak species Q. mongolicus, Q. acuttssima, and Q. dentate were identified as well as a few starch grains from broomcorn (Panicum miliaseum) and bean (Vigna sp.). Other starch grains were from unidenUfiable roots and grasses. A variety of starch grains indicates that the grinding stone tools were used to process not only cereals, but also other seeds or roots that had to be ground or husked, thus bringing into question the aforementioned cereal hypothesis. Because the numbers of starch grains from nuts and millets were so large, both gathering and cultivation might have been important economic patterns before 7000 years ago in Beijing area. Moreover, the starch remains are derived from plants that indicate that the paleoclimate of Beijing was wetter and warmer than today's.

  3. Starch grain analysis reveals function of grinding stone tools at Shangzhai site, Beijing

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Prehistoric groundstone tools including slabs (metate, mo-pan) and mullers (mano, mo-bang) are often considered to be tools that were used to process cereals in ancient China. Most archaeologists believe that groundstone tools are indicators of an agrarian economy. This study employed starch grain analysis to examine a slab and a muller excavated from the Shangzhai Site (7500-7000 cal a BP), Beijing. Identifiable starch grains recovered from the stone tools were classified into 9 genera and 12 species, most of which were from acorns and foxtail millets. Remains from the oak species Q. mongolicus, Q. acuttssima, and Q. dentate were identified as well as a few starch grains from broomcorn (Panicum miliaseum) and bean (Vigna sp.). Other starch grains were from unidentifiable roots and grasses. A variety of starch grains indicates that the grinding stone tools were used to process not only cereals, but also other seeds or roots that had to be ground or husked, thus bringing into question the aforementioned cereal hypothesis. Because the numbers of starch grains from nuts and millets were so large, both gathering and cultivation might have been important economic patterns before 7000 years ago in Beijing area. Moreover, the starch remains are derived from plants that indicate that the paleoclimate of Beijing was wetter and warmer than today’s.

  4. Functional Exercise and Physical Fitness Post Stroke: The Importance of Exercise Maintenance for Motor Control and Physical Fitness after Stroke

    Directory of Open Access Journals (Sweden)

    Birgitta Langhammer

    2012-01-01

    Full Text Available It is argued that all stroke patients, indifferent of disability, have the same possibility to improve with training. The aim of the study was to follow and register functional improvements in two groups with different functional capacities at baseline for a period of 36 months. Stroke patients were recruited and divided into groups related to their functional status at baseline. During the acute rehabilitation, both groups received functional task-oriented training, followed by regular self- or therapeutic driven training the first year after stroke and varied exercise patterns the following 24 months. The participants were tested on admission, and at three, six, twelve, and thirty-six months after the onset of stroke. Both groups improved functional activity up to six months which then stabilized up to twelve months to decline somewhat at thirty-six months after stroke. Change scores indicate a greater potential for rehabilitation in the MAS ≤35 in relation to group MAS >35 although the functional capacity was higher in the latter. This indicates the importance of maintaining exercise and training for all persons after stroke.

  5. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function

    DEFF Research Database (Denmark)

    Yatsenko, A S; Kucherenko, M M; Pantoja, M;

    2009-01-01

    BACKGROUND: Dystroglycan (Dg) is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC) which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C-terminal ......BACKGROUND: Dystroglycan (Dg) is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC) which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C...... function in the establishment of oocyte polarity in Drosophila. If either WW binding site is mutated, the Dg protein can still be active. However, simultaneous mutations in both WW binding sites abolish the Dg activities in both overexpression and loss-of-function oocyte polarity assays in vivo....... Additionally, sequence comparisons of WW binding sites in 12 species of Drosophila, as well as in humans, reveal a high level of conservation. This preservation throughout evolution supports the idea that both WW binding sites are functionally required. CONCLUSION: Based on the obtained results we propose...

  6. Molecular dynamics simulations and statistical coupling analysis of GPI12 in L. major: functional co-evolution and conservedness reveals potential drug-target sites.

    Science.gov (United States)

    Singh, Shailza; Mandlik, Vineetha; Shinde, Sonali

    2015-03-01

    GPI12 represents an important enzyme in the GPI biosynthetic pathway of several parasites like 'Leishmania'. GPI activity is generally regulated through either the hindrance in GPI complex assembly formation or the modulation of the lipophosphoglycan (LPG) flux to either reduce or enhance the pathogenicity in an organism. Of the various GPI molecules known, GPI12 is an important enzyme in the GPI biosynthetic pathway which can be exploited as a target due to the substrate specificity difference in parasites and humans. In the present study, the functional importance of the co-evolving residues of the GPI12 protein of Leishmania has been highlighted using the GPI proteins belonging to the GlcNAC-deacetylase family. Exploring the active site of the GPI12 protein and designing inhibitors against the functional residues provide ways and means to change the efficiency of deacetylation activity of the enzyme. The activity of de-N-acetylase is low in the absence of metal ions like zinc. Hence we designed eight small molecules in order to modulate the activity of GPI12. Compound 8 was found to be an appropriate choice to target the agonist (GPI12) active site thereby targeting the residues which were essential in the Zn binding and chelation activity. Inhibition of these sites offered a strong constraint to block the protein activity and in turn GPI biosynthesis.

  7. An important site in PBP2x of penicillin-resistant clinical isolates of Streptococcus pneumoniae: mutational analysis of Thr338.

    Science.gov (United States)

    Zerfass, Ilka; Hakenbeck, Regine; Denapaite, Dalia

    2009-03-01

    Penicillin-binding protein 2x (PBP2x) of Streptococcus pneumoniae represents a primary resistance determinant for beta-lactams, and low-affinity PBP2x variants can easily be selected with cefotaxime. Penicillin-resistant clinical isolates of S. pneumoniae frequently contain in their mosaic PBP2x the mutation T338A adjacent to the active site S337, and T338P as well as T338G substitutions are also known. Site-directed mutagenesis has now documented that a single point mutation at position T338 confers selectable levels of beta-lactam resistance preferentially to oxacillin. Despite the moderate impact on beta-lactam susceptibility, the function of the PBP2x mutants appears to be impaired, as can be documented in the absence of a functional CiaRH regulatory system, resulting in growth defects and morphological changes. The combination of low-affinity PBP2x and PBP1a encoded by mosaic genes is known to result in high cefotaxime resistance. In contrast, introduction of a mosaic pbp1a into the PBP2x(T338G) mutant did not lead to increased resistance. However, the mosaic PBP1a gene apparently complemented the PBP2x(T338G) defect, since Cia mutant derivatives grew normally. The data support the view that PBP2x and PBP1a interact with each other on some level and that alterations of both PBPs in resistant clinical isolates have evolved to ensure cooperation between both proteins.

  8. Androgen action via testicular arteriole smooth muscle cells is important for Leydig cell function, vasomotion and testicular fluid dynamics.

    Directory of Open Access Journals (Sweden)

    Michelle Welsh

    Full Text Available Regulation of blood flow through the testicular microvasculature by vasomotion is thought to be important for normal testis function as it regulates interstitial fluid (IF dynamics which is an important intra-testicular transport medium. Androgens control vasomotion, but how they exert these effects remains unclear. One possibility is by signalling via androgen receptors (AR expressed in testicular arteriole smooth muscle cells. To investigate this and determine the overall importance of this mechanism in testis function, we generated a blood vessel smooth muscle cell-specific AR knockout mouse (SMARKO. Gross reproductive development was normal in SMARKO mice but testis weight was reduced in adulthood compared to control littermates; this reduction was not due to any changes in germ cell volume or to deficits in testosterone, LH or FSH concentrations and did not cause infertility. However, seminiferous tubule lumen volume was reduced in adult SMARKO males while interstitial volume was increased, perhaps indicating altered fluid dynamics; this was associated with compensated Leydig cell failure. Vasomotion was impaired in adult SMARKO males, though overall testis blood flow was normal and there was an increase in the overall blood vessel volume per testis in adult SMARKOs. In conclusion, these results indicate that ablating arteriole smooth muscle AR does not grossly alter spermatogenesis or affect male fertility but does subtly impair Leydig cell function and testicular fluid exchange, possibly by locally regulating microvascular blood flow within the testis.

  9. Regions within the N-terminal domain of human topoisomerase I exert important functions during strand rotation and DNA binding

    DEFF Research Database (Denmark)

    Hougaard, Rikke Frølich; Andersen, Félicie Faucon; Westergaard, Ole

    2004-01-01

    The human topoisomerase I N-terminal domain is the only part of the enzyme still not crystallized and the function of this domain remains enigmatical. In the present study, we have addressed the specific functions of individual N-terminal regions of topoisomerase I by characterizing mutants lacking...... amino acid residues 1–202 or 191–206 or having tryptophane-205 substituted by glycine in a broad variety of in vitro activity assays. As a result of these investigations we find that mutants altered in the region 191–206 distinguished themselves from the wild-type enzyme by a faster strand rotation step...... support a model according to which tryptophane-205 and possibly other residues located between position 191–206 coordinates the restriction of free strand rotation during the topoisomerization step of catalysis. Moreover, tryptophane-205 appears important for the function of the bulk part of the N...

  10. Functional β-adrenoceptors are important for early muscle regeneration in mice through effects on myoblast proliferation and differentiation.

    Directory of Open Access Journals (Sweden)

    Jarrod E Church

    Full Text Available Muscles can be injured in different ways and the trauma and subsequent loss of function and physical capacity can impact significantly on the lives of patients through physical impairments and compromised quality of life. The relative success of muscle repair after injury will largely determine the extent of functional recovery. Unfortunately, regenerative processes are often slow and incomplete, and so developing novel strategies to enhance muscle regeneration is important. While the capacity to enhance muscle repair by stimulating β2-adrenoceptors (β-ARs using β2-AR agonists (β2-agonists has been demonstrated previously, the exact role β-ARs play in regulating the regenerative process remains unclear. To investigate β-AR-mediated signaling in muscle regeneration after myotoxic damage, we examined the regenerative capacity of tibialis anterior and extensor digitorum longus muscles from mice lacking either β1-AR (β1-KO and/or β2-ARs (β2-KO, testing the hypothesis that muscles from mice lacking the β2-AR would exhibit impaired functional regeneration after damage compared with muscles from β1-KO or β1/β2-AR null (β1/β2-KO KO mice. At 7 days post-injury, regenerating muscles from β1/β2-KO mice produced less force than those of controls but muscles from β1-KO or β2-KO mice did not exhibit any delay in functional restoration. Compared with controls, β1/β2-KO mice exhibited an enhanced inflammatory response to injury, which delayed early muscle regeneration, but an enhanced myoblast proliferation later during regeneration ensured a similar functional recovery (to controls by 14 days post-injury. This apparent redundancy in the β-AR signaling pathway was unexpected and may have important implications for manipulating β-AR signaling to improve the rate, extent and efficacy of muscle regeneration to enhance functional recovery after injury.

  11. Ground-level airborne particulate matter near important Portuguese Cultural Heritage sites in high polluted (Lisbon) and low polluted (Evora) urban environments

    Science.gov (United States)

    Schiavon, N.; Wagner, F.; Candeias, A.; Kandler, K.; Tobias, L.; Mirao, J.

    2012-04-01

    As part of a wider project on aerosol composition in the Southwestern part of the Iberian peninsula, an intensive field monitoring/sampling/analytical campaign has been conducted in August and December 2011 to assess indoor and outdoor atmospheric aerosol optical and microphysical parameters (Nephelometry), number/mass/size distribution (TEOM, MAAP, OPS) and single particle minero-chemical composition on filter collected samples (VP-SEM+EDS, XRD) at several sheltered and unsheltered locations close to important Cultural Heritage monuments in Evora and Lisbon, Portugal. Sites investigated included the Igreja do S. Francisco in Evora, the Cristo Rei sanctuary, Jeronimos Monastery, and Lisbon Castle in Lisbon. At Cristo Rei measurements at sea level, around 100m and around 180m were carried out in order to determine the vertical profile of the particle size distribution. Measurements were taken at different times of day reflecting changes in atmospheric mixing and air pollution levels. Measurements were also performed near an air quality monitoring station at Avenida de Libertade (the busiest traffic artery in Lisbon city center) during traffic peak hour. One of the aims of the campaign was to determine differences in airborne particulate matter compositions and concentrations between an urban coastal high pollution (Lisbon) and a low pollution (Evora) environments and how these could affect the nature of decay patterns and processes in the building materials of the monuments under investigation. Preliminary results indicate significant differences in particle properties between the 2 cities as well as between indoor and outdoor locations. One interesting result was the detection of considerable amounts of particle of oceanic origin (such as sodium chloride) in the Evora site even at 130 km away from the coast. Despite its relatively unpolluted location, single particle analysis by SEM+EDS at the Evora site reveals the presence of significant numbers of particle of

  12. GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.

    Science.gov (United States)

    Valencia, A; Kjeldgaard, M; Pai, E F; Sander, C

    1991-06-15

    GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calculation of residue-residue interactions, we analyzed the two subfamilies in terms of structural conservation, sequence conservation, and residue contact strength. There are three main results. (i) A structure-based alignment of p21 and elongation factor Tu. (ii) The definition of a common conserved structural core that may be useful as the basis of model building by homology of the three-dimensional structure of any GTPase domain. (iii) Identification of sequence regions, other than the effector loop and the nucleotide binding site, that may be involved in the functional cycle: they are loop L4, known to change conformation after GTP hydrolysis; helix alpha 2, especially Arg-73 and Met-67 in ras p21; loops L8 and L10, including ras p21 Arg-123, Lys-147, and Leu-120; and residues located spatially near the N and C termini. These regions are candidate sites for interaction either with the GTP/GDP exchange factor, with a GTPase-affected function, or with a molecule delivered to a destination site with the aid of the GTPase domain.

  13. Assessing the recovery of functional diversity after sustained sediment screening at an aggregate dredging site in the North Sea

    Science.gov (United States)

    Barrio Froján, Christopher R. S.; Cooper, Keith M.; Bremner, Julie; Defew, Emma C.; Wan Hussin, Wan M. R.; Paterson, David M.

    2011-05-01

    The effects of dredging the seabed for aggregate on benthic functional diversity were assessed using a suite of suitable indices on a recovering macrofaunal assemblage. Recovery was assessed as the return of a dredged assemblage to a state found in neighbouring undisturbed (reference) sites. In situ sediment screening was permitted during dredging operations; a difference in the sedimentary profile of the seabed between dredged and undisturbed reference sites was also observed. At sites of relatively high and low dredging intensity the sediment appeared more homogenous than reference sites after the selective removal of the coarser component. Initial assessment of the macrofaunal assemblage using univariate analytical techniques suggested a recovery of functional diversity at the low dredging intensity site after two years (according to the Infaunal Trophic Index, Taxonomic Distinctness index and Rao's Quadratic Entropy coefficient). However, multivariate analyses of the same data and of all indices except Taxonomic Distinctness indicated that assemblages at both high and low dredging intensity sites remained statistically indistinguishable from each other yet markedly different to the assemblage present in the reference area during the four-year study. The study concluded that recovery of functional diversity to a level found in a neighbouring undredged habitat had not occurred at either dredged site five years after the cessation of dredging. It is thought that the damage by dredging to functional diversity and to the capacity of the macrofaunal assemblage to recover is immediate and not so dependent on dredging intensity. The cumulative and wider ranging effects of sediment screening cannot be ignored or dismissed as a contributing factor to the similarities observed. The wider significance of these findings on the regulation of dredging activities is discussed.

  14. The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase.

    Science.gov (United States)

    Xiang, J; Sun, J; Sampson, N S

    2001-04-01

    We have determined the sequence requirements for the N-terminal protein hinge of the active-site lid of triosephosphate isomerase. The codons for the hinge (PVW) were replaced with a genetic library of all possible 8000 amino acid combinations. The most active of these 8000 mutants were selected using in vivo complementation of a triosephosphate isomerase-deficient strain of Escherichia coli, DF502. Approximately 0.3 % of the mutants complement DF502 with an activity that is between 10 and 70 % of wild-type activity. They all contain Pro at the first position. Furthermore, the sequences of these hinge mutants reveal that hydrophobic packing is very important for efficient formation of the enediol intermediate. However, the reduced catalytic activities observed are not due to increased rates of loop opening. To explore the relationship between the N-terminal and C-terminal hinges, three semi-active mutants from the N-terminal hinge selection experiment (PLH, PHS and PTF), and six active C-terminal hinge mutants from previous work (NSS, LWA, YSL, KTK, NPN, KVA) were combined to form 18 "double-hinge" mutants. The activities of these mutants suggest that the N-terminal and C-terminal hinge structures affect one another. It appears that specific side-chain interactions are important for forming a catalytically active enzyme, but not for preventing release of the unstable enediol intermediate from the active site of the enzyme. The independence of intermediate release on amino acid sequence is consistent with the absence of a "universal" hinge sequence in structurally related enzymes.

  15. Pharmacists' assessment of dispensing errors: risk factors, practice sites, professional functions, and satisfaction.

    Science.gov (United States)

    Bond, C A; Raehl, C L

    2001-05-01

    Certain demographic, practice, staffing, and pharmacist satisfaction variables may contribute to dispensing errors. A survey was randomly mailed to 7298 (50%) Texas pharmacists, of which 2862 were returned (39% response rate). Responders were 2437 pharmacists who indicated that they were in practice. Of these, 535 (23%) reported no risk to patients for dispensing errors and 793 (34%) reported at least one patient/week was at risk for such an error. There was a positive relationship between number of prescription orders filled/hour and the estimated risk of dispensing errors (r(s)=0.285, ppharmacies (risk score = 1.85 +/- 1.32), traditional chain store pharmacies (1.66 +/- 1.18), and hospital pharmacies (1.61 +/- 1.09) reported a higher risk than other groups. Pharmacists practicing in independent community pharmacies (0.75 +/- 0.84), home health care (0.83 +/- 0.99), grocery chain store pharmacies (1.30 +/- 0.96), and mass merchandise chain store pharmacies (1.30 +/- 1.08) reported a lower risk (H=260, df=8, p<0.001). Nine job satisfaction variables were strongly associated with the risk of dispensing errors (r(s) = between -0.3 and -0.422, p<0.001), as were prescription volume, practice site, staffing, training, pharmacist functions, and professional organization membership. The results of this survey should help pharmacists and management develop specific plans for reducing the risks of dispensing errors. These data should be useful for more in-depth study of such errors.

  16. rVISTA for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites

    Energy Technology Data Exchange (ETDEWEB)

    Loots, Gabriela G.; Ovcharenko, Ivan; Pachter, Lior; Dubchak, Inna; Rubin, Edward M.

    2002-03-08

    Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput discovery of cis-regulatory elements that combines transcription factor binding site prediction and the analysis of inter-species sequence conservation. Here, we illustrate the ability of rVISTA to identify true transcription factor binding sites through the analysis of AP-1 and NFAT binding sites in the 1 Mb well-annotated cytokine gene cluster1 (Hs5q31; Mm11). The exploitation of orthologous human-mouse data set resulted in the elimination of 95 percent of the 38,000 binding sites predicted upon analysis of the human sequence alone, while it identified 87 percent of the experimentally verified binding sites in this region.

  17. Actin polymerization negatively regulates p53 function by impairing its nuclear import in response to DNA damage.

    Directory of Open Access Journals (Sweden)

    Ling Wang

    Full Text Available Actin, one of the most evolutionarily conservative proteins in eukaryotes, is distributed both in the cytoplasm and the nucleus, and its dynamics plays important roles in numerous cellular processes. Previous evidence has shown that actin interacts with p53 and this interaction increases in the process of p53 responding to DNA damage, but the physiological significance of their interaction remains elusive. Here, we show that DNA damage induces both actin polymerization and p53 accumulation. To further understand the implication of actin polymerization in p53 function, cells were treated with actin aggregation agent. We find that the protein level of p53 decrease. The change in p53 is a consequence of the polymeric actin anchoring p53 in the cytoplasm, thus impairing p53 nuclear import. Analysis of phosphorylation and ubiquitination of p53 reveals that actin polymerization promotes the p53 phosphorylation at Ser315 and reduces the stabilization of p53 by recruiting Aurora kinase A. Taken together, our results suggest that the actin polymerization serves as a negative modulator leading to the impairment of nuclear import and destabilization of p53. On the basis of our results, we propose that actin polymerization might be a factor participating in the process of orchestrating p53 function in response to DNA damage.

  18. Functional Analysis of Multiple Transcription Factor Sites in a Regulatory Element of Human ε-Globin Gene

    Institute of Scientific and Technical Information of China (English)

    Chun-Hui HOU; Jian HUANG; Ruo-Lan QIAN

    2004-01-01

    The developmental control of the human ε-globin gene expression is mediated by transcriptional regulatory elements in the 5' flanking DNA of this gene. A previously identified negative regulatory element (-3028 to -2902 bp, termed ε-NRAII) was analyzed and one putative NF-κB site and two GATA sites locate at -3004 bp, -2975 bp and -2948 bp were characterized. Electrophoresis mobility shift assay (EMSA)showed that the putative NF-κB site was specifically bound by nuclear proteins of K562 cells. Data obtained from transient transfection showed that the expression of reporter gene could be upregulated about 50% or 100% respectively when ε-NRAII was inserted upstream of the SV40 promoter or ε-globin gene proximal promoter (-177 bp to +1 bp), suggesting that ε-NRAII might not be a classic silencer. Mutation in the putative NF-κB site or in the GATA site (at-2975 bp) slightly reduced the expression of reporter gene driven by SV40 promoter or ε-globin gene proximal promoter. However, the mutation of GATA site at -2948 bp remarkably reduced the reporter gene activity driven by SV40 promoter, but not by ε-globin gene proximal promoter. Further mutation analysis showed that the negative effect of mutation in GATA site at -2948 bp on SV40 promoter was not affected by the mutation of the putative NF-κB site, whereas it could be abolished by the mutation of GATA site at -2975 bp. Furthermore, the mutation of both GATA sites could synergistically reduce the reporter gene activity driven by ε-globin gene proximal promoter. Those results suggested that ε-NRAII might function differently on the SV40 promoter and ε-globin gene proximal promoter.

  19. The chicken miR-150 targets the avian orthologue of the functional zebrafish MYB 3'UTR target site

    Directory of Open Access Journals (Sweden)

    Guillon-Munos Audrey

    2010-09-01

    Full Text Available Abstract Background The c-myb proto-oncogene is the founding member of a family of transcription factors involved principally in haematopoiesis, in diverse organisms, from zebrafish to mammals. Its deregulation has been implicated in human leukaemogenesis and other cancers. The expression of c-myb is tightly regulated by post-transcriptional mechanisms involving microRNAs. MicroRNAs are small, highly conserved non-coding RNAs that inhibit translation and decrease mRNA stability by binding to regulatory motifs mostly located in the 3'UTR of target mRNAs conserved throughout evolution. MYB is an evolutionarily conserved miR-150 target experimentally validated in mice, humans and zebrafish. However, the functional miR-150 sites of humans and mice are orthologous, whereas that of zebrafish is different. Results We identified the avian mature miRNA-150-5P, Gallus gallus gga-miR-150 from chicken leukocyte small-RNA libraries and showed that, as expected, the gga-miR-150 sequence was highly conserved, including the seed region sequence present in the other miR-150 sequences listed in miRBase. Reporter assays showed that gga-miR-150 acted on the avian MYB 3'UTR and identified the avian MYB target site involved in gga-miR-150 binding. A comparative in silico analysis of the miR-150 target sites of MYB 3'UTRs from different species led to the identification of a single set of putative target sites in amphibians and zebrafish, whereas two sets of putative target sites were identified in chicken and mammals. However, only the target site present in the chicken MYB 3'UTR that was identical to that in zebrafish was functional, despite the additional presence of mammalian target sites in chicken. This specific miR-150 site usage was not cell-type specific and persisted when the chicken c-myb 3'UTR was used in the cell system to identify mammalian target sites, showing that this miR-150 target site usage was intrinsic to the chicken c-myb 3'UTR. Conclusion Our

  20. Impact of disruption of secondary binding site S2 on dopamine transporter function.

    Science.gov (United States)

    Zhen, Juan; Reith, Maarten E A

    2016-09-01

    The structures of the leucine transporter, drosophila dopamine transporter, and human serotonin transporter show a secondary binding site (designated S2 ) for drugs and substrate in the extracellular vestibule toward the membrane exterior in relation to the primary substrate recognition site (S1 ). The present experiments are aimed at disrupting S2 by mutating Asp476 and Ile159 to Ala. Both mutants displayed a profound decrease in [(3) H]DA uptake compared with wild-type associated with a reduced turnover rate kcat . This was not caused by a conformational bias as the mutants responded to Zn(2+) (10 μM) similarly as WT. The dopamine transporters with either the D476A or I159A mutation both displayed a higher Ki for dopamine for the inhibition of [3H](-)-2-β-carbomethoxy-3-β-(4-fluorophenyl)tropane binding than did the WT transporter, in accordance with an allosteric interaction between the S1 and S2 sites. The results provide evidence in favor of a general applicability of the two-site allosteric model of the Javitch/Weinstein group from LeuT to dopamine transporter and possibly other monoamine transporters. X-ray structures of transporters closely related to the dopamine (DA) transporter show a secondary binding site S2 in the extracellular vestibule proximal to the primary binding site S1 which is closely linked to one of the Na(+) binding sites. This work examines the relationship between S2 and S1 sites. We found that S2 site impairment severely reduced DA transport and allosterically reduced S1 site affinity for the cocaine analog [(3) H]CFT. Our results are the first to lend direct support for the application of the two-site allosteric model, advanced for bacterial LeuT, to the human DA transporter. The model states that, after binding of the first DA molecule (DA1 ) to the primary S1 site (along with Na(+) ), binding of a second DA (DA2 ) to the S2 site triggers, through an allosteric interaction, the release of DA1 and Na(+) into the cytoplasm. © 2016

  1. Adsorption and desorption of propane on Pd (111): A van der Waals density functional study. Energy binding sites and geometries

    Science.gov (United States)

    e Silva, Tadeu Leonardo Soares; Schmal, Martin

    2017-10-01

    Palladium supported catalysts used for the partial oxidation of propane reaction aiming the H2 production deserves specific characterizations and theoretical modeling for the explanation of the transition phase and energy needed for the adsorption and desorption of propane on top of the palladium atoms. On the other hand, the product distribution will depend on the adsorption and desorption capacity of the different compounds present during the reaction. In this work, the adsorption of propane on a Pd (111) surface was studied by using different approximations. A periodic method based on the Density Functional Theory (DFT) formalism employing vdW-DF functional was investigated for determining preferred binding sites of propane on palladium. The results show that the adsorption on hcp site is more stable than on top site and predictions fit well the experimental results.

  2. Evaluation of the effects of transvenous pacing site on left ventricular function and synchrony in healthy anesthetized dogs.

    Science.gov (United States)

    Maisenbacher, Herbert W; Estrada, Amara H; Prosek, Robert; Shih, Andre C; Vangilder, James M

    2009-04-01

    OBJECTIVE-To compare the acute effects of cardiac pacing from various transvenous pacing sites on left ventricular (LV) function and synchrony in clinically normal dogs. ANIMALS-10 healthy adult mixed-breed dogs. PROCEDURES-Dogs were anesthetized, and dual-chamber transvenous biventricular pacing systems were implanted. Dogs were paced in single-chamber mode from the right atrial appendage (RAA) alone and in dual-chamber mode from the right ventricular apex (RVA), from the left ventricular free wall (LVFW), and simultaneously from the RVA and LVFW (BiV). Standard ECG and echocardiographic measurements, cardiac output measured with the lithium dilution method (LiDCO), and tissue Doppler-derived measurements of LV synchrony were obtained during each of the pacing configurations. RESULTS-Placement of the biventricular pacing systems was possible in 8 of the 10 dogs. The QRS duration was significantly different among all pacing sites, and the order of increasing duration was RAA, BiV, LVFW, and RVA. Pacing sites did not differ with respect to fractional shortening; however, pacing from the RVA resulted in a significantly lower ejection fraction than pacing from all other sites. During RVA and LVFW pacing, LiDCO was significantly lower than that at other sites; there was no significant difference between RAA and BiV pacing with respect to LiDCO. Although the degree of dyssynchrony was significantly lower during pacing from the RAA versus other ventricular pacing sites, it was not significantly different among sites. CONCLUSIONS AND CLINICAL RELEVANCE-Ventricular activation by RAA pacing provided the best LV function and synchrony. Pacing from the RVA worsened LV function, and although pacing from the LVFW improved it, BiV pacing may provide additional improvement.

  3. Functional Importance of L- and P/Q-Type Voltage-Gated Calcium Channels in Human Renal Vasculature

    DEFF Research Database (Denmark)

    Hansen, Pernille B; Poulsen, Christian B; Walter, Steen

    2011-01-01

    in kidney function. It was hypothesized that human renal vascular excitation-contraction coupling involves different subtypes of channels. In human renal artery and dissected intrarenal blood vessels from nephrectomies, PCR analysis showed expression of L-type (Ca(v) 1.2), P/Q-type (Ca(v) 2.1), and T-type......, and L- and P/Q-type channels are of functional importance for the depolarization-induced vasoconstriction. The contribution of P/Q-type channels to contraction in the human vasculature is a novel mechanism for the regulation of renal blood flow and suggests that clinical treatment with calcium blockers......Calcium channel blockers are widely used for treatment of hypertension, because they decrease peripheral vascular resistance through inhibition of voltage-gated calcium channels. Animal studies of renal vasculature have shown expression of several types of calcium channels that are involved...

  4. Pre-implant right ventricular function might be an important predictor of the response to cardiac resynchronization therapy

    Directory of Open Access Journals (Sweden)

    Ring Margareta

    2011-10-01

    Full Text Available Abstract Objective Cardiac resynchronization therapy is proven efficacious in patients with heart failure (HF. Presence of biventricular HF is associated with a worse prognosis than having only left ventricular (LV HF and pacing might deteriorate heart function. The aim of the study was to assess a possible significance of right ventricular (RV pre-implant systolic function to predict response to CRT. Design We studied 22 HF-patients aged 72 ± 11 years, QRS-duration 155 ± 20 ms and with an LV ejection fraction (EF of 26 ± 6% before and four weeks after receiving a CRT-device. Results There were no changes in LV diameters or end systolic volume (ESV during the study. However, end diastolic volume (EDV decreased from 226 ± 71 to 211 ± 64 ml (p = 0.02 and systolic maximal velocities (SMV increased from 2.2 ± 0.4 to 2.6 ± 0.9 cm/s (p = 0.04. Pre-implant RV-SMV (6.2 ± 2.6 cm/s predicted postoperative increase in LV contractility, p = 0.032. Conclusions Pre-implant decreased RV systolic function might be an important way to predict a poor response to CRT implicating that other treatments should be considered. Furthermore we found that 3D- echocardiography and Tissue Doppler Imaging were feasible to detect short-term changes in LV function.

  5. Environmental radiological surveillance in perspective: the relative importance of environmental media as a function of effluent pathway and radionuclides

    Energy Technology Data Exchange (ETDEWEB)

    Denham, D.H.

    1977-10-01

    Most published guidelines for environmental surveillance emphasize the collection and analysis of specific media (e.g. air, water, milk, direct radiation) without total regard for the potential dose impact of the radionuclides expected in or actually present in the effluent streams from nuclear facilities. To determine the relative importance of medium/nuclide combinations in environmental surveillance, the experience at major ERDA sites and at operating nuclear power plants was reviewed. Typical release rates for nuclide groupings (tritium, noble gases, radioiodine, mixed fission or activation products, and transuranics) in those effluent streams were followed through various environmental pathways. By using this scheme the environmental medium which is most prominent in the critical dose pathway to man was determined. It was also possible to determine points of short-or long-term contaminant accumulation. Following these combination providing the relative importance of sampling specific environmental media with emphasis on the radiation dose to a critical population group. Finally, the results of these environmental pathway studies are presented in tabular form to provide ready reference for environmental surveillance program design or evaluation.

  6. Assigning Quantitative Function to Post-Translational Modifications Reveals Multiple Sites of Phosphorylation That Tune Yeast Pheromone Signaling Output

    Energy Technology Data Exchange (ETDEWEB)

    Pincus, David; Ryan, Christopher J.; Smith, Richard D.; Brent, Roger; Resnekov, Orna; Hakimi, Mohamed Ali

    2013-03-12

    Cell signaling systems transmit information by post-­translationally modifying signaling proteins, often via phosphorylation. While thousands of sites of phosphorylation have been identified in proteomic studies, the vast majority of sites have no known function. Assigning functional roles to the catalog of uncharacterized phosphorylation sites is a key research challenge. Here we present a general approach to address this challenge and apply it to a prototypical signaling pathway, the pheromone response pathway in Saccharomyces cerevisiae. The pheromone pathway includes a mitogen activated protein kinase (MAPK) cascade activated by a G-­protein coupled receptor (GPCR). We used mass spectrometry-based proteomics to identify sites whose phosphorylation changed when the system was active, and evolutionary conservation to assign priority to a list of candidate MAPK regulatory sites. We made targeted alterations in those sites, and measured the effects of the mutations on pheromone pathway output in single cells. Our work identified six new sites that quantitatively tuned system output. We developed simple computational models to find system architectures that recapitulated the quantitative phenotypes of the mutants. Our results identify a number of regulated phosphorylation events that contribute to adjust the input-­output relationship of this model eukaryotic signaling system. We believe this combined approach constitutes a general means not only to reveal modification sites required to turn a pathway on and off, but also those required for more subtle quantitative effects that tune pathway output. Our results further suggest that relatively small quantitative influences from individual regulatory phosphorylation events endow signaling systems with plasticity that evolution may exploit to quantitatively tailor signaling outcomes.

  7. The conserved WW-domain binding sites in Dystroglycan C-terminus are essential but partially redundant for Dystroglycan function

    DEFF Research Database (Denmark)

    Yatsenko, A S; Kucherenko, M M; Pantoja, M;

    2009-01-01

    BACKGROUND: Dystroglycan (Dg) is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC) which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C-terminal ......BACKGROUND: Dystroglycan (Dg) is a transmembrane protein that is a part of the Dystrophin Glycoprotein Complex (DGC) which connects the extracellular matrix to the actin cytoskeleton. The C-terminal end of Dg contains a number of putative SH3, SH2 and WW domain binding sites. The most C......-terminal PPXY motif has been established as a binding site for Dystrophin (Dys) WW-domain. However, our previous studies indicate that both Dystroglycan PPXY motives, WWbsI and WWbsII can bind Dystrophin protein in vitro. RESULTS: We now find that both WW binding sites are important for maintaining full Dg...

  8. A Random Forest Model for Predicting Allosteric and Functional Sites on Proteins.

    Science.gov (United States)

    Chen, Ava S-Y; Westwood, Nicholas J; Brear, Paul; Rogers, Graeme W; Mavridis, Lazaros; Mitchell, John B O

    2016-04-01

    We created a computational method to identify allosteric sites using a machine learning method trained and tested on protein structures containing bound ligand molecules. The Random Forest machine learning approach was adopted to build our three-way predictive model. Based on descriptors collated for each ligand and binding site, the classification model allows us to assign protein cavities as allosteric, regular or orthosteric, and hence to identify allosteric sites. 43 structural descriptors per complex were derived and were used to characterize individual protein-ligand binding sites belonging to the three classes, allosteric, regular and orthosteric. We carried out a separate validation on a further unseen set of protein structures containing the ligand 2-(N-cyclohexylamino) ethane sulfonic acid (CHES).

  9. Assessing the structural conservation of protein pockets to study functional and allosteric sites: implications for drug discovery

    Directory of Open Access Journals (Sweden)

    Daura Xavier

    2010-03-01

    Full Text Available Abstract Background With the classical, active-site oriented drug-development approach reaching its limits, protein ligand-binding sites in general and allosteric sites in particular are increasingly attracting the interest of medicinal chemists in the search for new types of targets and strategies to drug development. Given that allostery represents one of the most common and powerful means to regulate protein function, the traditional drug discovery approach of targeting active sites can be extended by targeting allosteric or regulatory protein pockets that may allow the discovery of not only novel drug-like inhibitors, but activators as well. The wealth of available protein structural data can be exploited to further increase our understanding of allosterism, which in turn may have therapeutic applications. A first step in this direction is to identify and characterize putative effector sites that may be present in already available structural data. Results We performed a large-scale study of protein cavities as potential allosteric and functional sites, by integrating publicly available information on protein sequences, structures and active sites for more than a thousand protein families. By identifying common pockets across different structures of the same protein family we developed a method to measure the pocket's structural conservation. The method was first parameterized using known active sites. We characterized the predicted pockets in terms of sequence and structural conservation, backbone flexibility and electrostatic potential. Although these different measures do not tend to correlate, their combination is useful in selecting functional and regulatory sites, as a detailed analysis of a handful of protein families shows. We finally estimated the numbers of potential allosteric or regulatory pockets that may be present in the data set, finding that pockets with putative functional and effector characteristics are widespread across

  10. Propofol Shares the Binding Site with Isoflurane and Sevoflurane on Leukocyte Function-Associated Antigen-1

    Science.gov (United States)

    Yuki, Koichi; Bu, Weiming; Xi, Jin; Shimaoka, Motomu; Eckenhoff, Roderic

    2013-01-01

    Background We previously demonstrated that propofol interacted with the leukocyte adhesion molecule leukocyte function–associated antigen-1 (LFA-1) and inhibited the production of interleukin-2 via LFA-1 in a dependent manner. However, the binding site(s) of propofol on LFA-1 remains unknown. Methods First, the inhibition of LFA-1's ligand binding by propofol was confirmed in an ELISA-type assay. The binding site of propofol on LFA-1 was probed with a photolabeling experiment using a photoactivatable propofol analog called azi-propofol-m. The adducted residues of LFA-1 by this compound were determined using liquid chromatography–mass spectrometry. In addition, the binding of propofol to the ligand-binding domain of LFA-1 was examined using 1-aminoanthracene (1-AMA) displacement assay. Furthermore, the binding site(s) of 1-AMA and propofol on LFA-1 was studied using the docking program GLIDE. Results We demonstrated that propofol impaired the binding of LFA-1 to its ligand intercellular adhesion molecule-1. The photolabeling experiment demonstrated that the adducted residues were localized in the allosteric cavity of the ligand-binding domain of LFA-1 called “lovastatin site. ” The shift of fluorescence spectra was observed when 1-AMA was coincubated with the low-affinity conformer of LFA-1 ligand-binding domain (wild-type [WT] αL I domain), not with the high-affinity conformer, suggesting that 1-AMA bound only to WT αL I domain. In the 1-AMA displacement assay, propofol decreased 1-AMA fluorescence signal (at 520 nm), suggesting that propofol competed with 1-AMA and bound to the WT αL I domain. The docking simulation demonstrated that both 1-AMA and propofol bound to the lovastatin site, which agreed with the photolabeling experiment. Conclusions We demonstrated that propofol bound to the lovastatin site in LFA-1. Previously we showed that the volatile anesthetics isoflurane and sevoflurane bound to this site. Taken together, the lovastatin site is an

  11. Energies of the adsorption of functional groups to calcium carbonate polymorphs: the importance of -OH and -COOH groups.

    Science.gov (United States)

    Okhrimenko, D V; Nissenbaum, J; Andersson, M P; Olsson, M H M; Stipp, S L S

    2013-09-01

    The adsorption behavior of calcium carbonate is an important factor in many processes in nature, industry, and biological systems. We determined and compared the adsorption energies for a series of small molecules of different sizes and polarities (i.e., water, several alcohols, and acetic acid) on three synthetic CaCO3 polymorphs (calcite, aragonite, and vaterite). We measured isosteric heats of adsorption from vapor adsorption isotherms for 273 < T < 293 K, and we used XRD and SEM to confirm that samples did not change phase during the experiments. Density functional calculations and molecular dynamics simulations complemented the experimental results and aided interpretation. Alcohols with molecular mass greater than that of methanol bind more strongly to the calcium carbonate polymorphs than water and acetic acid. The adsorption energies for the alcohols are typical of chemisorption and indicate alcohol displacement of water from calcium carbonate surfaces. This explains why organisms favor biomolecules that contain alcohol functional groups (-OH) to control which polymorph they use, the crystal face and orientation, and the particle shape and size in biomineralization processes. This new insight is also very useful in understanding organic molecule adsorption mechanisms in soils, sediments, and rocks, which is important for predicting the behavior of mineral-fluid interactions when the challenge is to remediate contaminated groundwater aquifers or to produce oil and gas from reservoirs.

  12. Experimental coccidiosis influences the expression of the ABCB1 gene, a physiological important functional marker of intestinal integrity in chickens.

    Science.gov (United States)

    Haritova, Aneliya; Koinarski, Vencislav; Stanilova, Spaska

    2013-01-01

    Efflux transporters belonging to the family of ABC transporters have an important functional role in the maintenance of the intestinal barrier. As efflux transporters they prevent the absorption of toxic substances from feed, while at the same time facilitating the excretion of metabolic waste products as well as drugs from the circulation into the intestinal lumen. As Eimeria tenella infection significantly affects the integrity of caecum, the effects of experimental E. tenella infection on the levels of expression of ABCB1 mRNAs in the intestines and livers of broilers were evaluated. ABCB1 mRNA expression was quantified by qRT-PCR. Its expression levels were significantly down-regulated in the caecum of infected animals. The levels of ABCB1 mRNA were not changed in the duodenum and the liver. After treatment of the animals with sulfapyrazine for three days, not only a significant improvement of the clinical appearance but also a normalization of the P-gp expression was noticed. Although the current study cannot distinguish between the direct effect of the drug on the host and the drug action on the parasite, these results suggest that the treatment of coccidiosis with sulfachlorpyrazine also restored the expression of the investigated efflux transporter in the caecum. This is of clinical significance as P-glycoproteins contribute to the integrity of intestines and their function as important biological barriers, protecting poultry from pathogens and toxic compounds in animal feeds.

  13. Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource.

    Science.gov (United States)

    Mann, Ishminder K; Wegrzyn, Jill L; Rajora, Om P

    2013-10-11

    EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change. We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified. We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also

  14. The first assessment of marine debris in a Site of Community Importance in the north-western Adriatic Sea (Mediterranean Sea).

    Science.gov (United States)

    Melli, Valentina; Angiolillo, Michela; Ronchi, Francesca; Canese, Simonepietro; Giovanardi, Otello; Querin, Stefano; Fortibuoni, Tomaso

    2017-01-30

    At present, few studies have investigated the marine litter abundance, composition and distribution on rocky bottoms due to sampling constraints. We surveyed by means of the ROV imaging technique a system of biogenic rocky outcrops classified as a Site of Community Importance in the Adriatic Sea. A mean density of 3.3 (±1.8) items/100m(2) was recorded, with a strong dominance of fishing- and aquaculture-related debris, accounting for 69.4% and 18.9% of the total, respectively. The abundance of litter over the rocky bottoms was significantly higher than that on soft substrates, and its spatial distribution proved to be related to hydrographic factors. Litter-fauna interactions were high, with most of the debris (65.7%) entangling or covering benthic organisms, in particular habitat constructors such as the endangered sea sponge Geodia cydonium. Unless appropriate measures are undertaken to address this problem, the abundance of marine litter in the area is likely to increase. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. A Novel Abetalipoproteinemia Missense Mutation Highlights the Importance of N-Terminal β-Barrel in Microsomal Triglyceride Transfer Protein Function

    Science.gov (United States)

    Walsh, Meghan T.; Iqbal, Jahangir; Josekutty, Joby; Soh, James; Di Leo, Enza; Özaydin, Eda; Gündüz, Mehmet; Tarugi, Patrizia; Hussain, M. Mahmood

    2015-01-01

    Background The use of microsomal triglyceride transfer protein (MTP) inhibitors is limited to severe hyperlipidemias due to associated hepatosteatosis and gastrointestinal adverse effects. Comprehensive knowledge about the structure-function of MTP might help design new molecules that avoid steatosis. Characterization of mutations in MTP causing abetalipoproteinemia have revealed that the central α-helical and C-terminal β-sheet domains are important for protein disulfide isomerase (PDI) binding and lipid transfer activity. Our aim was to identify and characterize mutations in the N-terminal domain to understand its function. Methods and Results We identified a novel missense mutation (D169V) in a 4-month old Turkish male with severe signs of ABL. To study the effect of this mutation on MTP function, we created mutants via site-directed mutagenesis. Although D169V was expressed in the endoplasmic reticulum and interacted with apoB17, it was unable to bind PDI, transfer lipids, and support apoB secretion. Computational modeling suggested that D169 could form an internal salt bridge with K187 and K189. Mutagenesis of these lysines to leucines abolished PDI heterodimerization, lipid transfer, and apoB secretion, without affecting apoB17 binding. Further, mutants with preserved charges (D169E, K187R, K189R) rescued these activities. Conclusions D169V is detrimental because it disrupts an internal salt bridge leading to loss of PDI binding and lipid transfer activities; however, it does not affect apoB-binding. Thus, the N-terminal domain of MTP is also important for its lipid transfer activity. PMID:26224785

  16. Isocitrate binding at two functionally distinct sites in yeast NAD+-specific isocitrate dehydrogenase.

    Science.gov (United States)

    Lin, An-Ping; McAlister-Henn, Lee

    2002-06-21

    Yeast NAD(+)-specific isocitrate dehydrogenase (IDH) is an octamer containing two types of homologous subunits. Ligand-binding analyses were conducted to examine effects of residue changes in putative catalytic and regulatory isocitrate-binding sites respectively contained in IDH2 and IDH1 subunits. Replacement of homologous serine residues in either subunit site, S98A in IDH2 or S92A in IDH1, was found to reduce by half the total number of holoenzyme isocitrate-binding sites, confirming a correlation between detrimental effects on isocitrate binding and respective kinetic defects in catalysis and allosteric activation by AMP. Replacement of both serine residues eliminates isocitrate binding and measurable catalytic activity. The putative isocitrate-binding sites of IDH1 and IDH2 contain five identical and four nonidentical residues. Reciprocal replacement of the four nonidentical residues in either or both subunits (A108R, F136Y, T241D, and N245D in IDH1 and/or R114A, Y142F, D248T, and D252N in IDH2) was found to be permissive for isocitrate binding. This provides further evidence for two types of binding sites in IDH, although the authentic residues have been shown to be necessary for normal kinetic contributions. Finally, the mutant enzymes with residue replacements in the IDH1 site were found to be unable to bind AMP, suggesting that allosteric activation is dependent both upon binding of isocitrate at the IDH1 site and upon the changes in the enzyme normally elicited by this binding.

  17. Functional microRNAs and target sites are created by lineage-specific transposition.

    Science.gov (United States)

    Spengler, Ryan M; Oakley, Clayton K; Davidson, Beverly L

    2014-04-01

    Transposable elements (TEs) account for nearly one-half of the sequence content in the human genome, and de novo germline transposition into regulatory or coding sequences of protein-coding genes can cause heritable disorders. TEs are prevalent in and around protein-coding genes, providing an opportunity to impart regulation. Computational studies reveal that microRNA (miRNA) genes and miRNA target sites reside within TE sequences, but there is little experimental evidence supporting a role for TEs in the birth of miRNAs, or as platform for gene regulation by miRNAs. In this work, we validate miRNAs and target sites derived from TE families prevalent in the human genome, including the ancient long interspersed nuclear element 2 (LINE2/L2), mammalian-wide interspersed repeat (MIR) retrotransposons and the primate-specific Alu family. We show that genes with 3' untranslated region (3' UTR) MIR elements are enriched for let-7 targets and that these sites are conserved and responsive to let-7 expression. We also demonstrate that 3' UTR-embedded Alus are a source of miR-24 and miR-122 target sites and that a subset of active genomic Alus provide for de novo target site creation. Finally, we report that although the creation of miRNA genes by Alu elements is relatively uncommon relative to their overall genomic abundance, Alu-derived miR-1285-1 is efficiently processed from its genomic locus and regulates genes with target sites contained within homologous elements. Taken together, our data provide additional evidence for TEs as a source for miRNAs and miRNA target sites, with instances of conservation through the course of mammalian evolution.

  18. Understanding sex differences in form and function of bird song: The importance of studying song learning processes

    Directory of Open Access Journals (Sweden)

    Katharina eRiebel

    2016-06-01

    Full Text Available Birdsong is a culturally transmitted mating signal. Due to historical and geographical biases, song (learning has been predominantly studied in the temperate zones, where female song is rare. Consequently, mechanisms and function of song learning have been almost exclusively studied in male birds and under the premise that inter- and intrasexual selection favoured larger repertoires and complex songs in males. However, female song is not rare outside the temperate zones and song in both sexes probably is the ancestral state in songbirds. Some song dimorphisms seen today might therefore be manifestations of secondary losses of female song. What selection pressures have favoured such losses and other sexual dimorphisms in song? Combined mapping of phylogenetic and ecological correlates of sex differences in song structure and function might provide important clues to the evolution of male and female song. This requires parameterization of the degree of sexual dimorphism. Simple comparison of male-female song might not provide enough resolution, because the same magnitude of difference (e.g. repertoire overlap could result from different processes: the sexes could differ in how well they learn (‘copying fidelity’ or from whom they learn (‘model selection’. Different learning mechanisms might provide important pointers towards different selection pressures. Investigating sex-specific learning could therefore help to identify the social and ecological selection pressures contributing to sex differences in adult song. The study of female song learning in particular could be crucial to our understanding of i song function in males and females and ii the evolution of sex-specific song.

  19. Syndecan-3: a cell-surface heparan sulfate proteoglycan important for chondrocyte proliferation and function during limb skeletogenesis.

    Science.gov (United States)

    Pacifici, Maurizio; Shimo, Tsuyoshi; Gentili, Chiara; Kirsch, Thorsten; Freeman, Theresa A; Enomoto-Iwamoto, Motomi; Iwamoto, Masahiro; Koyama, Eiki

    2005-01-01

    Syndecans are single-pass integral membrane components that serve as co-receptors for growth factors and cytokines and can elicit signal transduction via their cytoplasmic tails. We review here previous studies from our groups on syndecan-3 biology and function in the growth plates of developing long bones in chick and mouse embryos. Gain- and loss-of-function data indicate that syndecan-3 has important roles in restricting mitotic activity to the proliferative zone of growth plate and may do so in close cooperation and interaction with the signaling molecule Indian hedgehog (IHH). Biochemical and protein-modeling data suggest a dimeric/oligomeric syndecan-3 configuration on the chondrocyte's cell surface. Analyses of embryos misexpressing syndecan-3 or lacking IHH provide further clues on syndecan-3/IHH interdependence and interrelationships. The data and the conclusions reached provide insights into mechanisms fine-tuning chondrocyte proliferation, maturation, and function in the developing and growing skeleton and into how abnormalities in these fundamental mechanisms may subtend human congenital pathologies, including osteochondromas in hereditary multiple exostoses syndrome.

  20. SIRT1 Functions as an Important Regulator of Estrogen-Mediated Cardiomyocyte Protection in Angiotensin II-Induced Heart Hypertrophy

    Directory of Open Access Journals (Sweden)

    Tao Shen

    2014-01-01

    Full Text Available Background. Sirtuin 1 (SIRT1 is a member of the sirtuin family, which could activate cell survival machinery and has been shown to be protective in regulation of heart function. Here, we determined the mechanism by which SIRT1 regulates Angiotensin II- (AngII- induced cardiac hypertrophy and injury in vivo and in vitro. Methods. We analyzed SIRT1 expression in the hearts of control and AngII-induced mouse hypertrophy. Female C57BL/6 mice were ovariectomized and pretreated with 17β-estradiol to measure SIRT1 expression. Protein synthesis, cardiomyocyte surface area analysis, qRT-PCR, TUNEL staining, and Western blot were performed on AngII-induced mouse heart hypertrophy samples and cultured neonatal rat ventricular myocytes (NRVMs to investigate the function of SIRT1. Results. SIRT1 expression was slightly upregulated in AngII-induced mouse heart hypertrophy in vivo and in vitro, accompanied by elevated cardiomyocyte apoptosis. SIRT1 overexpression relieves AngII-induced cardiomyocyte hypertrophy and apoptosis. 17β-Estradiol was able to protect cardiomyocytes from AngII-induced injury with a profound upregulation of SIRT1 and activation of AMPK. Moreover, estrogen receptor inhibitor ICI 182,780 and SIRT1 inhibitor niacinamide could block SIRT1’s protective effect. Conclusions. These results indicate that SIRT1 functions as an important regulator of estrogen-mediated cardiomyocyte protection during AngII-induced heart hypertrophy and injury.

  1. Diverse functionalization of Aurora-A kinase at specified surface and buried sites by native chemical modification.

    Directory of Open Access Journals (Sweden)

    Fiona Rowan

    Full Text Available The ability to obtain a homogeneous sample of protein is invaluable when studying the effect of alterations such as post-translational modifications (PTMs. Selective functionalization of a protein to investigate the effect of PTMs on its structure or activity can be achieved by chemical modification of cysteine residues. We demonstrate here that one such technique, which involves conversion of cysteine to dehydroalanine followed by thiol nucleophile addition, is suitable for the site-specific installation of a wide range of chemical mimics of PTMs, including acetylated and dimethylated lysine, and other unnatural amino acids. These reactions, optimized for the clinically relevant kinase Aurora-A, readily proceed to completion as revealed by intact protein mass spectrometry. Moreover, these reactions proceed under non-denaturing conditions, which is desirable when working with large protein substrates. We have determined reactivity trends for a diverse range of thiol nucleophile addition reactions at two separate sites on Aurora-A, and we also highlight limitations when using thiol nucleophiles that contain basic functional groups. We show that chemical modification of cysteine residues is possible not only on a flexible surface-exposed loop, but also within a deep active site pocket at the conserved DFG motif, which reveals the potential use of this method in exploring enzyme function through modification of catalytic site residues.

  2. Identification of key functional residues in the active site of human {beta}1,4-galactosyltransferase 7: a major enzyme in the glycosaminoglycan synthesis pathway.

    Science.gov (United States)

    Talhaoui, Ibtissam; Bui, Catherine; Oriol, Rafael; Mulliert, Guillermo; Gulberti, Sandrine; Netter, Patrick; Coughtrie, Michael W H; Ouzzine, Mohamed; Fournel-Gigleux, Sylvie

    2010-11-26

    Glycosaminoglycans (GAGs) play a central role in many pathophysiological events, and exogenous xyloside substrates of β1,4-galactosyltransferase 7 (β4GalT7), a major enzyme of GAG biosynthesis, have interesting biomedical applications. To predict functional peptide regions important for substrate binding and activity of human β4GalT7, we conducted a phylogenetic analysis of the β1,4-galactosyltransferase family and generated a molecular model using the x-ray structure of Drosophila β4GalT7-UDP as template. Two evolutionary conserved motifs, (163)DVD(165) and (221)FWGWGREDDE(230), are central in the organization of the enzyme active site. This model was challenged by systematic engineering of point mutations, combined with in vitro and ex vivo functional assays. Investigation of the kinetic properties of purified recombinant wild-type β4GalT7 and selected mutants identified Trp(224) as a key residue governing both donor and acceptor substrate binding. Our results also suggested the involvement of the canonical carboxylate residue Asp(228) acting as general base in the reaction catalyzed by human β4GalT7. Importantly, ex vivo functional tests demonstrated that regulation of GAG synthesis is highly responsive to modification of these key active site amino acids. Interestingly, engineering mutants at position 224 allowed us to modify the affinity and to modulate the specificity of human β4GalT7 toward UDP-sugars and xyloside acceptors. Furthermore, the W224H mutant was able to sustain decorin GAG chain substitution but not GAG synthesis from exogenously added xyloside. Altogether, this study provides novel insight into human β4GalT7 active site functional domains, allowing manipulation of this enzyme critical for the regulation of GAG synthesis. A better understanding of the mechanism underlying GAG assembly paves the way toward GAG-based therapeutics.

  3. Impact of the permanent ventricular pacing site on left ventricular function in children: A retrospective multicentre survey

    NARCIS (Netherlands)

    I.E. van Geldorp (Irene); T. Delhaas (Tammo); R.A. Gebauer (Roman); P. Frias (Patrick); M. Tomaske (Maren); M.K. Friedberg (Mark); S. Tisma-Dupanovic (Svjetlana); J. Elders (Jan); A. Früh (Andreas); F. Gabbarini (Fulvio); P. Kubuš (Petr); V. Illikova (Viera); E.C. Tsao (Elisa); A.C. Blank (Andreas Christian); A. Hiippala (Anita); T. Sluysmans (Thierry); P. Karpawich (Peter); S.A. Clur (Sally-Ann); X. Ganame (Xavier); K.K. Collins (Kathryn); G.C. Dann (Greg); J.-B. Thambo (Jean-Benoît); C. Trigo (Conceição); B. Nagel (Bert); J. Papagiannis (John); A. Rackowitz (Annette); J. Marek (Josef); J.-H. Nürnberg (Jan-Hendrik); W.Y. Vanagt (Ward); F.W. Prinzen (Frits); J. Janousek (Jan)

    2011-01-01

    textabstractBackground: Chronic right ventricular (RV) pacing is associated with deleterious effects on cardiac function. Objective In an observational multicentre study in children with isolated atrioventricular (AV) block receiving chronic ventricular pacing, the importance of the ventricular paci

  4. Relative importance of modularity and other morphological attributes on different types of lithic point weapons: assessing functional variations.

    Science.gov (United States)

    González-José, Rolando; Charlin, Judith

    2012-01-01

    The specific using of different prehistoric weapons is mainly determined by its physical properties, which provide a relative advantage or disadvantage to perform a given, particular function. Since these physical properties are integrated to accomplish that function, examining design variables and their pattern of integration or modularity is of interest to estimate the past function of a point. Here we analyze a composite sample of lithic points from southern Patagonia likely formed by arrows, thrown spears and hand-held points to test if they can be viewed as a two-module system formed by the blade and the stem, and to evaluate the degree in which shape, size, asymmetry, blade: stem length ratio, and tip angle explain the observed variance and differentiation among points supposedly aimed to accomplish different functions. To do so we performed a geometric morphometric analysis on 118 lithic points, departing from 24 two-dimensional landmark and semi landmarks placed on the point's contour. Klingenberg's covariational modularity tests were used to evaluate different modularity hypotheses, and a composite PCA including shape, size, asymmetry, blade: stem length ratio, and tip angle was used to estimate the importance of each attribute to explaining variation patterns. Results show that the blade and the stem can be seen as "near decomposable units" in the points integrating the studied sample. However, this modular pattern changes after removing the effects of reduction. Indeed, a resharpened point tends to show a tip/rest of the point modular pattern. The composite PCA analyses evidenced three different patterns of morphometric attributes compatible with arrows, thrown spears, and hand-held tools. Interestingly, when analyzed independently, these groups show differences in their modular organization. Our results indicate that stone tools can be approached as flexible designs, characterized by a composite set of interacting morphometric attributes, and evolving

  5. Relative importance of modularity and other morphological attributes on different types of lithic point weapons: assessing functional variations.

    Directory of Open Access Journals (Sweden)

    Rolando González-José

    Full Text Available The specific using of different prehistoric weapons is mainly determined by its physical properties, which provide a relative advantage or disadvantage to perform a given, particular function. Since these physical properties are integrated to accomplish that function, examining design variables and their pattern of integration or modularity is of interest to estimate the past function of a point. Here we analyze a composite sample of lithic points from southern Patagonia likely formed by arrows, thrown spears and hand-held points to test if they can be viewed as a two-module system formed by the blade and the stem, and to evaluate the degree in which shape, size, asymmetry, blade: stem length ratio, and tip angle explain the observed variance and differentiation among points supposedly aimed to accomplish different functions. To do so we performed a geometric morphometric analysis on 118 lithic points, departing from 24 two-dimensional landmark and semi landmarks placed on the point's contour. Klingenberg's covariational modularity tests were used to evaluate different modularity hypotheses, and a composite PCA including shape, size, asymmetry, blade: stem length ratio, and tip angle was used to estimate the importance of each attribute to explaining variation patterns. Results show that the blade and the stem can be seen as "near decomposable units" in the points integrating the studied sample. However, this modular pattern changes after removing the effects of reduction. Indeed, a resharpened point tends to show a tip/rest of the point modular pattern. The composite PCA analyses evidenced three different patterns of morphometric attributes compatible with arrows, thrown spears, and hand-held tools. Interestingly, when analyzed independently, these groups show differences in their modular organization. Our results indicate that stone tools can be approached as flexible designs, characterized by a composite set of interacting morphometric

  6. Relative Importance of Modularity and Other Morphological Attributes on Different Types of Lithic Point Weapons: Assessing Functional Variations

    Science.gov (United States)

    González-José, Rolando; Charlin, Judith

    2012-01-01

    The specific using of different prehistoric weapons is mainly determined by its physical properties, which provide a relative advantage or disadvantage to perform a given, particular function. Since these physical properties are integrated to accomplish that function, examining design variables and their pattern of integration or modularity is of interest to estimate the past function of a point. Here we analyze a composite sample of lithic points from southern Patagonia likely formed by arrows, thrown spears and hand-held points to test if they can be viewed as a two-module system formed by the blade and the stem, and to evaluate the degree in which shape, size, asymmetry, blade: stem length ratio, and tip angle explain the observed variance and differentiation among points supposedly aimed to accomplish different functions. To do so we performed a geometric morphometric analysis on 118 lithic points, departing from 24 two-dimensional landmark and semi landmarks placed on the point's contour. Klingenberg's covariational modularity tests were used to evaluate different modularity hypotheses, and a composite PCA including shape, size, asymmetry, blade: stem length ratio, and tip angle was used to estimate the importance of each attribute to explaining variation patterns. Results show that the blade and the stem can be seen as “near decomposable units” in the points integrating the studied sample. However, this modular pattern changes after removing the effects of reduction. Indeed, a resharpened point tends to show a tip/rest of the point modular pattern. The composite PCA analyses evidenced three different patterns of morphometric attributes compatible with arrows, thrown spears, and hand-held tools. Interestingly, when analyzed independently, these groups show differences in their modular organization. Our results indicate that stone tools can be approached as flexible designs, characterized by a composite set of interacting morphometric attributes, and

  7. Cognitive and functional impairment in patients suffering from stroke: the importance of cognitive assessment for Occupational Therapy intervention

    Directory of Open Access Journals (Sweden)

    Andressa de Oliveira Ferro

    2013-12-01

    Full Text Available Abstract: Introduction: Stroke (CVA can generate motor, sensory and cognitive development deficits, affecting the individual’s performance in daily activities. Changes in any cognitive area can affect the individual’s occupational engagement. Objective: To evaluate the cognitive and functional capacity in patients suffering from stroke, showing the importance of cognitive assessment for occupational therapy intervention. Method: A comparative study with cross-sectional sampling of 44 subjects aged 30-80 years, both sexes. The subjects were divided in three groups: Adult: 11 individuals affected by stroke, 30-59 years old; Elderly: 10 individuals affected by stroke, 60-80 years old; Control: 23 normal subjects, 30-80 years old. Tests applied: MMSE, Clock Test, Test of tracks A and B, and functional capacity (BOMFAQ. Results: Cognitive changes were identified in the Adult and Elderly groups. The Adult group showed poorer performance on the Clock test (visuospatial and executive functions compared with the Control group. The Adult and Elderly groups presented worse performance in the Track A test (attention compared with the Control group. In the Track B test (visual attention, graphomotor skills, and mental flexibility, applied with absolute numbers, no significant differences were observed between the Adult and Elderly groups and the Control group, but cognitive impairment was perceived when the test was applied with categories. The Adult group showed higher prevalence of moderate/severe impairment in the carrying out of daily activities. Conclusion: As a rule, individuals suffering from stroke, in addition to having impaired functional capacity, present cognitive impairments that can negatively impact the performance of daily tasks, whether they are occupational, leisure or self-care activities. Accordingly, we observed the need to evaluate cognitive rehabilitation for better targeting and quality of life improvement.

  8. Functional link between surface low-coordination sites and the electrochemical durability of Pt nanoparticles

    Science.gov (United States)

    Chung, Dong Young; Shin, Heejong; Yoo, Ji Mun; Lee, Kug-Seung; Lee, Nam-Suk; Kang, Kisuk; Sung, Yung-Eun

    2016-12-01

    A promising strategy for achieving enhanced catalytic activity involves the use of nanoscale electrocatalysts; however, their low stability remains a major challenge. Among the various performance-degradation mechanisms, atomic dissolution is known to cause severe nanoparticle deactivation. To date, the factors influencing these catalysts' durability are not understood. Herein, we assess the role of low-coordination surface sites, focusing on the atomic dissolution of Pt nanoparticles. The density of low-coordination sites was finely controlled, and no significant size change occurred. Based on our findings, we suggest that the initial low-coordination sites trigger metal dissolution, which subsequently accelerates Pt dissolution. We believe that controlling the surface coordination number can open new routes for the design of highly durable nanoscale electrocatalysts.

  9. Simultaneous presence of both open metal sites and free functional organic sites in a noncentrosymmetric dynamic metal-organic framework with bimodal catalytic and sensing activities.

    Science.gov (United States)

    Saha, Rajat; Joarder, Biplab; Roy, Anupam Singha; Manirul Islam, Sk; Kumar, Sanjay

    2013-12-02

    Assimilation of open metal sites (OMSs) and free functional organic sites (FOSs) with a framework strut has opened up a new route for the fabrication of novel metal-organic materials, thereby providing a unique opportunity to explore their multiple functionalities. A new metal-organic framework (MOF), {[Cu(ina)2(H2O)][Cu(ina)2(bipy)]·2H2O}n (1) (ina=isonicotinate, bipy=4,4'-bipyridine), has been synthesized and characterized. Complex 1 is crystallized in the orthorhombic noncentrosymmetric space group Aba2 and consists of two different 2D coordination polymers, [Cu(ina)2(H2O)]n and [Cu(ina)2(bipy)]n, with entrapped solvent water molecules. Hydrogen-bonding interactions assemble these two different 2D coordination layers in a single-crystal structure with interdigitation of pendant 4,4'-bipy from one layer into the groove of another. Upon removal of guest molecules, 1 undergoes a structural transformation in single-crystal-to-single-crystal fashion with expansion of the effective void space. Each metal center is five-coordinated and thus can potentially behave as an OMS, and the free pyridyl groups of pendant 4,4'-bipy moieties and free -C=O groups can act as free FOSs. Thus, owing to presence of both OMSs and free FOSs, the framework exhibits multifunctional properties. Owing to the presence of OMSs, the framework can act as a Lewis acid catalyst as well as a small-molecule sensor material, and in a similar way, owing to the presence of free FOSs, it performs as a Lewis base catalyst and a cation sensor material. Furthermore, owing to noncentrosymmetry with large polarity along a particular direction, it shows strong second-harmonic generation/nonlinear optical (SHG-NLO) activity. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Expanding site productivity research to sustain non-timber forest functions

    Science.gov (United States)

    D. Andrew Scott; James A. Burger; Barbara Crane

    2006-01-01

    Southern forests produce multiple products and services including timber, wildlife habitat, species bio- and genetic divenity, water quality and control, waste remediation, recreation, and carbon sequestration. All of these benefits must be produced in a sustainable manner to meet today's societal needs without compromising future needs. A forest site is...

  11. Characterisation of the zebrafish serotonin transporter functionally links TM10 to the ligand binding site

    DEFF Research Database (Denmark)

    Severinsen, Kasper; Müller, Heidi Kaastrup; Wiborg, Ove

    2008-01-01

    and [(3)H]-escitalopram binding in transiently transfected human embryonic kidney cells; HEK-293-MSR. Residues responsible for altered affinities inhibitors were pinpointed by generating cross-species chimeras and subsequent point mutations by site directed mutagenesis. drSERT has a higher affinity...

  12. Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes

    NARCIS (Netherlands)

    Leveau, J.H.J.; Gerards, S.; Fritsche, K.; Zondag, G.; Van Veen, J.A.

    2006-01-01

    Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic D

  13. Modelling the decadal trend of ecosystem carbon fluxes demonstrates the important role of functional changes in a temperate deciduous forest

    DEFF Research Database (Denmark)

    Wu, Jian; Jansson, P.E.; van der Linden, Leon;

    2013-01-01

    Temperate forests are globally important carbon sinks and stocks. Trends in net ecosystem exchange have been observed in a Danish beech forest and this trend cannot be entirely attributed to changing climatic drivers. This study sought to clarify the mechanisms responsible for the observed trend......, the latent and sensible heat fluxes and the CO2 fluxes decreased the parameter uncertainty considerably compared to using CO2 fluxes as validation data alone. The fitted model was able to simulate the observed carbon fluxes well (R2=0.8, mean error=0.1gCm−2d−1) but did not reproduce the decadal (1997......–2009) trend in carbon uptake when global parameter estimates were used. Annual parameter estimates were able to reproduce the decadal scale trend; the yearly fitted posterior parameters (e.g. the light use efficiency) indicated a role for changes in the ecosystem functional properties. A possible role...

  14. Dimer monomer transition and dimer re-formation play important role for ATM cellular function during DNA repair.

    Science.gov (United States)

    Du, Fengxia; Zhang, Minjie; Li, Xiaohua; Yang, Caiyun; Meng, Hao; Wang, Dong; Chang, Shuang; Xu, Ye; Price, Brendan; Sun, Yingli

    2014-10-03

    The ATM protein kinase, is a serine/threonine protein kinase that is recruited and activated by DNA double-strand breaks, mediates responses to ionizing radiation in mammalian cells. Here we show that ATM is held inactive in unirradiated cells as a dimer and phosphorylates the opposite strand of the dimer in response to DNA damage. Cellular irradiation induces rapid intermolecular autophosphorylation of serine 1981 that causes dimer dissociation and initiates cellular ATM kinase activity. ATM cannot phosphorylate the substrates when it could not undergo dimer monomer transition. After DNA repair, the active monomer will undergo dephosphorylation to form dimer again and dephosphorylation is critical for dimer re-formation. Our work reveals novel function of ATM dimer monomer transition and explains why ATM dimer monomer transition plays such important role for ATM cellular activity during DNA repair.

  15. Microbial community characterization and functional gene quantification in RDX-degrading microcosms derived from sediment and groundwater at two naval sites.

    Science.gov (United States)

    Wilson, Fernanda Paes; Cupples, Alison M

    2016-08-01

    The explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has long been recognized as a problematic environmental pollutant, and efforts to remediate contaminated soils, sediments, and groundwater have been going on for decades. In recent years, much interest has focused on using bioremediation to clean up these sites. The current study investigated the microorganisms (16S rRNA genes, Illumina) and functional genes (xenA, xenB, and xplA) linked to RDX biodegradation in microcosms composed of sediment or groundwater from two Navy sites. For this, experiments included sediment samples from three depths (5 to 30 ft) from two wells located in one Navy site. In addition, the groundwater upstream and downstream of an emulsified oil biobarrier was examined from another Navy site. Further, for the groundwater experiments, the effect of glucose addition was explored. For the sediment experiments, the most enriched phylotypes during RDX degradation varied over time, by depth and well locations. However, several trends were noted, including the enrichment of Pseudomonas, Rhodococcus, Arthrobacter, and Sporolactobacillus in the sediment microcosms. For the groundwater-based experiments, Pseudomonas, unclassified Rhodocyclaceae, Sphingomonas, and Rhodococcus were also highly abundant during RDX degradation. The abundance of both xplA and xenA significantly increased during RDX degradation compared to the control microcosms for many treatments (both groundwater and sediment microcosms). In a limited number of microcosms, the copy number of the xenB gene increased. Phylotype data were correlated with functional gene data to highlight potentially important biomarkers for RDX biodegradation at these two Navy sites.

  16. Serum amyloid A: an ozone-induced circulating factor with potentially important functions in the lung-brain axis.

    Science.gov (United States)

    Erickson, Michelle A; Jude, Joseph; Zhao, Hengjiang; Rhea, Elizabeth M; Salameh, Therese S; Jester, William; Pu, Shelley; Harrowitz, Jenna; Nguyen, Ngan; Banks, William A; Panettieri, Reynold A; Jordan-Sciutto, Kelly L

    2017-09-01

    Accumulating evidence suggests that O3 exposure may contribute to CNS dysfunction. Here, we posit that inflammatory and acute-phase proteins in the circulation increase after O3 exposure and systemically convey signals of O3 exposure to the CNS. To model acute O3 exposure, female Balb/c mice were exposed to 3 ppm O3 or forced air for 2 h and were studied after 6 or 24 h. Of 23 cytokines and chemokines, only KC/CXCL1 was increased in blood 6 h after O3 exposure. The acute-phase protein serum amyloid A (A-SAA) was significantly increased by 24 h, whereas C-reactive protein was unchanged. A-SAA in blood correlated with total leukocytes, macrophages, and neutrophils in bronchoalveolar lavage from O3-exposed mice. A-SAA mRNA and protein were increased in the liver. We found that both isoforms of A-SAA completely crossed the intact blood-brain barrier, although the rate of SAA2.1 influx was approximately 5 times faster than that of SAA1.1. Finally, A-SAA protein, but not mRNA, was increased in the CNS 24 h post-O3 exposure. Our findings suggest that A-SAA is functionally linked to pulmonary inflammation in our O3 exposure model and that A-SAA could be an important systemic signal of O3 exposure to the CNS.-Erickson, M. A., Jude, J., Zhao, H., Rhea, E. M., Salameh, T. S., Jester, W., Pu, S., Harrowitz, J., Nguyen, N., Banks, W. A., Panettieri, R. A., Jr., Jordan-Sciutto, K. L. Serum amyloid A: an ozone-induced circulating factor with potentially important functions in the lung-brain axis. © FASEB.

  17. Cyclophilin A is an important mediator of platelet function by regulating integrin αIIbβ3 bidirectional signalling.

    Science.gov (United States)

    Wang, Lian; Soe, Nwe Nwe; Sowden, Mark; Xu, Yingqian; Modjeski, Kristina; Baskaran, Padmamalini; Kim, Yeonghwan; Smolock, Elaine M; Morrell, Craig N; Berk, Bradford C

    2014-05-05

    Cyclophilin A (CyPA) is an important mediator in cardiovascular diseases. It possesses peptidyl-prolyl cis-trans isomerase activity (PPIase) and chaperone functions, which regulate protein folding, intracellular trafficking and reactive oxygen species (ROS) production. Platelet glycoprotein receptor αIIbβ3 integrin activation is the common pathway for platelet activation. It was our objective to understand the mechanism by which CyPA-regulates αIIbβ3 activation in platelets. Mice deficient for CyPA (CyPA-/-) had prolonged tail bleeding time compared to wild-type (WT) controls despite equivalent platelet numbers. In vitro studies revealed that CyPA-/- platelets exhibited dramatically decreased thrombin-induced platelet aggregation. In vivo, formation of occlusive thrombi following FeCl3 injury was also significantly impaired in CyPA-/- mice compared with WT-controls. Furthermore, CyPA deficiency inhibited flow-induced thrombus formation in vitro. Flow cytometry demonstrated that thrombin-induced ROS production and αIIbβ3 activation were reduced in CyPA-/- platelets. Coimmunoprecipitation studies showed ROS-dependent increased association of CyPA and αIIbβ3. This association was dependent upon the PPIase activity of CyPA. Significantly, fibrinogen-platelet binding, platelet spreading and cytoskeleton reorganisation were also altered in CyPA-/- platelets. Moreover, CyPA deficiency prevented thrombin-induced αIIbβ3 and cytoskeleton association. In conclusion, CyPA is an important mediator in platelet function by regulation of αIIbβ3 bidirectionalsignalling through increased ROS production and facilitating interaction between αIIbβ3 and the cell cytoskeleton.

  18. Numbers of presynaptic Ca(2+) channel clusters match those of functionally defined vesicular docking sites in single central synapses.

    Science.gov (United States)

    Miki, Takafumi; Kaufmann, Walter A; Malagon, Gerardo; Gomez, Laura; Tabuchi, Katsuhiko; Watanabe, Masahiko; Shigemoto, Ryuichi; Marty, Alain

    2017-06-27

    Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such "simple synapses" indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1-10) and 2.03 at 4 wk (range: 1-4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1-8) and 2.37 at 4 wk (range: 1-5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm(2) to 0.0234 μm(2)), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels.

  19. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses

    Science.gov (United States)

    Miki, Takafumi; Kaufmann, Walter A.; Malagon, Gerardo; Gomez, Laura; Tabuchi, Katsuhiko; Watanabe, Masahiko; Shigemoto, Ryuichi; Marty, Alain

    2017-01-01

    Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. PMID:28607047

  20. The importance of object geometric properties for trajectory modeling of functional reach-to-grasp robotic therapy tasks - biomed 2009.

    Science.gov (United States)

    Nathan, Dominic; Jeutter, Dean C

    2009-01-01

    Reaching-to-grasp is essential for the performance of activities of daily living. Pathologies such as stroke, spinal cord injury, cerebral palsy, etc. limit individuals from being able to perform meaningful upper extremity movements, leading to a reduced quality of life. Robotic aided therapy is gaining prevalence as a rehabilitation tool because it can provide consistent and quantitative therapy. Such systems are dependent upon models to generate trajectories that dictate their movements. Time scaled polynomial techniques have been extensively used for robotic model development and trajectory generation. However, this approach is limited because it cannot support functional therapy tasks. This is largely due to the influence of cognitive complexity not completely considered with regards to the activity performed. We examine the influence of task cognitive complexity as manifested through the geometric properties of each object on the movement trajectories and kinematic dependent variables tasks through a motion analysis study using healthy subjects (N=8). We then compare the predicted results from several robotic trajectory models with the actual motion analysis data. Our results show that there are differences present, between the trajectory data and kinematic properties for each task, that are specific to the geometric properties of each object. In addition, the predicted results from the robotic trajectory models do not fully correlate with the actual movement information. This study is important as it will help provide some insight with regards to factors that need to be considered during the development of future robotic trajectory models and controllers for upper extremity functional rehabilitation tasks.

  1. Recombinant γT305A fibrinogen indicates severely impaired fibrin polymerization due to the aberrant function of hole 'A' and calcium binding sites.

    Science.gov (United States)

    Ikeda, Minami; Kobayashi, Tamaki; Arai, Shinpei; Mukai, Saki; Takezawa, Yuka; Terasawa, Fumiko; Okumura, Nobuo

    2014-08-01

    We examined a 6-month-old girl with inherited fibrinogen abnormality and no history of bleeding or thrombosis. Routine coagulation screening tests showed a markedly low level of plasma fibrinogen determined by functional measurement and also a low level by antigenic measurement (functional/antigenic ratio=0.295), suggesting hypodysfibrinogenemia. DNA sequence analysis was performed, and γT305A fibrinogen was synthesized in Chinese hamster ovary cells based on the results. We then functionally analyzed and compared with that of nearby recombinant γN308K fibrinogen. DNA sequence analysis revealed a heterozygous γT305A substitution (mature protein residue number). The γT305A fibrinogen indicated markedly impaired thrombin-catalyzed fibrin polymerization both in the presence or absence of 1mM calcium ion compared with that of γN308K fibrinogen. Protection of plasmin degradation in the presence of calcium ion or Gly-Pro-Arg-Pro peptide (analogue for so-called knob 'A') and factor XIIIa-catalyzed fibrinogen crosslinking demonstrated that the calcium binding sites, hole 'a' and D:D interaction sites were all markedly impaired, whereas γN308Kwas impaired at the latter two sites. Molecular modeling demonstrated that γT305 is localized at a shorter distance than γN308 from the high affinity calcium binding site and hole 'a'. Our findings suggest that γT305 might be important for construction of the overall structure of the γ module of fibrinogen. Substitution of γT305A leads to both dysfibrinogenemic and hypofibrinogenemic characterization, namely hypodysfibrinogenemia. We have already reported that recombinant γT305A fibrinogen was synthesized normally and secreted slightly, but was significantly reduced. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Prefrontal hemodynamic mapping by functional near-infrared spectroscopy in response to thermal stimulations over three body sites.

    Science.gov (United States)

    Yennu, Amarnath; Tian, Fenghua; Gatchel, Robert J; Liu, Hanli

    2016-10-01

    Functional near-infrared spectroscopy (fNIRS) was used to examine hemodynamic responses in the prefrontal cortex (PFC) during noxious thermal pain, induced by thermal stimulations over three different body sites over the right forearm, right temporomandibular joint, and left forearm. Functional NIRS measurements were obtained from three groups of healthy volunteers, one group for each body region. Each group was subjected to both low-pain stimulation (LPS) and high-pain stimulation (HPS) by a [Formula: see text] thermode of a temperature-controlled thermal stimulator over the respective three body sites. Our results showed that HPS given at three sites induced significant increases ([Formula: see text]) in oxy-hemoglobin concentration ([Formula: see text]) in the PFC with similar temporal patterns in relatively spread PFC areas. In contrast, LPS did not cause any significant [Formula: see text] in the PFC of any subject group. Our observed PFC activations induced by acute HPS were generally consistent with previous reports by fMRI studies. The study also found a peculiar global trend of postpain deactivation in the PFC, which is attributed to global vasoconstriction due to acute nocuous pain. Overall, these results indicate that hemodynamic activities in PFC exhibit consistent temporal and spatial patterns in response to acute thermal stimulation given across all three body sites.

  3. New aspects of the role of histamine in cardiovascular function: identification, characterization, and potential pathophysiological importance of H3 receptors.

    Science.gov (United States)

    Göthert, M; Garbarg, M; Hey, J A; Schlicker, E; Schwartz, J C; Levi, R

    1995-05-01

    As a result of intensive research during several decades, the distribution, function, and pathophysiological role of cardiovascular H1 and H2 receptors are well known, whereas reports on the occurrence and function of H3 receptors in blood vessels and the heart have not become available before the last 7 years (i.e., 4 years after the first description of these receptors in the central nervous system in 1983). The development of selective and potent H3 receptor agonists and antagonists was a prerequisite for convenient investigations of cardiovascular H3 receptors, which like H1 and H2 receptors are G-protein coupled but unlike them have not yet been cloned. Both in blood vessels and the heart, H3 receptors are located on noradrenergic nerve endings and upon stimulation mediate an inhibition of noradrenaline release. Whereas it remains to be clarified under which conditions the vascular H3 receptors may be stimulated by endogenous histamine, those in the heart become activated in the early phases of myocardial ischemia characterized by an increased histamine spillover. The H3 receptors in the central nervous system also appear to be of importance for the control of vascular function. Inhibitory presynaptic H3 receptors occur on trigeminal sensory C fibres supplying blood vessels in the dura mater. Release of neuropeptides from these fibres induces a neurogenic inflammation, which has been suggested to be involved in the pathogenesis of migraine. An interaction, involving presynaptic H3 receptors, between sensory C fibres and mast cells in close apposition to these fibres plays a role in the control of histamine synthesis in the dura mater.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Impaired social cognition 30 years after hemispherectomy for intractable epilepsy: the importance of the right hemisphere in complex social functioning.

    Science.gov (United States)

    Fournier, N M; Calverley, K L; Wagner, J P; Poock, J L; Crossley, M

    2008-04-01

    Clinical research with individuals following hemispherectomy typically quantifies the success of surgical outcomes by focusing primarily on the achievement of seizure control and the preservation of general brain functions, such as movement, sensation, language, and memory. In addition to these outcomes, careful study of individuals following hemispherectomy also has the potential to contribute to our understanding of functional brain asymmetries involving other complex cognitive behaviors. In this study, we report preliminary evidence for the lateralization of social perception. We administered a series of neuropsychological tests that were developed to assess emotional recognition and the formation of social inferences and advanced social cognitive judgments, as they occur in everyday situations, to two adult participants who underwent complete anatomic left- or right-sided hemispherectomy. Our results show that despite a 30-year postsurgical period of recovery and consistent and high levels of family support and social engagement, distinct cognitive profiles are still evident between our right- and left-sided participants. In particular, participant S.M., who underwent an anatomic right hemispherectomy, showed the most severe impairments in identifying negative emotional expressions and conversational exchanges involving lies and sarcasm and in "mentalizing" the intent of others. In contrast, participant J.H., who underwent an anatomic left hemispherectomy was highly skilled interpersonally, despite evident language-related limitations, and showed only mild difficulties when asked to identify emotional expressions involving disgust and anger. These results suggest that the right hemisphere plays a particularly important role in social cognitive functioning and reasoning. Further examination of the extent of social perceptual difficulties prior to and following surgical intervention for epilepsy may guide the development of effective social skills training

  5. Quantifying the importance of orbital over spin correlations in delta-Pu within density-functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Soderlind, P; Wolfer, W

    2007-07-27

    Spin and orbital and electron correlations are known to be important when treating the high-temperature {delta} phase of plutonium within the framework of density-functional theory (DFT). One of the more successful attempts to model {delta}-Pu within this approach has included condensed-matter generalizations of Hund's three rules for atoms, i.e., spin polarization, orbital polarization, and spin-orbit coupling. Here they perform a quantitative analysis of these interactions relative rank for the bonding and electronic structure in {delta}-Pu within the DFT model. The result is somewhat surprising in that spin-orbit coupling and orbital polarization are far more important than spin polarization for a realistic description of {delta}-Pu. They show that these orbital correlations on their own, without any formation of magnetic spin moments, can account for the low atomic density of the {delta} phase with a reasonable equation-of-state. In addition, this unambiguously non-magnetic (NM) treatment produces a one-electron spectra with resonances close to the Fermi level consistent with experimental valence band photoemission spectra.

  6. Structure-function studies of DNA binding domain of response regulator KdpE reveals equal affinity interactions at DNA half-sites.

    Directory of Open Access Journals (Sweden)

    Anoop Narayanan

    Full Text Available Expression of KdpFABC, a K(+ pump that restores osmotic balance, is controlled by binding of the response regulator KdpE to a specific DNA sequence (kdpFABC(BS via the winged helix-turn-helix type DNA binding domain (KdpE(DBD. Exploration of E. coli KdpE(DBD and kdpFABC(BS interaction resulted in the identification of two conserved, AT-rich 6 bp direct repeats that form half-sites. Despite binding to these half-sites, KdpE(DBD was incapable of promoting gene expression in vivo. Structure-function studies guided by our 2.5 Å X-ray structure of KdpE(DBD revealed the importance of residues R193 and R200 in the α-8 DNA recognition helix and T215 in the wing region for DNA binding. Mutation of these residues renders KdpE incapable of inducing expression of the kdpFABC operon. Detailed biophysical analysis of interactions using analytical ultracentrifugation revealed a 2∶1 stoichiometry of protein to DNA with dissociation constants of 200±100 and 350±100 nM at half-sites. Inactivation of one half-site does not influence binding at the other, indicating that KdpE(DBD binds independently to the half-sites with approximately equal affinity and no discernable cooperativity. To our knowledge, these data are the first to describe in quantitative terms the binding at half-sites under equilibrium conditions for a member of the ubiquitous OmpR/PhoB family of proteins.

  7. Random and Site-Specific Mutagenesis of the Helicobacter pylori Ferric Uptake Regulator Provides Insight into Fur Structure-Function Relationships

    Science.gov (United States)

    Gilbreath, Jeremy J.; Pich, Oscar Q.; Benoit, Stéphane L.; Besold, Angelique N.; Cha, Jeong-Heon; Maier, Robert J.; Michel, Sarah L.J.; Maynard, Ernest L.; Merrell, D. Scott

    2013-01-01

    Summary The ferric uptake regulator (Fur) of Helicobacter pylori is a global regulator that is important for colonization and survival within the gastric mucosa. H. pylori Fur is unique in its ability to activate and repress gene expression in both the iron-bound (Fe-Fur) and apo forms (apo-Fur). In the current study we combined random and site-specific mutagenesis to identify amino acid residues important for both Fe-Fur and apo-Fur function. We identified 25 mutations that affected Fe-Fur repression and 23 mutations that affected apo-Fur repression, as determined by transcriptional analyses of the Fe-Fur target gene amiE, and the apo-Fur target gene, pfr. In addition, eight of these mutations also significantly affected levels of Fur in the cell. Based on regulatory phenotypes, we selected several representative mutations to characterize further. Of those selected, we purified the wildtype (HpFurWT) and three mutant Fur proteins (HpFurE5A, HpFurA92T, and HpFurH134Y), which represent mutations in the N-terminal extension, the regulatory metal binding site (S2) and the structural metal binding site (S3), respectively. Purified proteins were evaluated for secondary structure by circular dichroism spectroscopy, iron-binding by atomic absorption spectrophotometry, oligomerization in iron-substituted and apo conditions by in vitro cross-linking assays, and DNA binding to Fe-Fur and apo-Fur target sequences by fluorescence anisotropy. The results showed that the N-terminal, S2, and S3 regions play distinct roles in terms of Fur structure-function relationships. Overall, these studies provide novel information regarding the role of these residues in Fur function, and provide mechanistic insight into how H. pylori Fur regulates gene expression in both the iron-bound and apo forms of the protein. PMID:23710935

  8. Functional importance of GGXG sequence motifs in putative reentrant loops of 2HCT and ESS transport proteins.

    Science.gov (United States)

    Dobrowolski, Adam; Lolkema, Juke S

    2009-08-11

    The 2HCT and ESS families are two families of secondary transporters. Members of the two families are unrelated in amino acid sequence but share similar hydropathy profiles, which suggest a similar folding of the proteins in membranes. Structural models show two homologous domains containing five transmembrane segments (TMSs) each, with a reentrant or pore loop between the fourth and fifth TMSs in each domain. Here we show that GGXG sequence motifs present in the putative reentrant loops are important for the activity of the transporters. Mutation of the conserved Gly residues to Cys in the motifs of the Na(+)-citrate transporter CitS in the 2HCT family and the Na(+)-glutamate transporter GltS in the ESS family resulted in strongly reduced transport activity. Similarly, mutation of the variable residue "X" to Cys in the N-terminal half of GltS essentially inactivated the transporter. The corresponding mutations in the N- and C-terminal halves of CitS reduced transport activity to 60 and 25% of that of the wild type, respectively. Residual activity of any of the mutants could be further reduced by treatment with the membrane permeable thiol reagent N-ethylmaleimide (NEM). The X to Cys mutation (S405C) in the cytoplasmic loop in the C-terminal half of CitS rendered the protein sensitive to the bulky, membrane impermeable thiol reagent 4-acetamido-4'-maleimidylstilbene-2,2'-disulfonic acid (AmdiS) added at the periplasmic side of the membrane, providing further evidence that this part of the loop is positioned between the transmembrane segments. The putative reentrant loop in the C-terminal half of the ESS family does not contain the GGXG motif, but a conserved stretch rich in Gly residues. Cysteine-scanning mutagenesis of a stretch of 18 residues in the GltS protein revealed two residues important for function. Mutant N356C was completely inactivated by treatment with NEM, and mutant P351C appeared to be the counterpart of mutant S405C of CitS; the mutant was

  9. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

    Directory of Open Access Journals (Sweden)

    Hong Jin

    Full Text Available The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  10. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures.

    Science.gov (United States)

    Jin, Hong; Stojnic, Robert; Adryan, Boris; Ozdemir, Anil; Stathopoulos, Angelike; Frasch, Manfred

    2013-01-01

    The NK homeodomain factor Tinman is a crucial regulator of early mesoderm patterning and, together with the GATA factor Pannier and the Dorsocross T-box factors, serves as one of the key cardiogenic factors during specification and differentiation of heart cells. Although the basic framework of regulatory interactions driving heart development has been worked out, only about a dozen genes involved in heart development have been designated as direct Tinman target genes to date, and detailed information about the functional architectures of their cardiac enhancers is lacking. We have used immunoprecipitation of chromatin (ChIP) from embryos at two different stages of early cardiogenesis to obtain a global overview of the sequences bound by Tinman in vivo and their linked genes. Our data from the analysis of ~50 sequences with high Tinman occupancy show that the majority of such sequences act as enhancers in various mesodermal tissues in which Tinman is active. All of the dorsal mesodermal and cardiac enhancers, but not some of the others, require tinman function. The cardiac enhancers feature diverse arrangements of binding motifs for Tinman, Pannier, and Dorsocross. By employing these cardiac and non-cardiac enhancers in machine learning approaches, we identify a novel motif, termed CEE, as a classifier for cardiac enhancers. In vivo assays for the requirement of the binding motifs of Tinman, Pannier, and Dorsocross, as well as the CEE motifs in a set of cardiac enhancers, show that the Tinman sites are essential in all but one of the tested enhancers; although on occasion they can be functionally redundant with Dorsocross sites. The enhancers differ widely with respect to their requirement for Pannier, Dorsocross, and CEE sites, which we ascribe to their different position in the regulatory circuitry, their distinct temporal and spatial activities during cardiogenesis, and functional redundancies among different factor binding sites.

  11. Mechanical Control of ATP Synthase Function: Activation Energy Difference between Tight and Loose Binding Sites

    KAUST Repository

    Beke-Somfai, Tamás

    2010-01-26

    Despite exhaustive chemical and crystal structure studies, the mechanistic details of how FoF1-ATP synthase can convert mechanical energy to chemical, producing ATP, are still not fully understood. On the basis of quantum mechanical calculations using a recent highresolution X-ray structure, we conclude that formation of the P-O bond may be achieved through a transition state (TS) with a planar PO3 - ion. Surprisingly, there is a more than 40 kJ/mol difference between barrier heights of the loose and tight binding sites of the enzyme. This indicates that even a relatively small change in active site conformation, induced by the γ-subunit rotation, may effectively block the back reaction in βTP and, thus, promote ATP. © 2009 American Chemical Society.

  12. Modeling injury rates as a function of industrialized versus on-site construction techniques.

    Science.gov (United States)

    Rubio-Romero, J C; Suárez-Cebador, M; Abad, Jesús

    2014-05-01

    It is often predicted that the industrialization of building activities will lead to a reduction of accident rates in the construction sector, particularly as a result of switching activities from building sites to factories. However, to date no scientific research has provided objective quantitative results to back up this claim. The aim of this paper is to evaluate how industrialization affects the accident rate in different industrialized building systems in Spain. Our results revealed that the industrialized steel modular system presents the lowest accident rate, while the highest accident rate was recorded in the construction method with cast-in-place concrete. The lightweight construction system also presents a high accident rate. Accordingly, industrialized building systems cannot claim to be safer than traditional ones. The different types of "on-site work" seem to be the main variable which would explain the accident rates recorded in industrialized construction systems.

  13. AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.

    Science.gov (United States)

    Uehara, Shota; Tanaka, Shigenori

    2016-11-23

    Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.

  14. An Atlas of Peroxiredoxins Created Using an Active Site Profile-Based Approach to Functionally Relevant Clustering of Proteins

    Science.gov (United States)

    Babbitt, Patricia C.; Ferrin, Thomas E.

    2017-01-01

    Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles in proliferation, differentiation, and apoptosis. Prx superfamily members are widespread across phylogeny and multiple methods have been developed to classify them. Here we present an updated atlas of the Prx superfamily identified using a novel method called MISST (Multi-level Iterative Sequence Searching Technique). MISST is an iterative search process developed to be both agglomerative, to add sequences containing similar functional site features, and divisive, to split groups when functional site features suggest distinct functionally-relevant clusters. Superfamily members need not be identified initially—MISST begins with a minimal representative set of known structures and searches GenBank iteratively. Further, the method’s novelty lies in the manner in which isofunctional groups are selected; rather than use a single or shifting threshold to identify clusters, the groups are deemed isofunctional when they pass a self-identification criterion, such that the group identifies itself and nothing else in a search of GenBank. The method was preliminarily validated on the Prxs, as the Prxs presented challenges of both agglomeration and division. For example, previous sequence analysis clustered the Prx functional families Prx1 and Prx6 into one group. Subsequent expert analysis clearly identified Prx6 as a distinct functionally relevant group. The MISST process distinguishes these two closely related, though functionally distinct, families. Through MISST search iterations, over 38,000 Prx sequences were identified, which the method divided into six isofunctional clusters, consistent with previous expert analysis. The results represent the most complete computational functional analysis of proteins comprising the Prx superfamily. The feasibility of this novel method is demonstrated

  15. Variation in stratum corneum protein content as a function of anatomical site and ethnic group.

    Science.gov (United States)

    Raj, N; Voegeli, R; Rawlings, A V; Gibbons, S; Munday, M R; Summers, B; Lane, M E

    2016-06-01

    Quantification of stratum corneum (SC) protein levels from tape strippings is frequently used to investigate skin conditions, to correct for amounts of SC protein removed in SC biomarker studies and to determine distribution of topically applied ingredients. In recent years, a rapid and convenient method for SC protein quantification from tape strippings has become available using infrared densitometry (IRD). However, standard curves have only been generated for Caucasian forearm and shoulder SC and have been assumed to be correct not only for facial SC but also for SC samples of other ethnic groups. The aim of this study was to investigate whether the use of IRD for SC protein measurement is valid for other body sites such as the cheek and for measuring SC protein content of darkly pigmented skin types. Ten Caucasian and ten Black African female subjects with self-assessed normal skin participated in the study. Tape strippings were collected from two different body sites (forearm and cheek). First from the tape strippings, the SC optical absorption was determined densitometrically. This obtained absorption (%) was compared with absolute SC protein extracted from the same tapes using a colorimetric microbicinchoninic acid (μBCA) assay. Higher amounts of SC protein were removed from the forearm compared with the cheek (P 0.05). The overall coefficient of determination (R(2) ) shows a good fit to the regression line between the two methods in both sites (forearm = 0.82, cheek = 0.77). Also, both ethnicities showed good correlation (R(2) ≥ 0.69, P = 0.01). Facial SC is morphologically distinct from the forearm, as demonstrated by the differences in amounts of SC removed. Although the data distribution in different subject groups varied, the regression was always quite similar between the two body sites and both ethnic groups. Also, the correlations were similar to previously published data on other body sites. The resultant calibration curves can be used as a rapid

  16. ATR-FTIR characterization of organic functional groups and inorganic ions in ambient aerosols at a rural site

    Science.gov (United States)

    Coury, Charity; Dillner, Ann M.

    An Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopic method was used to measure organic functional groups and inorganic ions at Tonto National Monument (TNM), an Interagency Monitoring of Protected Visual Environments (IMPROVE) sampling site in a rural area near Phoenix, Arizona. Functional groups and ions from common aerosol compound classes such as aliphatic and aromatic CH, methylene, methyl, aldehydes/ketones, carboxylic acids, ammonium sulfate and nitrate as well as functional groups from difficult to measure compound classes such as esters/lactones, acid anhydrides, carbohydrate hydroxyl and ethers, amino acids, and amines were quantified. On average, ˜33% of the PM 1.0 mass was composed of organic aerosol. The average (standard deviation) composition of the organic aerosol at TNM was 34% (6%) biogenic functional groups, 21% (5%) oxygenated functional groups, 28% (7%) aliphatic hydrocarbon functional groups (aliphatic CH, methylene and methyl) and 17% (1%) aromatic hydrocarbon functional groups. Compositional analysis, functional group correlations, and back trajectories were used to identify three types of events with source signatures: primary biogenic-influenced, urban-influenced, and regional background. The biogenic-influenced event had high concentrations of amino acids and carbohydrate hydroxyl and ether, as well as aliphatic CH and aromatic CH functional groups and qualitatively high levels of silicate. The urban-influenced events had back trajectories traveling directly from the Phoenix area and high concentrations of hydrocarbons, oxygenated functional groups, and inorganic ions. This aerosol characterization suggests that both primary emissions in Phoenix and secondary formation of aerosols from Phoenix emissions had a major impact on the aerosol composition and concentration at TNM. The regional background source had low concentrations of all functional groups, but had higher concentrations of biogenic functional

  17. Importance of congestive heart failure and interaction of congestive heart failure and left ventricular systolic function on prognosis in patients with acute myocardial infarction

    DEFF Research Database (Denmark)

    Køber, L; Torp-Pedersen, C; Pedersen, O D;

    1996-01-01

    Left ventricular (LV) systolic function and congestive heart failure (CHF) are important predictors of long-term mortality after acute myocardial infarction. The importance of transient CHF and the interaction of CHF and LV function on prognosis has not been studied in detail previously...

  18. The Importance of Medical Students' Attitudes Regarding Cognitive Competence for Teaching Applied Statistics: Multi-Site Study and Meta-Analysis

    Science.gov (United States)

    Milic, Natasa M.; Masic, Srdjan; Milin-Lazovic, Jelena; Trajkovic, Goran; Bukumiric, Zoran; Savic, Marko; Milic, Nikola V.; Cirkovic, Andja; Gajic, Milan; Kostic, Mirjana; Ilic, Aleksandra; Stanisavljevic, Dejana

    2016-01-01

    Background The scientific community increasingly is recognizing the need to bolster standards of data analysis given the widespread concern that basic mistakes in data analysis are contributing to the irreproducibility of many published research findings. The aim of this study was to investigate students’ attitudes towards statistics within a multi-site medical educational context, monitor their changes and impact on student achievement. In addition, we performed a systematic review to better support our future pedagogical decisions in teaching applied statistics to medical students. Methods A validated Serbian Survey of Attitudes Towards Statistics (SATS-36) questionnaire was administered to medical students attending obligatory introductory courses in biostatistics from three medical universities in the Western Balkans. A systematic review of peer-reviewed publications was performed through searches of Scopus, Web of Science, Science Direct, Medline, and APA databases through 1994. A meta-analysis was performed for the correlation coefficients between SATS component scores and statistics achievement. Pooled estimates were calculated using random effects models. Results SATS-36 was completed by 461 medical students. Most of the students held positive attitudes towards statistics. Ability in mathematics and grade point average were associated in a multivariate regression model with the Cognitive Competence score, after adjusting for age, gender and computer ability. The results of 90 paired data showed that Affect, Cognitive Competence, and Effort scores demonstrated significant positive changes. The Cognitive Competence score showed the largest increase (M = 0.48, SD = 0.95). The positive correlation found between the Cognitive Competence score and students’ achievement (r = 0.41; p<0.001), was also shown in the meta-analysis (r = 0.37; 95% CI 0.32–0.41). Conclusion Students' subjective attitudes regarding Cognitive Competence at the beginning of the

  19. Corn stover fractions as a function of hybrid, maturity, site and year

    Energy Technology Data Exchange (ETDEWEB)

    Lizotte, P.L. [Laval Univ., Quebec City, PQ (Canada). Dept. des sols et de genie agroalimentaire; Savoie, P. [Agriculture and Agri-Food Canada, Quebec City, PQ (Canada); Lefsrud, M. [McGill Univ., Macdonald College, Ste-Anne-de-Bellevue, PQ (Canada). Dept. of Biosystems Engineering

    2010-07-01

    Corn stover is usually left on the ground following corn harvest so that it can be incorp