Sample records for functionally relevant sites
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Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.
2017-01-01
Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422
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Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S
2017-04-01
Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
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Biological and functional relevance of CASP predictions
Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D.
2017-01-01
Abstract Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. PMID:28975675
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Biological and functional relevance of CASP predictions.
Liu, Tianyun; Ish-Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D; Altman, Russ B
2018-03-01
Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and Ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc.
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Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance.
Jann, Oliver C; Werling, Dirk; Chang, Jung-Su; Haig, David; Glass, Elizabeth J
2008-10-20
There is accumulating evidence that polymorphism in Toll-like receptor (TLR) genes might be associated with disease resistance or susceptibility traits in livestock. Polymorphic sites affecting TLR function should exhibit signatures of positive selection, identified as a high ratio of non-synonymous to synonymous nucleotide substitutions (omega). Phylogeny based models of codon substitution based on estimates of omega for each amino acid position can therefore offer a valuable tool to predict sites of functional relevance. We have used this approach to identify such polymorphic sites within the bovine TLR2 genes from ten Bos indicus and Bos taurus cattle breeds. By analysing TLR2 gene phylogeny in a set of mammalian species and a subset of ruminant species we have estimated the selective pressure on individual sites and domains and identified polymorphisms at sites of putative functional importance. The omega were highest in the mammalian TLR2 domains thought to be responsible for ligand binding and lowest in regions responsible for heterodimerisation with other TLR-related molecules. Several positively-selected sites were detected in or around ligand-binding domains. However a comparison of the ruminant subset of TLR2 sequences with the whole mammalian set of sequences revealed that there has been less selective pressure among ruminants than in mammals as a whole. This suggests that there have been functional changes during ruminant evolution. Twenty newly-discovered non-synonymous polymorphic sites were identified in cattle. Three of them were localised at positions shaped by positive selection in the ruminant dataset (Leu227Phe, His305Pro, His326Gln) and in domains involved in the recognition of ligands. His326Gln is of particular interest as it consists of an exchange of differentially-charged amino acids at a position which has previously been shown to be crucial for ligand binding in human TLR2. Within bovine TLR2, polymorphisms at amino acid positions 227, 305 and 326 map to functionally important sites of TLR2 and should be considered as candidate SNPs for immune related traits in cattle. A final proof of their functional relevance requires further studies to determine their functional effect on the immune response after stimulation with relevant ligands and/or their association with immune related traits in animals.
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RNA Editome in Rhesus Macaque Shaped by Purifying Selection
Yang, Xin-Zhuang; Tan, Bertrand Chin-Ming; Fang, Huaying; Liu, Chu-Jun; Shi, Mingming; Ye, Zhi-Qiang; Zhang, Yong E.; Deng, Minghua; Zhang, Xiuqin; Li, Chuan-Yun
2014-01-01
Understanding of the RNA editing process has been broadened considerably by the next generation sequencing technology; however, several issues regarding this regulatory step remain unresolved – the strategies to accurately delineate the editome, the mechanism by which its profile is maintained, and its evolutionary and functional relevance. Here we report an accurate and quantitative profile of the RNA editome for rhesus macaque, a close relative of human. By combining genome and transcriptome sequencing of multiple tissues from the same animal, we identified 31,250 editing sites, of which 99.8% are A-to-G transitions. We verified 96.6% of editing sites in coding regions and 97.5% of randomly selected sites in non-coding regions, as well as the corresponding levels of editing by multiple independent means, demonstrating the feasibility of our experimental paradigm. Several lines of evidence supported the notion that the adenosine deamination is associated with the macaque editome – A-to-G editing sites were flanked by sequences with the attributes of ADAR substrates, and both the sequence context and the expression profile of ADARs are relevant factors in determining the quantitative variance of RNA editing across different sites and tissue types. In support of the functional relevance of some of these editing sites, substitution valley of decreased divergence was detected around the editing site, suggesting the evolutionary constraint in maintaining some of these editing substrates with their double-stranded structure. These findings thus complement the “continuous probing” model that postulates tinkering-based origination of a small proportion of functional editing sites. In conclusion, the macaque editome reported here highlights RNA editing as a widespread functional regulation in primate evolution, and provides an informative framework for further understanding RNA editing in human. PMID:24722121
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Common Anesthetic-binding Site for Inhibition of Pentameric Ligand-gated Ion Channels.
Kinde, Monica N; Bu, Weiming; Chen, Qiang; Xu, Yan; Eckenhoff, Roderic G; Tang, Pei
2016-03-01
Identifying functionally relevant anesthetic-binding sites in pentameric ligand-gated ion channels (pLGICs) is an important step toward understanding the molecular mechanisms underlying anesthetic action. The anesthetic propofol is known to inhibit cation-conducting pLGICs, including a prokaryotic pLGIC from Erwinia chrysanthemi (ELIC), but the sites responsible for functional inhibition remain undetermined. We photolabeled ELIC with a light-activated derivative of propofol (AziPm) and performed fluorine-19 nuclear magnetic resonance experiments to support propofol binding to a transmembrane domain (TMD) intrasubunit pocket. To differentiate sites responsible for propofol inhibition from those that are functionally irrelevant, we made an ELIC-γ-aminobutyric acid receptor (GABAAR) chimera that replaced the ELIC-TMD with the α1β3GABAAR-TMD and compared functional responses of ELIC-GABAAR and ELIC with propofol modulations. Photolabeling showed multiple AziPm-binding sites in the extracellular domain (ECD) but only one site in the TMD with labeled residues M265 and F308 in the resting state of ELIC. Notably, this TMD site is an intrasubunit pocket that overlaps with binding sites for anesthetics, including propofol, found previously in other pLGICs. Fluorine-19 nuclear magnetic resonance experiments supported propofol binding to this TMD intrasubunit pocket only in the absence of agonist. Functional measurements of ELIC-GABAAR showed propofol potentiation of the agonist-elicited current instead of inhibition observed on ELIC. The distinctly different responses of ELIC and ELIC-GABAAR to propofol support the functional relevance of propofol binding to the TMD. Combining the newly identified TMD intrasubunit pocket in ELIC with equivalent TMD anesthetic sites found previously in other cationic pLGICs, we propose this TMD pocket as a common site for anesthetic inhibition of pLGICs.
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Harper, Angela F; Leuthaeuser, Janelle B; Babbitt, Patricia C; Morris, John H; Ferrin, Thomas E; Poole, Leslie B; Fetrow, Jacquelyn S
2017-02-01
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 by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences.
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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 by the Prx superfamily results, laying the foundation for potential functionally relevant clustering of the universe of protein sequences. PMID:28187133
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Text Mining Improves Prediction of Protein Functional Sites
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
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Shai, Nadav; Yifrach, Eden; van Roermund, Carlo W T; Cohen, Nir; Bibi, Chen; IJlst, Lodewijk; Cavellini, Laetitia; Meurisse, Julie; Schuster, Ramona; Zada, Lior; Mari, Muriel C; Reggiori, Fulvio M; Hughes, Adam L; Escobar-Henriques, Mafalda; Cohen, Mickael M; Waterham, Hans R; Wanders, Ronald J A; Schuldiner, Maya; Zalckvar, Einat
2018-05-02
The understanding that organelles are not floating in the cytosol, but rather held in an organized yet dynamic interplay through membrane contact sites, is altering the way we grasp cell biological phenomena. However, we still have not identified the entire repertoire of contact sites, their tethering molecules and functions. To systematically characterize contact sites and their tethering molecules here we employ a proximity detection method based on split fluorophores and discover four potential new yeast contact sites. We then focus on a little-studied yet highly disease-relevant contact, the Peroxisome-Mitochondria (PerMit) proximity, and uncover and characterize two tether proteins: Fzo1 and Pex34. We genetically expand the PerMit contact site and demonstrate a physiological function in β-oxidation of fatty acids. Our work showcases how systematic analysis of contact site machinery and functions can deepen our understanding of these structures in health and disease.
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Disrupting the brain to validate hypotheses on the neurobiology of language
Papeo, Liuba; Pascual-Leone, Alvaro; Caramazza, Alfonso
2013-01-01
Comprehension of words is an important part of the language faculty, involving the joint activity of frontal and temporo-parietal brain regions. Transcranial Magnetic Stimulation (TMS) enables the controlled perturbation of brain activity, and thus offers a unique tool to test specific predictions about the causal relationship between brain regions and language understanding. This potential has been exploited to better define the role of regions that are classically accepted as part of the language-semantic network. For instance, TMS has contributed to establish the semantic relevance of the left anterior temporal lobe, or to solve the ambiguity between the semantic vs. phonological function assigned to the left inferior frontal gyrus (LIFG). We consider, more closely, the results from studies where the same technique, similar paradigms (lexical-semantic tasks) and materials (words) have been used to assess the relevance of regions outside the classically-defined language-semantic network—i.e., precentral motor regions—for the semantic analysis of words. This research shows that different aspects of the left precentral gyrus (primary motor and premotor sites) are sensitive to the action-non action distinction of words' meanings. However, the behavioral changes due to TMS over these sites are incongruent with what is expected after perturbation of a task-relevant brain region. Thus, the relationship between motor activity and language-semantic behavior remains far from clear. A better understanding of this issue could be guaranteed by investigating functional interactions between motor sites and semantically-relevant regions. PMID:23630480
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Improved ATLAS HammerCloud Monitoring for Local Site Administration
NASA Astrophysics Data System (ADS)
Böhler, M.; Elmsheuser, J.; Hönig, F.; Legger, F.; Mancinelli, V.; Sciacca, G.
2015-12-01
Every day hundreds of tests are run on the Worldwide LHC Computing Grid for the ATLAS, and CMS experiments in order to evaluate the performance and reliability of the different computing sites. All this activity is steered, controlled, and monitored by the HammerCloud testing infrastructure. Sites with failing functionality tests are auto-excluded from the ATLAS computing grid, therefore it is essential to provide a detailed and well organized web interface for the local site administrators such that they can easily spot and promptly solve site issues. Additional functionality has been developed to extract and visualize the most relevant information. The site administrators can now be pointed easily to major site issues which lead to site blacklisting as well as possible minor issues that are usually not conspicuous enough to warrant the blacklisting of a specific site, but can still cause undesired effects such as a non-negligible job failure rate. This paper summarizes the different developments and optimizations of the HammerCloud web interface and gives an overview of typical use cases.
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ERIC Educational Resources Information Center
Giron, Maria D.; Salto, Rafael
2011-01-01
Structure-function relationship studies in proteins are essential in modern Cell Biology. Laboratory exercises that allow students to familiarize themselves with basic mutagenesis techniques are essential in all Genetic Engineering courses to teach the relevance of protein structure. We have implemented a laboratory course based on the…
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Hamid, Azzmer Azzar Abdul; Hamid, Tengku Haziyamin Tengku Abdul; Wahab, Roswanira Abdul; Huyop, Fahrul
2015-03-01
The non-stereospecific α-haloalkanoic acid dehalogenase DehE from Rhizobium sp. RC1 catalyzes the removal of the halide from α-haloalkanoic acid D,L-stereoisomers and, by doing so, converts them into hydroxyalkanoic acid L,D-stereoisomers, respectively. DehE has been extensively studied to determine its potential to act as a bioremediation agent, but its structure/function relationship has not been characterized. For this study, we explored the functional relevance of several putative active-site amino acids by site-specific mutagenesis. Ten active-site residues were mutated individually, and the dehalogenase activity of each of the 10 resulting mutants in soluble cell lysates against D- and L-2-chloropropionic acid was assessed. Interestingly, the mutants W34→A,F37→A, and S188→A had diminished activity, suggesting that these residues are functionally relevant. Notably, the D189→N mutant had no activity, which strongly implies that it is a catalytically important residue. Given our data, we propose a dehalogenation mechanism for DehE, which is the same as that suggested for other non-stereospecific α-haloalkanoic acid dehalogenases. To the best of our knowledge, this is the first report detailing a functional aspect for DehE, and our results could help pave the way for the bioengineering of haloalkanoic acid dehalogenases with improved catalytic properties. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Recreation and procreation: A critical view of sex in the human female.
Levin, Roy J
2015-04-01
This review deals critically with many aspects of the functional genital anatomy of the human female in relation to inducing sexual arousal and its relevance to procreation and recreation. Various controversial problems are discussed including: the roles of clitorally versus coitally induced arousal and orgasm in relation to the health of women, the various sites of induction of orgasm and the difficulty women find in specifically identifying them because of "'ambiguity problems" and "genital site pareidolia," the cervix and sexual arousal, why there are so many sites for arousal, why multiple orgasms occur, genital reflexes and coitus, the sites of arousal and their representation in the brain, and identifying aspects and functions of the genitalia with appropriate new nomenclature. © 2014 Wiley Periodicals, Inc.
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Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S
2015-09-01
The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
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Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S
2015-01-01
The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648
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Mowrey, David D; Liu, Qiang; Bondarenko, Vasyl; Chen, Qiang; Seyoum, Edom; Xu, Yan; Wu, Jie; Tang, Pei
2013-12-13
Nicotinic acetylcholine receptors (nAChRs) are targets of general anesthetics, but functional sensitivity to anesthetic inhibition varies dramatically among different subtypes of nAChRs. Potential causes underlying different functional responses to anesthetics remain elusive. Here we show that in contrast to the α7 nAChR, the α7β2 nAChR is highly susceptible to inhibition by the volatile anesthetic isoflurane in electrophysiology measurements. Isoflurane-binding sites in β2 and α7 were found at the extracellular and intracellular end of their respective transmembrane domains using NMR. Functional relevance of the identified β2 site was validated via point mutations and subsequent functional measurements. Consistent with their functional responses to isoflurane, β2 but not α7 showed pronounced dynamics changes, particularly for the channel gate residue Leu-249(9'). These results suggest that anesthetic binding alone is not sufficient to generate functional impact; only those sites that can modulate channel dynamics upon anesthetic binding will produce functional effects.
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Chen, Yuanyuan; Farquhar, Erik R.; Chance, Mark R.; Palczewski, Krzysztof; Kiser, Philip D.
2012-01-01
Aminopeptidases are key enzymes involved in the regulation of signaling peptide activity. Here, we present a detailed biochemical and structural analysis of an evolutionary highly conserved aspartyl aminopeptidase called DNPEP. We show that this peptidase can cleave multiple physiologically relevant substrates, including angiotensins, and thus may play a key role in regulating neuron function. Using a combination of x-ray crystallography, x-ray absorption spectroscopy, and single particle electron microscopy analysis, we provide the first detailed structural analysis of DNPEP. We show that this enzyme possesses a binuclear zinc-active site in which one of the zinc ions is readily exchangeable with other divalent cations such as manganese, which strongly stimulates the enzymatic activity of the protein. The plasticity of this metal-binding site suggests a mechanism for regulation of DNPEP activity. We also demonstrate that DNPEP assembles into a functionally relevant tetrahedral complex that restricts access of peptide substrates to the active site. These structural data allow rationalization of the enzyme's preference for short peptide substrates with N-terminal acidic residues. This study provides a structural basis for understanding the physiology and bioinorganic chemistry of DNPEP and other M18 family aminopeptidases. PMID:22356908
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van Hazel, Ilke; Dungan, Sarah Z; Hauser, Frances E; Morrow, James M; Endler, John A; Chang, Belinda S W
2016-07-01
Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates. © 2016 The Protein Society.
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Sommer, Felix; Bäckhed, Fredrik
2016-05-01
Interactions between the host and its associated microbiota differ spatially and the local cross talk determines organ function and physiology. Animals and their organs are not uniform but contain several functional and cellular compartments and gradients. In the intestinal tract, different parts of the gut carry out different functions, tissue structure varies accordingly, epithelial cells are differentially distributed and gradients exist for several physicochemical parameters such as nutrients, pH, or oxygen. Consequently, the microbiota composition also differs along the length of the gut, but also between lumen and mucosa of the same intestinal segment, and even along the crypt-villus axis in the epithelium. Thus, host-microbiota interactions are highly site-specific and the local cross talk determines intestinal function and physiology. Here we review recent advances in our understanding of site-specific host-microbiota interactions and discuss their functional relevance for host physiology. © 2016 WILEY Periodicals, Inc.
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Surface Functionalization and Targeting Strategies of Liposomes in Solid Tumor Therapy: A Review
Riaz, Muhammad Kashif; Riaz, Muhammad Adil; Zhang, Xue; Lin, Congcong; Wong, Ka Hong; Chen, Xiaoyu; Lu, Aiping
2018-01-01
Surface functionalization of liposomes can play a key role in overcoming the current limitations of nanocarriers to treat solid tumors, i.e., biological barriers and physiological factors. The phospholipid vesicles (liposomes) containing anticancer agents produce fewer side effects than non-liposomal anticancer formulations, and can effectively target the solid tumors. This article reviews information about the strategies for targeting of liposomes to solid tumors along with the possible targets in cancer cells, i.e., extracellular and intracellular targets and targets in tumor microenvironment or vasculature. Targeting ligands for functionalization of liposomes with relevant surface engineering techniques have been described. Stimuli strategies for enhanced delivery of anticancer agents at requisite location using stimuli-responsive functionalized liposomes have been discussed. Recent approaches for enhanced delivery of anticancer agents at tumor site with relevant surface functionalization techniques have been reviewed. Finally, current challenges of functionalized liposomes and future perspective of smart functionalized liposomes have been discussed. PMID:29315231
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van Hazel, Ilke; Dungan, Sarah Z.; Hauser, Frances E.; Morrow, James M.; Endler, John A.
2016-01-01
Abstract Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well‐characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein‐coupled receptors. While this substitution is present in some dim‐light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site‐directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue‐shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light‐activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure‐function as well as their evolutionary significance for dim‐light vision across vertebrates. PMID:26889650
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Riecke, B; Assaf, A T; Heiland, M; Al-Dam, A; Gröbe, A; Blessmann, M; Wikner, J
2015-08-01
A novel technique to reduce donor site morbidity after radial forearm free flap (RFFF) harvest, using a local full-thickness skin graft (FTSG), is described. Thirty consecutive patients undergoing RFFF for head and neck reconstruction were enrolled in a prospective study. Donor site defect closure was performed with spindle-shaped FTSGs excised from the wavelike skin incision made for the vascular pedicle. Both the removal site of the FTSG on the volar forearm and the covered RFFF donor site healed uneventfully in 29 cases, with no impairment of function related to the skin graft. No skin graft failure and no exposure, tenting, or adherence of the flexor tendons occurred. All patients expressed satisfaction with postoperative pain, the functional outcome, and cosmetic appearance. Primary donor site defect closure could be achieved in all cases with the use of a local FTSG. This graft can be gained at the access incision for the vascular pedicle, avoids expansion of the incision for a local flap technique, and does not prolong wound healing, and thus reduces both donor site and graft site morbidity of the RFFF. This technique leads to an inconspicuous aesthetic result with no apparent relevant functional deficits and avoids the need for a second donor site. Copyright © 2015 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.
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van Leeuwen, Marieke; Husson, Olga; Alberti, Paola; Arraras, Juan Ignacio; Chinot, Olivier L; Costantini, Anna; Darlington, Anne-Sophie; Dirven, Linda; Eichler, Martin; Hammerlid, Eva B; Holzner, Bernhard; Johnson, Colin D; Kontogianni, Meropi; Kjær, Trille Kristina; Morag, Ofir; Nolte, Sandra; Nordin, Andrew; Pace, Andrea; Pinto, Monica; Polz, Katja; Ramage, John; Reijneveld, Jaap C; Serpentini, Samantha; Tomaszewski, Krzysztof A; Vassiliou, Vassilios; Verdonck-de Leeuw, Irma M; Vistad, Ingvild; Young, Teresa E; Aaronson, Neil K; van de Poll-Franse, Lonneke V
2018-06-04
The number of cancer survivors is growing steadily and increasingly, clinical trials are being designed to include long-term follow-up to assess not only survival, but also late effects and health-related quality of life (HRQOL). Therefore it is is essential to develop patient-reported outcome measures (PROMs) that capture the full range of issues relevant to disease-free cancer survivors. The objectives of this project are: 1) to develop a European Organisation for Research and Treatment of Cancer (EORTC) questionnaire that captures the full range of physical, mental and social HRQOL issues relevant to disease-free cancer survivors; and 2) to determine at which minimal time since completion of treatment the questionnaire should be used. We reviewed 134 publications on cancer survivorship and interviewed 117 disease-free cancer survivors with 11 different types of cancer across 14 countries in Europe to generate an exhaustive, provisional list of HRQOL issues relevant to cancer survivors. The resulting issue list, the EORTC core questionnaire (QLQ-C30), and site-specific questionnaire modules were completed by a second group of 458 survivors. We identified 116 generic survivorship issues. These issues covered body image, cognitive functioning, health behaviors, negative and positive outlook, health distress, mental health, fatigue, sleep problems, physical functioning, pain, several physical symptoms, social functioning, and sexual problems. Patients rated most of the acute symptoms of cancer and its treatment (e.g. nausea) as no longer relevant approximately one year after completion of treatment. Compared to existing cancer survivorship questionnaires, our findings underscore the relevance of assessing issues related to chronic physical side effects of treatment such as neuropathy and joint pain. We will further develop a core survivorship questionnaire and three site-specific modules for disease-free adult cancer survivors who are at least one year post-treatment.
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Wells, Stephen A; van der Kamp, Marc W; McGeagh, John D; Mulholland, Adrian J
2015-01-01
Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes.
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McGeagh, John D.; Mulholland, Adrian J.
2015-01-01
Large-scale conformational change is a common feature in the catalytic cycles of enzymes. Many enzymes function as homodimers with active sites that contain elements from both chains. Symmetric and anti-symmetric cooperative motions in homodimers can potentially lead to correlated active site opening and/or closure, likely to be important for ligand binding and release. Here, we examine such motions in two different domain-swapped homodimeric enzymes: the DcpS scavenger decapping enzyme and citrate synthase. We use and compare two types of all-atom simulations: conventional molecular dynamics simulations to identify physically meaningful conformational ensembles, and rapid geometric simulations of flexible motion, biased along normal mode directions, to identify relevant motions encoded in the protein structure. The results indicate that the opening/closure motions are intrinsic features of both unliganded enzymes. In DcpS, conformational change is dominated by an anti-symmetric cooperative motion, causing one active site to close as the other opens; however a symmetric motion is also significant. In CS, we identify that both symmetric (suggested by crystallography) and asymmetric motions are features of the protein structure, and as a result the behaviour in solution is largely non-cooperative. The agreement between two modelling approaches using very different levels of theory indicates that the behaviours are indeed intrinsic to the protein structures. Geometric simulations correctly identify and explore large amplitudes of motion, while molecular dynamics simulations indicate the ranges of motion that are energetically feasible. Together, the simulation approaches are able to reveal unexpected functionally relevant motions, and highlight differences between enzymes. PMID:26241964
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Analysis of functional importance of binding sites in the Drosophila gap gene network model.
Kozlov, Konstantin; Gursky, Vitaly V; Kulakovskiy, Ivan V; Dymova, Arina; Samsonova, Maria
2015-01-01
The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.
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Lysine Ubiquitination and Acetylation of Human Cardiac 20S Proteasomes
Lau, Edward; Choi, Howard JH; Ng, Dominic CM; Meyer, David; Fang, Caiyun; Li, Haomin; Wang, Ding; Zelaya, Ivette M; Yates, John R; Lam, Maggie PY
2016-01-01
Purpose Altered proteasome functions are associated with multiple cardiomyopathies. While the proteasome targets poly-ubiquitinated proteins for destruction, it itself is modifiable by ubiquitination. We aim to identify the exact ubiquitination sites on cardiac proteasomes and examine whether they are also subject to acetylations. Experimental design Assembled cardiac 20S proteasome complexes were purified from five human hearts with ischemic cardiomyopathy, then analyzed by high-resolution MS to identify ubiquitination and acetylation sites. We developed a library search strategy that may be used to complement database search in identifying PTM in different samples. Results We identified 63 ubiquitinated lysines from intact human cardiac 20S proteasomes. In parallel, 65 acetylated residues were also discovered, 39 of which shared with ubiquitination sites. Conclusion and clinical relevance This is the most comprehensive characterization of cardiac proteasome ubiquitination to-date. There are significant overlaps between the discovered ubiquitination and acetylation sites, permitting potential crosstalk in regulating proteasome functions. The information presented here will aid future therapeutic strategies aimed at regulating the functions of cardiac proteasomes. PMID:24957502
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Binding Leverage as a Molecular Basis for Allosteric Regulation
Mitternacht, Simon; Berezovsky, Igor N.
2011-01-01
Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design. PMID:21935347
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Raguz Nakic, Zrinka; Seisenbacher, Gerhard; Posas, Francesc; Sauer, Uwe
2016-11-15
Coordinated through a complex network of kinases and phosphatases, protein phosphorylation regulates essentially all cellular processes in eukaryotes. Recent advances in proteomics enable detection of thousands of phosphorylation sites (phosphosites) in single experiments. However, functionality of the vast majority of these sites remains unclear and we lack suitable approaches to evaluate functional relevance at a pace that matches their detection. Here, we assess functionality of 26 phosphosites by introducing phosphodeletion and phosphomimic mutations in 25 metabolic enzymes and regulators from the TOR and HOG signaling pathway in Saccharomyces cerevisiae by phenotypic analysis and untargeted metabolomics. We show that metabolomics largely outperforms growth analysis and recovers 10 out of the 13 previously characterized phosphosites and suggests functionality for several novel sites, including S79 on the TOR regulatory protein Tip41. We analyze metabolic profiles to identify consequences underlying regulatory phosphorylation events and detecting glycerol metabolism to have a so far unknown influence on arginine metabolism via phosphoregulation of the glycerol dehydrogenases. Further, we also find S508 in the MAPKK Pbs2 as a potential link for cross-talking between HOG signaling and the cell wall integrity pathway. We demonstrate that metabolic profiles can be exploited for gaining insight into regulatory consequences and biological roles of phosphosites. Altogether, untargeted metabolomics is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of phosphosites.
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Garazha, Andrew; Ivanova, Alena; Suntsova, Maria; Malakhova, Galina; Roumiantsev, Sergey; Zhavoronkov, Alex; Buzdin, Anton
2015-01-01
Endogenous retroviruses (ERVs) and LTR retrotransposons (LRs) occupy ∼8% of human genome. Deep sequencing technologies provide clues to understanding of functional relevance of individual ERVs/LRs by enabling direct identification of transcription factor binding sites (TFBS) and other landmarks of functional genomic elements. Here, we performed the genome-wide identification of human ERVs/LRs containing TFBS according to the ENCODE project. We created the first interactive ERV/LRs database that groups the individual inserts according to their familial nomenclature, number of mapped TFBS and divergence from their consensus sequence. Information on any particular element can be easily extracted by the user. We also created a genome browser tool, which enables quick mapping of any ERV/LR insert according to genomic coordinates, known human genes and TFBS. These tools can be used to easily explore functionally relevant individual ERV/LRs, and for studying their impact on the regulation of human genes. Overall, we identified ∼110,000 ERV/LR genomic elements having TFBS. We propose a hypothesis of "domestication" of ERV/LR TFBS by the genome milieu including subsequent stages of initial epigenetic repression, partial functional release, and further mutation-driven reshaping of TFBS in tight coevolution with the enclosing genomic loci.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Carra,J.; McHugh, C.; Mulligan, S.
2007-01-01
We found that amide ligands can bind weakly but specifically to the ricin active site, producing significant shifts in positions of the critical active site residues Arg180 and Tyr80. These results indicate that fragment-based drug discovery methods are capable of identifying minimal bonding determinants of active-site side-chain rearrangements and the mechanistic origins of spectroscopic shifts. Our results suggest that tryptophan fluorescence provides a sensitive probe for the geometric relationship of arginine-tryptophan pairs, which often have significant roles in protein function. Using the unusual characteristics of the RTA system, we measured the still controversial thermodynamic changes of site-specific urea binding tomore » a protein, results that are relevant to understanding the physical mechanisms of protein denaturation.« less
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NASA Astrophysics Data System (ADS)
Hawley, R. J.; Vietz, G. J.; Wooten, M. S.
2016-12-01
The threshold discharge that initiates streambed mobilization (Qcritical) is one of the most mechanistically-important flows for geomorphic function and biological integrity in stream ecosystems. Increased frequency and duration of flows that exceed Qcritical are a dominant driver of geomorphic instability and excess benthic disturbance in urban/suburban streams (i.e. the urban disturbance regime). Qcritical frequency also corresponds to measures of stream integrity in reference streams, with both geomorphic stability and biological indices significantly correlated to time since a Qcritical event in one 7-y study. Indeed, reference site macroinvertebrate communities during years with atypically frequent Qcritical events were more similar to sites draining watersheds with 30% imperviousness than to reference site communities of more typical rainfall years. Despite its biophysical relevance to stream ecosystems, Qcritical is one of the most overlooked and misunderstood flows in the stormwater management and stream restoration fields. Regional stormwater policies and stream restoration design guidance are often based on the misplaced assumption that streambed erosion does not occur at sub-bankfull events (often assumed to correspond to the 1-y recurrence discharge). Using an international database of nearly 200 sites we show that Qcritical varies by several orders of magnitude as a function of streambed particle size. Qcritical in sand-dominated streams is likely to be orders of magnitude less than the 1-yr discharge, whereas Qcritical in cobble/boulder dominated streams could be much larger than the 1-yr discharge, implying that stormwater/restoration policies focused on the 1-yr event could lack efficacy in many stream settings. Qcritical is a geomorphically- and biologically-relevant discharge threshold when developing stormwater management policies intended to protect streams from excess erosion, designing watershed-scale restoration efforts to restore a more natural disturbance regime, or reconstructing stream reaches designed to restore sediment continuity. Incorporation of Qcritical into such restoration and management efforts ensures that designs are actually tailored to the mechanisms that drive channel erosion and disturbance to the benthos.
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Expansion of Protein Farnesyltransferase Specificity Using “Tunable” Active Site Interactions
Hougland, James L.; Gangopadhyay, Soumyashree A.; Fierke, Carol A.
2012-01-01
Post-translational modifications play essential roles in regulating protein structure and function. Protein farnesyltransferase (FTase) catalyzes the biologically relevant lipidation of up to several hundred cellular proteins. Site-directed mutagenesis of FTase coupled with peptide selectivity measurements demonstrates that molecular recognition is determined by a combination of multiple interactions. Targeted randomization of these interactions yields FTase variants with altered and, in some cases, bio-orthogonal selectivity. We demonstrate that FTase specificity can be “tuned” using a small number of active site contacts that play essential roles in discriminating against non-substrates in the wild-type enzyme. This tunable selectivity extends in vivo, with FTase variants enabling the creation of bioengineered parallel prenylation pathways with altered substrate selectivity within a cell. Engineered FTase variants provide a novel avenue for probing both the selectivity of prenylation pathway enzymes and the effects of prenylation pathway modifications on the cellular function of a protein. PMID:22992747
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Chakraborty, Saumen; Pallada, Stavroula; Pedersen, Jeppe T; Jancso, Attila; Correia, Joao G; Hemmingsen, Lars
2017-09-19
Metalloproteins are essential to numerous reactions in nature, and constitute approximately one-third of all known proteins. Molecular dynamics of proteins has been elucidated with great success both by experimental and theoretical methods, revealing atomic level details of function involving the organic constituents on a broad spectrum of time scales. However, the characterization of dynamics at biomolecular metal sites on nanosecond time scales is scarce in the literature. The aqua ions of many biologically relevant metal ions exhibit exchange of water molecules on the nanosecond time scale or faster, often defining their reactivity in aqueous solution, and this is presumably also a relevant time scale for the making and breaking of coordination bonds between metal ions and ligands at protein metal sites. Ligand exchange dynamics is critical for a variety of elementary steps of reactions in metallobiochemistry, for example, association and dissociation of metal bound water, association of substrate and dissociation of product in the catalytic cycle of metalloenzymes, at regulatory metal sites which require binding and dissociation of metal ions, as well as in the transport of metal ions across cell membranes or between proteins involved in metal ion homeostasis. In Perturbed Angular Correlation of γ-rays (PAC) spectroscopy, the correlation in time and space of two γ-rays emitted successively in a nuclear decay is recorded, reflecting the hyperfine interactions of the PAC probe nucleus with the surroundings. This allows for characterization of molecular and electronic structure as well as nanosecond dynamics at the PAC probe binding site. Herein, selected examples describing the application of PAC spectroscopy in probing the dynamics at protein metal sites are presented, including (1) exchange of Cd 2+ bound water in de novo designed synthetic proteins, and the effect of remote mutations on metal site dynamics; (2) dynamics at the β-lactamase active site, where the metal ion appears to jump between the two adjacent sites; (3) structural relaxation in small blue copper proteins upon 111 Ag + to 111 Cd 2+ transformation in radioactive nuclear decay; (4) metal ion transfer between two HAH1 proteins with change in coordination number; and (5) metal ion sensor proteins with two coexisting metal site structures. With this Account, we hope to make our modest contribution to the field and perhaps spur additional interest in dynamics at protein metal sites, which we consider to be severely underexplored. Relatively little is known about detailed atomic motions at metal sites, for example, how ligand exchange processes affect protein function, and how the amino acid composition of the protein may control this facet of metal site characteristics. We also aim to provide the reader with a qualitative impression of the possibilities offered by PAC spectroscopy in bioinorganic chemistry, especially when elucidating dynamics at protein metal sites, and finally present data that may serve as benchmarks on a relevant time scale for development and tests of theoretical molecular dynamics methods applied to biomolecular metal sites.
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Complement Factor B Mutations in Atypical Hemolytic Uremic Syndrome—Disease-Relevant or Benign?
Marinozzi, Maria Chiara; Vergoz, Laura; Rybkine, Tania; Ngo, Stephanie; Bettoni, Serena; Pashov, Anastas; Cayla, Mathieu; Tabarin, Fanny; Jablonski, Mathieu; Hue, Christophe; Smith, Richard J.; Noris, Marina; Halbwachs-Mecarelli, Lise; Donadelli, Roberta; Fremeaux-Bacchi, Veronique
2014-01-01
Atypical hemolytic uremic syndrome (aHUS) is a genetic ultrarare renal disease associated with overactivation of the alternative pathway of complement. Four gain-of-function mutations that form a hyperactive or deregulated C3 convertase have been identified in Factor B (FB) ligand binding sites. Here, we studied the functional consequences of 10 FB genetic changes recently identified from different aHUS cohorts. Using several tests for alternative C3 and C5 convertase formation and regulation, we identified two gain-of-function and potentially disease-relevant mutations that formed either an overactive convertase (M433I) or a convertase resistant to decay by FH (K298Q). One mutation (R178Q) produced a partially cleaved protein with no ligand binding or functional activity. Seven genetic changes led to near-normal or only slightly reduced ligand binding and functional activity compared with the most common polymorphism at position 7, R7. Notably, none of the algorithms used to predict the disease relevance of FB mutations agreed completely with the experimental data, suggesting that in silico approaches should be undertaken with caution. These data, combined with previously published results, suggest that 9 of 15 FB genetic changes identified in patients with aHUS are unrelated to disease pathogenesis. This study highlights that functional assessment of identified nucleotide changes in FB is mandatory to confirm disease association. PMID:24652797
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Barbiturates Bind in the GLIC Ion Channel Pore and Cause Inhibition by Stabilizing a Closed State*♦
Fourati, Zaineb; Ruza, Reinis Reinholds; Laverty, Duncan; Drège, Emmanuelle; Delarue-Cochin, Sandrine; Joseph, Delphine; Koehl, Patrice; Smart, Trevor; Delarue, Marc
2017-01-01
Barbiturates induce anesthesia by modulating the activity of anionic and cationic pentameric ligand-gated ion channels (pLGICs). Despite more than a century of use in clinical practice, the prototypic binding site for this class of drugs within pLGICs is yet to be described. In this study, we present the first X-ray structures of barbiturates bound to GLIC, a cationic prokaryotic pLGIC with excellent structural homology to other relevant channels sensitive to general anesthetics and, as shown here, to barbiturates, at clinically relevant concentrations. Several derivatives of barbiturates containing anomalous scatterers were synthesized, and these derivatives helped us unambiguously identify a unique barbiturate binding site within the central ion channel pore in a closed conformation. In addition, docking calculations around the observed binding site for all three states of the receptor, including a model of the desensitized state, showed that barbiturates preferentially stabilize the closed state. The identification of this pore binding site sheds light on the mechanism of barbiturate inhibition of cationic pLGICs and allows the rationalization of several structural and functional features previously observed for barbiturates. PMID:27986812
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Serrano-Hervás, Eila; Casadevall, Guillem; Garcia-Borràs, Marc; Feixas, Ferran; Osuna, Sílvia
2018-04-06
The conformational landscape of Bacillus megaterium epoxide hydrolase (BmEH) and how it is altered by mutations that confer the enzyme the ability to accept bulky epoxide substrates has been investigated. Extensive molecular dynamics (MD) simulations coupled to active site volume calculations have unveiled relevant features of the enzyme conformational dynamics and function. Our long-timescale MD simulations identify key conformational states not previously observed by means of X-ray crystallography and short MD simulations that present the loop containing one of the catalytic residues, Asp239, in a wide-open conformation, which is likely involved in the binding of the epoxide substrate. Introduction of mutations M145S and F128A dramatically alters the conformational landscape of the enzyme. These singly mutated variants can accept bulky epoxide substrates due to the disorder induced by mutation in the α-helix containing the catalytic Tyr144 and some parts of the lid domain. These changes impact the enzyme active site, which is substantially wider and more complementary to the bulky pharmacologically relevant epoxide substrates. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Pollastrini, Martina; Holland, Vera; Brüggemann, Wolfgang; Bruelheide, Helge; Dănilă, Iulian; Jaroszewicz, Bogdan; Valladares, Fernando; Bussotti, Filippo
2016-10-01
The variability of chlorophyll a fluorescence (ChlF) parameters of forest tree species was investigated in 209 stands belonging to six European forests, from Mediterranean to boreal regions. The modifying role of environmental factors, forest structure and tree diversity (species richness and composition) on ChlF signature was analysed. At the European level, conifers showed higher potential performance than broadleaf species. Forests in central Europe performed better than those in Mediterranean and boreal regions. At the site level, homogeneous clusters of tree species were identified by means of a principal component analysis (PCA) of ChlF parameters. The discrimination of the clusters of species was influenced by their taxonomic position and ecological characteristics. The species richness influenced the tree ChlF properties in different ways depending on tree species and site. Tree species and site also affected the relationships between ChlF parameters and other plant functional traits (specific leaf area, leaf nitrogen content, light-saturated photosynthesis, wood density, leaf carbon isotope composition). The assessment of the photosynthetic properties of tree species, by means of ChlF parameters, in relation to their functional traits, is a relevant issue for studies in forest ecology. The connections of data from field surveys with remotely assessed parameters must be carefully explored. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.
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Knight, Rodney R.; Murphy, Jennifer C.; Wolfe, William J.; Saylor, Charles F.; Wales, Amy K.
2014-01-01
Ecological limit functions relating streamflow and aquatic ecosystems remain elusive despite decades of research. We investigated functional relationships between species richness and changes in streamflow characteristics at 662 fish sampling sites in the Tennessee River basin. Our approach included the following: (1) a brief summary of relevant literature on functional relations between fish and streamflow, (2) the development of ecological limit functions that describe the strongest discernible relationships between fish species richness and streamflow characteristics, (3) the evaluation of proposed definitions of hydrologic reference conditions, and (4) an investigation of the internal structures of wedge-shaped distributions underlying ecological limit functions.Twenty-one ecological limit functions were developed across three ecoregions that relate the species richness of 11 fish groups and departures from hydrologic reference conditions using multivariate and quantile regression methods. Each negatively sloped function is described using up to four streamflow characteristics expressed in terms of cumulative departure from hydrologic reference conditions. Negative slopes indicate increased departure results in decreased species richness.Sites with the highest measured fish species richness generally had near-reference hydrologic conditions for a given ecoregion. Hydrology did not generally differ between sites with the highest and lowest fish species richness, indicating that other environmental factors likely limit species richness at sites with reference hydrology.Use of ecological limit functions to make decisions regarding proposed hydrologic regime changes, although commonly presented as a management tool, is not as straightforward or informative as often assumed. We contend that statistical evaluation of the internal wedge structure below limit functions may provide a probabilistic understanding of how aquatic ecology is influenced by altered hydrology and may serve as the basis for evaluating the potential effect of proposed hydrologic changes.
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The miR-29 family: genomics, cell biology, and relevance to renal and cardiovascular injury.
Kriegel, Alison J; Liu, Yong; Fang, Yi; Ding, Xiaoqiang; Liang, Mingyu
2012-02-27
The human miR-29 family of microRNAs has three mature members, miR-29a, miR-29b, and miR-29c. miR-29s are encoded by two gene clusters. Binding sites for several transcriptional factors have been identified in the promoter regions of miR-29 genes. The miR-29 family members share a common seed region sequence and are predicted to target largely overlapping sets of genes. However, the miR-29 family members exhibit differential regulation in several cases and different subcellular distribution, suggesting their functional relevance may not be identical. miR-29s directly target at least 16 extracellular matrix genes, providing a dramatic example of a single microRNA targeting a large group of functionally related genes. Strong antifibrotic effects of miR-29s have been demonstrated in heart, kidney, and other organs. miR-29s have also been shown to be proapoptotic and involved in the regulation of cell differentiation. It remains to be explored how various cellular effects of miR-29s determine functional relevance of miR-29s to specific diseases and how the miR-29 family members may function cooperatively or separately.
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Designing Hydrolytic Zinc Metalloenzymes
2015-01-01
Zinc is an essential element required for the function of more than 300 enzymes spanning all classes. Despite years of dedicated study, questions regarding the connections between primary and secondary metal ligands and protein structure and function remain unanswered, despite numerous mechanistic, structural, biochemical, and synthetic model studies. Protein design is a powerful strategy for reproducing native metal sites that may be applied to answering some of these questions and subsequently generating novel zinc enzymes. From examination of the earliest design studies introducing simple Zn(II)-binding sites into de novo and natural protein scaffolds to current studies involving the preparation of efficient hydrolytic zinc sites, it is increasingly likely that protein design will achieve reaction rates previously thought possible only for native enzymes. This Current Topic will review the design and redesign of Zn(II)-binding sites in de novo-designed proteins and native protein scaffolds toward the preparation of catalytic hydrolytic sites. After discussing the preparation of Zn(II)-binding sites in various scaffolds, we will describe relevant examples for reengineering existing zinc sites to generate new or altered catalytic activities. Then, we will describe our work on the preparation of a de novo-designed hydrolytic zinc site in detail and present comparisons to related designed zinc sites. Collectively, these studies demonstrate the significant progress being made toward building zinc metalloenzymes from the bottom up. PMID:24506795
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Girard, Eric; Marchal, Stéphane; Perez, Javier; Finet, Stéphanie; Kahn, Richard; Fourme, Roger; Marassio, Guillaume; Dhaussy, Anne-Claire; Prangé, Thierry; Giffard, Marion; Dulin, Fabienne; Bonneté, Françoise; Lange, Reinhard; Abraini, Jacques H.; Mezouar, Mohamed; Colloc'h, Nathalie
2010-01-01
Abstract Structure-function relationships in the tetrameric enzyme urate oxidase were investigated using pressure perturbation. As the active sites are located at the interfaces between monomers, enzyme activity is directly related to the integrity of the tetramer. The effect of hydrostatic pressure on the enzyme was investigated by x-ray crystallography, small-angle x-ray scattering, and fluorescence spectroscopy. Enzymatic activity was also measured under pressure and after decompression. A global model, consistent with all measurements, discloses structural and functional details of the pressure-induced dissociation of the tetramer. Before dissociating, the pressurized protein adopts a conformational substate characterized by an expansion of its substrate binding pocket at the expense of a large neighboring hydrophobic cavity. This substate should be adopted by the enzyme during its catalytic mechanism, where the active site has to accommodate larger intermediates and product. The approach, combining several high-pressure techniques, offers a new (to our knowledge) means of exploring structural and functional properties of transient states relevant to protein mechanisms. PMID:20483346
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Alam, Aftab; Johnson, Duane D.
Cerium and its technologically relevant compounds are examples of anomalous mixed valency, originating from two competing oxidation states—itinerant Ce4+ and localized Ce3+. Under applied stress, anomalous transitions are observed but not well understood. Here we treat mixed valency as an “alloy” problem involving two valences with competing and numerous site-occupancy configurations. We use density-functional theory with Hubbard U (i.e., DFT+U) to evaluate the effective valence and predict properties, including controlling the valence by pseudoternary alloying. For Ce and its compounds, such as (Ce,La)2(Fe,Co)14B permanent magnets, we find a stable mixed-valent α state near the spectroscopic value of νs=3.53. Ce valencymore » in compounds depends on its steric volume and local chemistry. For La doping, Ce valency shifts towards γ-like Ce3+, as expected from steric volume; for Co doping, valency depends on local Ce-site chemistry and steric volume. Our approach captures the key origins of anomalous valency and site-preference chemistry in complex compounds.« less
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Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution
Rao, Reshma R.; Kolb, Manuel J.; Halck, Niels Bendtsen; ...
2017-11-17
While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2O on the coordinatively unsaturated Ru sites (CUS)more » and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.« less
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Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution
DOE Office of Scientific and Technical Information (OSTI.GOV)
Rao, Reshma R.; Kolb, Manuel J.; Halck, Niels Bendtsen
While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2O on the coordinatively unsaturated Ru sites (CUS)more » and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.« less
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Cork, David M.W.; Darby, Steven; Ryan-Munden, Claudia A.; Nakjang, Sirintra; Mendes Côrtes, Leticia; Treumann, Achim; Gaughan, Luke
2017-01-01
Abstract The androgen receptor (AR) is the main driver of prostate cancer (PC) development and progression, and the primary therapeutic target in PC. To date, two functional ubiquitination sites have been identified on AR, both located in its C-terminal ligand binding domain (LBD). Recent reports highlight the emergence of AR splice variants lacking the LBD that can arise during disease progression and contribute to castrate resistance. Here, we report a novel N-terminal ubiquitination site at lysine 311. Ubiquitination of this site plays a role in AR stability and is critical for its transcriptional activity. Inactivation of this site causes AR to accumulate on chromatin and inactivates its transcriptional function as a consequence of inability to bind to p300. Additionally, mutation at lysine 311 affects cellular transcriptome altering the expression of genes involved in chromatin organization, signaling, adhesion, motility, development and metabolism. Even though this site is present in clinically relevant AR-variants it can only be ubiquitinated in cells when AR retains LBD suggesting a role for AR C-terminus in E2/E3 substrate recognition. We report that as a consequence AR variants lacking the LBD cannot be ubiquitinated in the cellular environment and their protein turnover must be regulated via an alternate pathway. PMID:27903893
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Nanaware, Padma P; Ramteke, Manoj P; Somavarapu, Arun K; Venkatraman, Prasanna
2014-07-01
Gankyrin, a non-ATPase component of the proteasome and a chaperone of proteasome assembly, is also an oncoprotein. Gankyrin regulates a variety of oncogenic signaling pathways in cancer cells and accelerates degradation of tumor suppressor proteins p53 and Rb. Therefore gankyrin may be a unique hub integrating signaling networks with the degradation pathway. To identify new interactions that may be crucial in consolidating its role as an oncogenic hub, crystal structure of gankyrin-proteasome ATPase complex was used to predict novel interacting partners. EEVD, a four amino acid linear sequence seems a hot spot site at this interface. By searching for EEVD in exposed regions of human proteins in PDB database, we predicted 34 novel interactions. Eight proteins were tested and seven of them were found to interact with gankyrin. Affinity of four interactions is high enough for endogenous detection. Others require gankyrin overexpression in HEK 293 cells or occur endogenously in breast cancer cell line- MDA-MB-435, reflecting lower affinity or presence of a deregulated network. Mutagenesis and peptide inhibition confirm that EEVD is the common hot spot site at these interfaces and therefore a potential polypharmacological drug target. In MDA-MB-231 cells in which the endogenous CLIC1 is silenced, trans-expression of Wt protein (CLIC1_EEVD) and not the hot spot site mutant (CLIC1_AAVA) resulted in significant rescue of the migratory potential. Our approach can be extended to identify novel functionally relevant protein-protein interactions, in expansion of oncogenic networks and in identifying potential therapeutic targets. © 2013 Wiley Periodicals, Inc.
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Multisite Reliability of Cognitive BOLD Data
Brown, Gregory G.; Mathalon, Daniel H.; Stern, Hal; Ford, Judith; Mueller, Bryon; Greve, Douglas N.; McCarthy, Gregory; Voyvodic, Jim; Glover, Gary; Diaz, Michele; Yetter, Elizabeth; Burak Ozyurt, I.; Jorgensen, Kasper W.; Wible, Cynthia G.; Turner, Jessica A.; Thompson, Wesley K.; Potkin, Steven G.
2010-01-01
Investigators perform multi-site functional magnetic resonance imaging studies to increase statistical power, to enhance generalizability, and to improve the likelihood of sampling relevant subgroups. Yet undesired site variation in imaging methods could off-set these potential advantages. We used variance components analysis to investigate sources of variation in the blood oxygen level dependent (BOLD) signal across four 3T magnets in voxelwise and region of interest (ROI) analyses. Eighteen participants traveled to four magnet sites to complete eight runs of a working memory task involving emotional or neutral distraction. Person variance was more than 10 times larger than site variance for five of six ROIs studied. Person-by-site interactions, however, contributed sizable unwanted variance to the total. Averaging over runs increased between-site reliability, with many voxels showing good to excellent between-site reliability when eight runs were averaged and regions of interest showing fair to good reliability. Between-site reliability depended on the specific functional contrast analyzed in addition to the number of runs averaged. Although median effect size was correlated with between-site reliability, dissociations were observed for many voxels. Brain regions where the pooled effect size was large but between-site reliability was poor were associated with reduced individual differences. Brain regions where the pooled effect size was small but between-site reliability was excellent were associated with a balance of participants who displayed consistently positive or consistently negative BOLD responses. Although between-site reliability of BOLD data can be good to excellent, acquiring highly reliable data requires robust activation paradigms, ongoing quality assurance, and careful experimental control. PMID:20932915
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Nuechterlein, Keith H.; Green, Michael F.; Calkins, Monica E.; Greenwood, Tiffany A.; Gur, Raquel E.; Gur, Ruben C.; Lazzeroni, Laura C.; Light, Gregory A.; Radant, Allen D.; Seidman, Larry J.; Siever, Larry J.; Silverman, Jeremy M.; Sprock, Joyce; Stone, William S.; Sugar, Catherine A.; Swerdlow, Neal R.; Tsuang, Debby W.; Tsuang, Ming T.; Turetsky, Bruce I.; Braff, David L.
2015-01-01
Attention/vigilance impairments are present in individuals with schizophrenia across psychotic and remitted states and in their first-degree relatives. An important question is whether deficits in attention/vigilance can be consistently and reliably measured across sites varying in many participant demographic, clinical, and functional characteristics, as needed for large-scale genetic studies of endophenotypes. We examined Continuous Performance Test (CPT) data from Phase 2 of the Consortium on the Genetics of Schizophrenia (COGS-2), the largest-scale assessment of cognitive and psychophysiological endophenotypes relevant to schizophrenia. CPT data from 2251 participants from five sites were examined. A perceptual-load vigilance task (the Degraded Stimulus CPT or DS-CPT) and a memory-load vigilance task (CPT - Identical Pairs or CPT-IP) were utilized. Schizophrenia patients performed more poorly than healthy comparison subjects (HCS) across sites, despite significant site differences in participant age, sex, education, and racial distribution. Patient-HCS differences in signal/noise discrimination (d’) in the DS-CPT varied significantly across sites, but averaged a medium effect size. CPT-IP performance showed large patient-HCS differences across sites. Poor CPT performance was independent of or weakly correlated with symptom severity, but was significantly associated with lower educational achievement and functional capacity. Current smoking was associated with poorer CPT-IP d’. Patients taking both atypical and typical antipsychotic medication performed more poorly than those on no or atypical antipsychotic medications, likely reflecting their greater severity of illness. We conclude that CPT deficits in schizophrenia can be reliably detected across sites, are relatively independent of current symptom severity, and are related to functional capacity. PMID:25749017
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Nuechterlein, Keith H; Green, Michael F; Calkins, Monica E; Greenwood, Tiffany A; Gur, Raquel E; Gur, Ruben C; Lazzeroni, Laura C; Light, Gregory A; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Sprock, Joyce; Stone, William S; Sugar, Catherine A; Swerdlow, Neal R; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L
2015-04-01
Attention/vigilance impairments are present in individuals with schizophrenia across psychotic and remitted states and in their first-degree relatives. An important question is whether deficits in attention/vigilance can be consistently and reliably measured across sites varying in many participant demographic, clinical, and functional characteristics, as needed for large-scale genetic studies of endophenotypes. We examined Continuous Performance Test (CPT) data from phase 2 of the Consortium on the Genetics of Schizophrenia (COGS-2), the largest-scale assessment of cognitive and psychophysiological endophenotypes relevant to schizophrenia. The CPT data from 2251 participants from five sites were examined. A perceptual-load vigilance task (the Degraded Stimulus CPT or DS-CPT) and a memory-load vigilance task (CPT-Identical Pairs or CPT-IP) were utilized. Schizophrenia patients performed more poorly than healthy comparison subjects (HCS) across sites, despite significant site differences in participant age, sex, education, and racial distribution. Patient-HCS differences in signal/noise discrimination (d') in the DS-CPT varied significantly across sites, but averaged a medium effect size. CPT-IP performance showed large patient-HCS differences across sites. Poor CPT performance was independent of or weakly correlated with symptom severity, but was significantly associated with lower educational achievement and functional capacity. Current smoking was associated with poorer CPT-IP d'. Patients taking both atypical and typical antipsychotic medication performed more poorly than those on no or atypical antipsychotic medications, likely reflecting their greater severity of illness. We conclude that CPT deficits in schizophrenia can be reliably detected across sites, are relatively independent of current symptom severity, and are related to functional capacity. Copyright © 2015 Elsevier B.V. All rights reserved.
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SpliceRover: Interpretable Convolutional Neural: Networks for Improved Splice Site Prediction.
Zuallaert, Jasper; Godin, Fréderic; Kim, Mijung; Soete, Arne; Saeys, Yvan; De Neve, Wesley
2018-06-21
During the last decade, improvements in high-throughput sequencing have generated a wealth of genomic data. Functionally interpreting these sequences and finding the biological signals that are hallmarks of gene function and regulation is currently mostly done using automated genome annotation platforms, which mainly rely on integrated machine learning frameworks to identify different functional sites of interest, including splice sites. Splicing is an essential step in the gene regulation process, and the correct identification of splice sites is a major cornerstone in a genome annotation system. In this paper, we present SpliceRover, a predictive deep learning approach that outperforms the state-of-the-art in splice site prediction. SpliceRover uses convolutional neural networks (CNNs), which have been shown to obtain cutting edge performance on a wide variety of prediction tasks. We adapted this approach to deal with genomic sequence inputs, and show it consistently outperforms already existing approaches, with relative improvements in prediction effectiveness of up to 80.9% when measured in terms of false discovery rate. However, a major criticism of CNNs concerns their "black box" nature, as mechanisms to obtain insight into their reasoning processes are limited. To facilitate interpretability of the SpliceRover models, we introduce an approach to visualize the biologically relevant information learnt. We show that our visualization approach is able to recover features known to be important for splice site prediction (binding motifs around the splice site, presence of polypyrimidine tracts and branch points), as well as reveal new features (e.g., several types of exclusion patterns near splice sites). SpliceRover is available as a web service. The prediction tool and instructions can be found at http://bioit2.irc.ugent.be/splicerover/. Supplementary materials are available at Bioinformatics online.
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Pérez-Izquierdo, Leticia; Zabal-Aguirre, Mario; Flores-Rentería, Dulce; González-Martínez, Santiago C; Buée, Marc; Rincón, Ana
2017-04-01
Fungi provide relevant ecosystem services contributing to primary productivity and the cycling of nutrients in forests. These fungal inputs can be decisive for the resilience of Mediterranean forests under global change scenarios, making necessary an in-deep knowledge about how fungal communities operate in these ecosystems. By using high-throughput sequencing and enzymatic approaches, we studied the fungal communities associated with three genotypic variants of Pinus pinaster trees, in 45-year-old common garden plantations. We aimed to determine the impact of biotic (i.e., tree genotype) and abiotic (i.e., season, site) factors on the fungal community structure, and to explore whether structural shifts triggered functional responses affecting relevant ecosystem processes. Tree genotype and spatial-temporal factors were pivotal structuring fungal communities, mainly by influencing their assemblage and selecting certain fungi. Diversity variations of total fungal community and of that of specific fungal guilds, together with edaphic properties and tree's productivity, explained relevant ecosystem services such as processes involved in carbon turnover and phosphorous mobilization. A mechanistic model integrating relations of these variables and ecosystem functional outcomes is provided. Our results highlight the importance of structural shifts in fungal communities because they may have functional consequences for key ecosystem processes in Mediterranean forests. © 2017 Society for Applied Microbiology and John Wiley and Sons Ltd.
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The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics
DOE Office of Scientific and Technical Information (OSTI.GOV)
Auerbach, Tamar; Mermershtain, Inbal; Davidovich, Chen
2010-04-26
Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by Streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. Biochemical and functional studies verified this finding and showed interference with peptide bond formation. Chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. These two antibiotics can bind to the ribosome simultaneously and display synergy in inhibiting bacterial growth. The binding site of lankacidin and lankamycin partially overlap with the binding site of another pair of synergistic antibiotics, themore » streptogramins. Thus, at least two pairs of structurally dissimilar compounds have been selected in the course of evolution to act synergistically by targeting neighboring sites in the ribosome. These results underscore the importance of the corresponding ribosomal sites for development of clinically relevant synergistic antibiotics and demonstrate the utility of structural analysis for providing new directions for drug discovery.« less
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Garrido-Martín, Diego; Pazos, Florencio
2018-02-27
The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. These results are informative for the methods' developers and final users, and may have implications in the design of new sequencing initiatives.
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PRISM offers a comprehensive genomic approach to transcription factor function prediction
Wenger, Aaron M.; Clarke, Shoa L.; Guturu, Harendra; Chen, Jenny; Schaar, Bruce T.; McLean, Cory Y.; Bejerano, Gill
2013-01-01
The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells. PMID:23382538
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Doucet, Nicolas
2011-04-01
Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.
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In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases
Li, Mingai; Xu, Jia; Algarra Alarcon, Alberto; Carlin, Silvia; Barbaro, Enrico; Cappellin, Luca; Velikova, Violeta; Vrhovsek, Urska; Loreto, Francesco; Varotto, Claudio
2017-01-01
Abstract Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance. PMID:28637270
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An alternate binding site for PPARγ ligands
Hughes, Travis S.; Giri, Pankaj Kumar; de Vera, Ian Mitchelle S.; Marciano, David P.; Kuruvilla, Dana S.; Shin, Youseung; Blayo, Anne-Laure; Kamenecka, Theodore M.; Burris, Thomas P.; Griffin, Patrick R.; Kojetin, Douglas J.
2014-01-01
PPARγ is a target for insulin sensitizing drugs such as glitazones, which improve plasma glucose maintenance in patients with diabetes. Synthetic ligands have been designed to mimic endogenous ligand binding to a canonical ligand-binding pocket to hyperactivate PPARγ. Here we reveal that synthetic PPARγ ligands also bind to an alternate site, leading to unique receptor conformational changes that impact coregulator binding, transactivation and target gene expression. Using structure-function studies we show that alternate site binding occurs at pharmacologically relevant ligand concentrations, and is neither blocked by covalently bound synthetic antagonists nor by endogenous ligands indicating non-overlapping binding with the canonical pocket. Alternate site binding likely contributes to PPARγ hyperactivation in vivo, perhaps explaining why PPARγ full and partial or weak agonists display similar adverse effects. These findings expand our understanding of PPARγ activation by ligands and suggest that allosteric modulators could be designed to fine tune PPARγ activity without competing with endogenous ligands. PMID:24705063
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Evidence and Function Relevance of Native DOR-MOR Heteromers.
Cahill, Catherine M; Ong, Edmund
2018-04-10
Opioid receptors are the sites of action for morphine and most other clinically used opioid drugs. Abundant evidence now demonstrates that different opioid receptor types can physically associate to form heteromers. Owing to their constituent monomers' involvement in analgesia, mu/delta opioid receptor (M/DOR) heteromers have been a particular focus of attention. Understandings of the physiological relevance and indisputable proof of M/DOR formation in vivo are still evolving. This aspect of the field has been slow to progress in large part by the limitations of most available experimental models; recently however, promising progress is being made. As a result, the long-repeated promise of opioid receptor heteromers as selective therapeutic targets is now being realized.
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2010-01-01
Background Comparative genomics methods such as phylogenetic profiling can mine powerful inferences from inherently noisy biological data sets. We introduce Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL), a method that applies the Partial Phylogenetic Profiling (PPP) approach locally within a protein sequence to discover short sequence signatures associated with functional sites. The approach is based on the basic scoring mechanism employed by PPP, namely the use of binomial distribution statistics to optimize sequence similarity cutoffs during searches of partitioned training sets. Results Here we illustrate and validate the ability of the SIMBAL method to find functionally relevant short sequence signatures by application to two well-characterized protein families. In the first example, we partitioned a family of ABC permeases using a metabolic background property (urea utilization). Thus, the TRUE set for this family comprised members whose genome of origin encoded a urea utilization system. By moving a sliding window across the sequence of a permease, and searching each subsequence in turn against the full set of partitioned proteins, the method found which local sequence signatures best correlated with the urea utilization trait. Mapping of SIMBAL "hot spots" onto crystal structures of homologous permeases reveals that the significant sites are gating determinants on the cytosolic face rather than, say, docking sites for the substrate-binding protein on the extracellular face. In the second example, we partitioned a protein methyltransferase family using gene proximity as a criterion. In this case, the TRUE set comprised those methyltransferases encoded near the gene for the substrate RF-1. SIMBAL identifies sequence regions that map onto the substrate-binding interface while ignoring regions involved in the methyltransferase reaction mechanism in general. Neither method for training set construction requires any prior experimental characterization. Conclusions SIMBAL shows that, in functionally divergent protein families, selected short sequences often significantly outperform their full-length parent sequence for making functional predictions by sequence similarity, suggesting avenues for improved functional classifiers. When combined with structural data, SIMBAL affords the ability to localize and model functional sites. PMID:20102603
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Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores.
Gómez-Sánchez, Rubén; Rose, Jaqueline; Guimarães, Rodrigo; Mari, Muriel; Papinski, Daniel; Rieter, Ester; Geerts, Willie J; Hardenberg, Ralph; Kraft, Claudine; Ungermann, Christian; Reggiori, Fulvio
2018-05-30
The autophagy-related (Atg) proteins play a key role in the formation of autophagosomes, the hallmark of autophagy. The function of the cluster composed by Atg2, Atg18, and transmembrane Atg9 is completely unknown despite their importance in autophagy. In this study, we provide insights into the molecular role of these proteins by identifying and characterizing Atg2 point mutants impaired in Atg9 binding. We show that Atg2 associates to autophagosomal membranes through lipid binding and independently from Atg9. Its interaction with Atg9, however, is key for Atg2 confinement to the growing phagophore extremities and subsequent association of Atg18. Assembly of the Atg9-Atg2-Atg18 complex is important to establish phagophore-endoplasmic reticulum (ER) contact sites. In turn, disruption of the Atg2-Atg9 interaction leads to an aberrant topological distribution of both Atg2 and ER contact sites on forming phagophores, which severely impairs autophagy. Altogether, our data shed light in the interrelationship between Atg9, Atg2, and Atg18 and highlight the possible functional relevance of the phagophore-ER contact sites in phagophore expansion. © 2018 Gómez-Sánchez et al.
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A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome*
Tatham, Michael H.; Cole, Christian; Scullion, Paul; Wilkie, Ross; Westwood, Nicholas J.; Stark, Lesley A.; Hay, Ronald T.
2017-01-01
Aspirin, or acetylsalicylic acid is widely used to control pain, inflammation and fever. Important to this function is its ability to irreversibly acetylate cyclooxygenases at active site serines. Aspirin has the potential to acetylate other amino acid side-chains, leading to the possibility that aspirin-mediated lysine acetylation could explain some of its as-yet unexplained drug actions or side-effects. Using isotopically labeled aspirin-d3, in combination with acetylated lysine purification and LC-MS/MS, we identified over 12000 sites of lysine acetylation from cultured human cells. Although aspirin amplifies endogenous acetylation signals at the majority of detectable endogenous sites, cells tolerate aspirin mediated acetylation very well unless cellular deacetylases are inhibited. Although most endogenous acetylations are amplified by orders of magnitude, lysine acetylation site occupancies remain very low even after high doses of aspirin. This work shows that while aspirin has enormous potential to alter protein function, in the majority of cases aspirin-mediated acetylations do not accumulate to levels likely to elicit biological effects. These findings are consistent with an emerging model for cellular acetylation whereby stoichiometry correlates with biological relevance, and deacetylases act to minimize the biological consequences of nonspecific chemical acetylations. PMID:27913581
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On-Site Inspection RadioIsotopic Spectroscopy (Osiris) System Development
DOE Office of Scientific and Technical Information (OSTI.GOV)
Caffrey, Gus J.; Egger, Ann E.; Krebs, Kenneth M.
2015-09-01
We have designed and tested hardware and software for the acquisition and analysis of high-resolution gamma-ray spectra during on-site inspections under the Comprehensive Nuclear-Test-Ban Treaty (CTBT). The On-Site Inspection RadioIsotopic Spectroscopy—Osiris—software filters the spectral data to display only radioisotopic information relevant to CTBT on-site inspections, e.g.,132I. A set of over 100 fission-product spectra was employed for Osiris testing. These spectra were measured, where possible, or generated by modeling. The synthetic test spectral compositions include non-nuclear-explosion scenarios, e.g., a severe nuclear reactor accident, and nuclear-explosion scenarios such as a vented underground nuclear test. Comparing its computer-based analyses to expert visual analysesmore » of the test spectra, Osiris correctly identifies CTBT-relevant fission product isotopes at the 95% level or better.The Osiris gamma-ray spectrometer is a mechanically-cooled, battery-powered ORTEC Transpec-100, chosen to avoid the need for liquid nitrogen during on-site inspections. The spectrometer was used successfully during the recent 2014 CTBT Integrated Field Exercise in Jordan. The spectrometer is controlled and the spectral data analyzed by a Panasonic Toughbook notebook computer. To date, software development has been the main focus of the Osiris project. In FY2016-17, we plan to modify the Osiris hardware, integrate the Osiris software and hardware, and conduct rigorous field tests to ensure that the Osiris system will function correctly during CTBT on-site inspections. The planned development will raise Osiris to technology readiness level TRL-8; transfer the Osiris technology to a commercial manufacturer, and demonstrate Osiris to potential CTBT on-site inspectors.« less
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Pescador, David S.; de Bello, Francesco; Valladares, Fernando; Escudero, Adrián
2015-01-01
Assessing changes in plant functional traits along gradients is useful for understanding the assembly of communities and their response to global and local environmental drivers. However, these changes may reflect the effects of species composition (i.e. composition turnover), species abundance (i.e. species interaction), and intra-specific trait variability (i.e. species plasticity). In order to determine the relevance of the latter, trait variation can be assessed under minimal effects of composition turnover. Nine sampling sites were established along an altitudinal gradient in a Mediterranean high mountain grassland community with low composition turnover (Madrid, Spain; 1940 m–2419 m). Nine functional traits were also measured for ten individuals of around ten plant species at each site, for a total of eleven species across all sites. The relative importance of different sources of variability (within/between site and intra-/inter-specific functional diversity) and trait variation at species and community level along the considered gradients were explored. We found a weak individual species response to altitude and other environmental variables although in some cases, individuals were smaller and leaves were thicker at higher elevations. This lack of species response was most likely due to greater within- than between-site species variation. At the community level, inter-specific functional diversity was generally greater than the intra-specific component except for traits linked to leaf element content (leaf carbon content, leaf nitrogen content, δ13C and δ15N). Inter-specific functional diversity decreased with lower altitude for four leaf traits (specific leaf area, leaf dry matter content, δ13C and δ15N), suggesting trait convergence between species at lower elevations, where water shortage may have a stronger environmental filtering effect than colder temperatures at higher altitudes. Our results suggest that, within a vegetation type encompassing various environmental gradients, both, changes in species abundance and intra-specific trait variability adjust for the community functional response to environmental changes. PMID:25774532
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Pescador, David S; de Bello, Francesco; Valladares, Fernando; Escudero, Adrián
2015-01-01
Assessing changes in plant functional traits along gradients is useful for understanding the assembly of communities and their response to global and local environmental drivers. However, these changes may reflect the effects of species composition (i.e. composition turnover), species abundance (i.e. species interaction), and intra-specific trait variability (i.e. species plasticity). In order to determine the relevance of the latter, trait variation can be assessed under minimal effects of composition turnover. Nine sampling sites were established along an altitudinal gradient in a Mediterranean high mountain grassland community with low composition turnover (Madrid, Spain; 1940 m-2419 m). Nine functional traits were also measured for ten individuals of around ten plant species at each site, for a total of eleven species across all sites. The relative importance of different sources of variability (within/between site and intra-/inter-specific functional diversity) and trait variation at species and community level along the considered gradients were explored. We found a weak individual species response to altitude and other environmental variables although in some cases, individuals were smaller and leaves were thicker at higher elevations. This lack of species response was most likely due to greater within- than between-site species variation. At the community level, inter-specific functional diversity was generally greater than the intra-specific component except for traits linked to leaf element content (leaf carbon content, leaf nitrogen content, δ13C and δ15N). Inter-specific functional diversity decreased with lower altitude for four leaf traits (specific leaf area, leaf dry matter content, δ13C and δ15N), suggesting trait convergence between species at lower elevations, where water shortage may have a stronger environmental filtering effect than colder temperatures at higher altitudes. Our results suggest that, within a vegetation type encompassing various environmental gradients, both, changes in species abundance and intra-specific trait variability adjust for the community functional response to environmental changes.
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Dawar, Farman Ullah; Tu, Jiagang; Xiong, Yang; Lan, Jiangfeng; Dong, Xing Xing; Liu, Xiaoling; Khattak, Muhammad Nasir Khan; Mei, Jie; Lin, Li
2016-01-01
Fish skin mucus is a dynamic barrier for invading pathogens with a variety of anti-microbial enzymes, including cyclophilin A (CypA), a multi-functional protein with peptidyl-prolyl cis/trans isomerase (PPIase) activity. Beside various other immunological functions, CypA induces leucocytes migration in vitro in teleost. In the current study, we have discovered several novel immune-relevant proteins in yellow catfish skin mucus by mass spectrometry (MS). The CypA present among them was further detected by Western blot. Moreover, the CypA present in the skin mucus displayed strong chemotactic activity for yellow catfish leucocytes. Interestingly, asparagine (like arginine in mammals) at position 69 was the critical site in yellow catfish CypA involved in leucocyte attraction. These novel efforts do not only highlight the enzymatic texture of skin mucus, but signify CypA to be targeted for anti-inflammatory therapeutics. PMID:27589721
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Probst, Olivia C.; Karayel, Evren; Schida, Nicole; Nimmerfall, Elisabeth; Hehenberger, Elisabeth; Puxbaum, Verena; Mach, Lukas
2013-01-01
The M6P (mannose 6-phosphate)/IGF2R (insulin-like growth factor II receptor) interacts with a variety of factors that impinge on tumour invasion and metastasis. It has been shown that expression of wild-type M6P/IGF2R reduces the tumorigenic and invasive properties of receptor-deficient SCC-VII squamous cell carcinoma cells. We have now used mutant forms of M6P/IGF2R to assess the relevance of the different ligand-binding sites of the receptor for its biological activities in this cellular system. The results of the present study demonstrate that M6P/IGF2R does not require a functional binding site for insulin-like growth factor II for inhibition of anchorage-independent growth and matrix invasion by SCC-VII cells. In contrast, the simultaneous mutation of both M6P-binding sites is sufficient to impair all cellular functions of the receptor tested. These findings highlight that the interaction between M6P/IGF2R and M6P-modified ligands is not only important for intracellular accumulation of lysosomal enzymes and formation of dense lysosomes, but is also crucial for the ability of the receptor to suppress SCC-VII growth and invasion. The present study also shows that some of the biological activities of M6P/IGF2R in SCC-VII cells strongly depend on a functional M6P-binding site within domain 3, thus providing further evidence for the non-redundant cellular functions of the individual carbohydrate-binding domains of the receptor. PMID:23347038
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Redox-Assisted Protein Folding Systems in Eukaryotic Parasites
Haque, Saikh Jaharul; Majumdar, Tanmay
2012-01-01
Abstract Significance: The cysteine (Cys) residues of proteins play two fundamentally important roles. They serve as sites of post-translational redox modifications as well as influence the conformation of the protein through the formation of disulfide bonds. Recent Advances: Redox-related and redox-associated protein folding in protozoan parasites has been found to be a major mode of regulation, affecting myriad aspects of the parasitic life cycle, host-parasite interactions, and the disease pathology. Available genome sequences of various parasites have begun to complement the classical biochemical and enzymological studies of these processes. In this article, we summarize the reversible Cys disulfide (S-S) bond formation in various classes of strategically important parasitic proteins, and its structural consequence and functional relevance. Critical Issues: Molecular mechanisms of folding remain under-studied and often disconnected from functional relevance. Future Directions: The clinical benefit of redox research will require a comprehensive characterization of the various isoforms and paralogs of the redox enzymes and their concerted effect on the structure and function of the specific parasitic client proteins. Antioxid. Redox Signal. 17, 674–683. PMID:22122448
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Remote carboxylation of halogenated aliphatic hydrocarbons with carbon dioxide
NASA Astrophysics Data System (ADS)
Juliá-Hernández, Francisco; Moragas, Toni; Cornella, Josep; Martin, Ruben
2017-05-01
Catalytic carbon-carbon bond formation has enabled the streamlining of synthetic routes when assembling complex molecules. It is particularly important when incorporating saturated hydrocarbons, which are common motifs in petrochemicals and biologically relevant molecules. However, cross-coupling methods that involve alkyl electrophiles result in catalytic bond formation only at specific and previously functionalized sites. Here we describe a catalytic method that is capable of promoting carboxylation reactions at remote and unfunctionalized aliphatic sites with carbon dioxide at atmospheric pressure. The reaction occurs via selective migration of the catalyst along the hydrocarbon side-chain with excellent regio- and chemoselectivity, representing a remarkable reactivity relay when compared with classical cross-coupling reactions. Our results demonstrate that site-selectivity can be switched and controlled, enabling the functionalization of less-reactive positions in the presence of a priori more reactive ones. Furthermore, we show that raw materials obtained in bulk from petroleum processing, such as alkanes and unrefined mixtures of olefins, can be used as substrates. This offers an opportunity to integrate a catalytic platform en route to valuable fatty acids by transforming petroleum-derived feedstocks directly.
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Yang, Yunfeng; Wu, Linwei; Lin, Qiaoyan; Yuan, Mengting; Xu, Depeng; Yu, Hao; Hu, Yigang; Duan, Jichuang; Li, Xiangzhen; He, Zhili; Xue, Kai; van Nostrand, Joy; Wang, Shiping; Zhou, Jizhong
2013-02-01
Microbes play key roles in various biogeochemical processes, including carbon (C) and nitrogen (N) cycling. However, changes of microbial community at the functional gene level by livestock grazing, which is a global land-use activity, remain unclear. Here we use a functional gene array, GeoChip 4.0, to examine the effects of free livestock grazing on the microbial community at an experimental site of Tibet, a region known to be very sensitive to anthropogenic perturbation and global warming. Our results showed that grazing changed microbial community functional structure, in addition to aboveground vegetation and soil geochemical properties. Further statistical tests showed that microbial community functional structures were closely correlated with environmental variables, and variations in microbial community functional structures were mainly controlled by aboveground vegetation, soil C/N ratio, and NH4 (+) -N. In-depth examination of N cycling genes showed that abundances of N mineralization and nitrification genes were increased at grazed sites, but denitrification and N-reduction genes were decreased, suggesting that functional potentials of relevant bioprocesses were changed. Meanwhile, abundances of genes involved in methane cycling, C fixation, and degradation were decreased, which might be caused by vegetation removal and hence decrease in litter accumulation at grazed sites. In contrast, abundances of virulence, stress, and antibiotics resistance genes were increased because of the presence of livestock. In conclusion, these results indicated that soil microbial community functional structure was very sensitive to the impact of livestock grazing and revealed microbial functional potentials in regulating soil N and C cycling, supporting the necessity to include microbial components in evaluating the consequence of land-use and/or climate changes. © 2012 Blackwell Publishing Ltd.
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In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases.
Li, Mingai; Xu, Jia; Algarra Alarcon, Alberto; Carlin, Silvia; Barbaro, Enrico; Cappellin, Luca; Velikova, Violeta; Vrhovsek, Urska; Loreto, Francesco; Varotto, Claudio
2017-10-01
Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolated and functionally validated in Arabidopsis the first isoprene synthase gene, AdoIspS, from a monocotyledonous species (Arundo donax L., Poaceae). Phylogenetic reconstruction indicates that AdoIspS and dicots isoprene synthases most likely originated by parallel evolution from TPS-b monoterpene synthases. Site-directed mutagenesis demonstrated invivo the functional and evolutionary relevance of the residues considered diagnostic for IspS function. One of these positions was identified by saturating mutagenesis as a major determinant of substrate specificity in AdoIspS able to cause invivo a dramatic change in total volatile emission from hemi- to monoterpenes and supporting evolution of isoprene synthases from ocimene synthases. The mechanism responsible for IspS neofunctionalization by active site size modulation by a single amino acid mutation demonstrated in this study might be general, as the very same amino acidic position is implicated in the parallel evolution of different short-chain terpene synthases from both angiosperms and gymnosperms. Based on these results, we present a model reconciling in a unified conceptual framework the apparently contrasting patterns previously observed for isoprene synthase evolution in plants. These results indicate that parallel evolution may be driven by relatively simple biophysical constraints, and illustrate the intimate molecular evolutionary links between the structural and functional bases of traits with global relevance. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
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Brain oscillatory substrates of visual short-term memory capacity.
Sauseng, Paul; Klimesch, Wolfgang; Heise, Kirstin F; Gruber, Walter R; Holz, Elisa; Karim, Ahmed A; Glennon, Mark; Gerloff, Christian; Birbaumer, Niels; Hummel, Friedhelm C
2009-11-17
The amount of information that can be stored in visual short-term memory is strictly limited to about four items. Therefore, memory capacity relies not only on the successful retention of relevant information but also on efficient suppression of distracting information, visual attention, and executive functions. However, completely separable neural signatures for these memory capacity-limiting factors remain to be identified. Because of its functional diversity, oscillatory brain activity may offer a utile solution. In the present study, we show that capacity-determining mechanisms, namely retention of relevant information and suppression of distracting information, are based on neural substrates independent of each other: the successful maintenance of relevant material in short-term memory is associated with cross-frequency phase synchronization between theta (rhythmical neural activity around 5 Hz) and gamma (> 50 Hz) oscillations at posterior parietal recording sites. On the other hand, electroencephalographic alpha activity (around 10 Hz) predicts memory capacity based on efficient suppression of irrelevant information in short-term memory. Moreover, repetitive transcranial magnetic stimulation at alpha frequency can modulate short-term memory capacity by influencing the ability to suppress distracting information. Taken together, the current study provides evidence for a double dissociation of brain oscillatory correlates of visual short-term memory capacity.
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van Pelt, Philomine A; Drossaert, Constance H C; Kruize, Aike A; Huisman, Jaap; Dolhain, Radboud J E M; Wulffraat, Nico M
2015-10-01
To evaluate the frequency of use and relevance of health-related Internet (HRI) sites and online peer support groups and their association with demographic, disease-related and psychosocial variables in young people with JIA. In a cross-sectional study, 176 young people (10-27 years of age) with JIA were asked to complete a questionnaire. The frequency of using HRI sites (regarding information, medication use and aspects of JIA relating to social life), online peer contact and perceived relevance of HRI sites and online peer communication were determined. Associations with demographic variables, disease activity, medication, emotional behaviour and coping were also examined. Seventy-one per cent of the 142 respondents had used the Internet to search for general information on JIA, but specific topics, such as medication, were searched for less often. Twenty-five per cent of respondents had visited a forum or had contacted peers online. The perceived relevance of HRI sites and online peer contact was rated low (median 2.0 and 1.0, respectively; scale 0-10). Apart from female gender (P < 0.01), none of the demographic and disease-related factors were associated with HRI site use. Coping styles, confrontation and reassuring thoughts were associated with increased HRI site use, but only in males. Internalizing and externalizing problem behaviour were not significantly associated. The frequency of HRI site use among young people with JIA was less than expected and was considered of low relevance. HRI sites in their present form cannot replace traditional information as an additional source to increase knowledge. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
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Copper attachment to a non-octarepeat site in prion protein
NASA Astrophysics Data System (ADS)
Hodak, Miroslav; Bernholc, Jerry
2010-03-01
Prion protein, PrP, plays a causative role in several neurodegenerative diseases, including mad cow disease in cattle and Creutzfeldt-Jakob disease in humans. The PrP is known to efficiently bind copper ions and this ability has been linked to its function. PrP contains up to six binding sites, four of which are located in the so-called octarepeat region and are now well known. The binding sites outside this region are still largely undetermined, despite evidence of their relevance to prion diseases. Using a hybrid DFT/DFT, which combines Kohn-Sham DFT with orbital-free DFT to achieve accurate and efficient description of solvent effects in ab initio calculations, we have investigated copper attachment to the sequence GGGTH, which represents the copper binding site located at His96. We have considered both NNNN and NNNO types of copper coordination, as suggested by experiments. Our calculations have determined the geometry of copper attachment site and its energetics. Comparison to the already known binding sites provides insight into the process of copper uptake in PrP.
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Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick
2014-02-01
Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.
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Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie
2014-01-01
Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329
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A comparative analysis of anorexia nervosa groups on Facebook.
Teufel, Martin; Hofer, Eva; Junne, Florian; Sauer, Helene; Zipfel, Stephan; Giel, Katrin Elisabeth
2013-12-01
To analyze the content and culture of anorexia nervosa (AN)-related communication on the current major social network site (SNS) Facebook. We searched for groups and sites related to AN on Facebook by means of a faux profile of a young female. Identified groups/sites were analyzed with respect to (1) category (education, self-help, professional help, pro-ana, anti pro-ana), (2) activity, (3) motivational aspects (prose, pictures), and (4) social support. Numerous relevant groups were found in all categories except that professional help was almost nonexistent. Pro-ana groups were found to be the most active, best organized, and offered the highest levels of social support. Prose motivation was distinctly offered in all categories. Motivation with pictures was particularly evident in pro-ana groups. The most functional motivation was found in self-help groups. SNS appears to be a relevant way for young females suffering from AN to communicate and exchange disease and health-related ideas. Caregivers, researchers, and institutions in the field of eating disorders should be aware of the existence, possibilities, dysfunctions, and influence of SNS. Whether SNS can help persons with AN to get therapeutic assistance as well as whether it can be integrated into psychotherapeutic strategies should be examined in future studies.
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Beta-globin locus activation regions: conservation of organization, structure, and function.
Li, Q L; Zhou, B; Powers, P; Enver, T; Stamatoyannopoulos, G
1990-01-01
The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function. Images PMID:2236034
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Land Management in the Anthropocene: Is History Still Relevant?
NASA Astrophysics Data System (ADS)
Safford, Hugh D.; Betancourt, Julio L.; Hayward, Gregory D.; Wiens, John A.; Regan, Claudia M.
2008-09-01
Incorporating Historical Ecology and Climate Change Into Land Management; Lansdowne, Virginia, 22-25 April 2008; Ecological restoration, conservation, and land management are often based on comparisons with reference sites or time periods, which are assumed to represent ``natural'' or ``properly functioning'' conditions. Such reference conditions can provide a vision of the conservation or management goal and a means to measure progress toward that vision. Although historical ecology has been used successfully to guide resource management in many parts of the world, the continuing relevance of history is now being questioned. Some scientists doubt that lessons from the past can inform management in what may be a dramatically different future, given profound climate change, accelerated land use, and an onslaught of plant and animal invasions.
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Long-Range Control of Gene Expression: Emerging Mechanisms and Disruption in Disease
Kleinjan, Dirk A.; van Heyningen, Veronica
2005-01-01
Transcriptional control is a major mechanism for regulating gene expression. The complex machinery required to effect this control is still emerging from functional and evolutionary analysis of genomic architecture. In addition to the promoter, many other regulatory elements are required for spatiotemporally and quantitatively correct gene expression. Enhancer and repressor elements may reside in introns or up- and downstream of the transcription unit. For some genes with highly complex expression patterns—often those that function as key developmental control genes—the cis-regulatory domain can extend long distances outside the transcription unit. Some of the earliest hints of this came from disease-associated chromosomal breaks positioned well outside the relevant gene. With the availability of wide-ranging genome sequence comparisons, strong conservation of many noncoding regions became obvious. Functional studies have shown many of these conserved sites to be transcriptional regulatory elements that sometimes reside inside unrelated neighboring genes. Such sequence-conserved elements generally harbor sites for tissue-specific DNA-binding proteins. Developmentally variable chromatin conformation can control protein access to these sites and can regulate transcription. Disruption of these finely tuned mechanisms can cause disease. Some regulatory element mutations will be associated with phenotypes distinct from any identified for coding-region mutations. PMID:15549674
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Sacchetti, P; Zvara, P; Plante, M K
1999-06-01
The information revolution triggered by the rapid growth of the Internet has allowed healthcare providers and patients to access a rapidly expanding volume of information. To address the quality of this information, a survey of the data on a single urology-related topic available on the Internet was performed. The search on the World Wide Web (Web) was performed using the search engine HotBot and search directory Yahoo. The Web pages were assessed according to their relevancy to the topic chosen. Relevance rates were derived from the number of relevant sites divided by the total number of sites found. Relevant sites were subsequently ranked for quality on the basis of their accuracy, comprehensiveness, and objectivity. HotBot was then subsequently divided by domain, with each assessed separately. Yahoo was analyzed in its entirety. The resources were then compared for relevance and quality of information. When using the keyword "Viagra," HotBot responded with 15,109 hits. Yahoo presented 51 hits under the category, "Health: Pharmacy: Drugs and Medications: Specific Drugs and Medications: Viagra (Sildenafil)." The relevance rate for the first 50 hits in the search engine HotBot was 0.08. The relevance rates for the edu and org domains found by HotBot were 0.22 and 0.24, respectively; those for com and net were both 0.10. The relevance rate for the search directory Yahoo was 0.20. For relevant sites, the quality of the information presented was significantly higher in the Yahoo and in the HotBot domains hosted by nonprofit organizations when compared with HotBot in general and with its commercially oriented domains. HotBot overall was found to contain seven excellent sites, of which only three were found within Yahoo. Although the medical information available on the Web has proliferated at a remarkable rate, the number of Web sites providing complete, nonbiased information continues to represent only a small portion of the total. We have shown that the search directory Yahoo reduced the number of irrelevant sites significantly, but at the same time, some very valuable information available in HotBot was missing. At present, it may be useful to conduct searches within Yahoo followed by a review of both the edu and org HotBot domains.
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Seal, S N; Davis, D L; Burch, J B
1991-05-01
The endogenous chicken vitellogenin II (VTGII) gene is transcribed exclusively in hepatocytes in response to estrogen. We previously identified two estrogen response elements (EREs) upstream of this gene. We now present an analysis of the VTGII promoter activated by these EREs in response to estrogen. Chimeric VTGII-CAT genes were cotransfected into LMH chicken hepatoma cells along with an estrogen receptor expression vector, and transient CAT expression was assayed after culturing the cells in the absence or presence of estrogen. An analysis of constructs bearing deletions downstream of the more proximal ERE indicated that promoter elements relevant to transcription in LMH cells extend to between -113 and -96. The relative importance of sequences within the VTGII promoter was examined by using 10 contiguous linker scanner mutations spanning the region from -117 to -24. Although most of these mutations compromised VTGII promoter function, one dramatically increased expression in LMH cells and also rendered the VTGII promoter capable of being activated by cis-linked EREs in fibroblasts cotransfected with an estrogen receptor expression vector. Gel retardation and DNase I footprinting assays revealed four factor-binding sites within this promoter. We demonstrate that three of these sites bind C/EBP, SP1, and USF (or related factors), respectively; the fourth site binds a factor that we denote TF-V beta. The biological relevance of these findings is suggested by the fact that three of these binding sites map to sites previously shown to be occupied in vivo in response to estrogen.
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Mosher, M J; Melton, P E; Stapleton, P; Schanfield, M S; Crawford, M H
2016-04-01
DNA methylation is the most widely studied of epigenetic mechanisms, with environmental effects recorded through patterned attachments of methyl groups along the DNA that are capable of modifying gene expression without altering the DNA sequencing. The degree to which these patterns of DNA methylation are heritable, the expected range of normality across populations, and the phenotypic relevance of pattern variation remain unclear. Genes regulating metabolic pathways appear to be vulnerable to ongoing nutritional programming over the life course, as dietary nutrients are significant environmental determinants of DNA methylation, supplying both the methyl groups and energy to generate the methylation process. Here we examine methylation patterns along a region of the metabolic gene leptin (LEP). LEP's putative functions include regulation of energy homeostasis, with its signals affecting energy intake and expenditure, adipogenesis and energy storage, lipid and glucose metabolism, bone metabolism, and reproductive endocrine function. A pattern of differential methylation across CpG sites of the LEP core promoter has been previously identified; however, any consistency of pattern or its phenotypic significance is not fully elucidated among populations. Using DNA extracted from unfractionated white blood cells of peripheral blood samples, our pilot study, divided into two parts, examined the significance of variation in DNA methylation patterns along the leptin core promoter in four populations (phase 1) and used biomarkers reflecting leptin's functional process in two of those populations, western Buryat of Siberia and the Mennonite of central Kansas, to investigate the relevance of the ethnic variation identified in the DNA methylation (phase 2). LEP's core promoter region contains both the binding site for C/EBPα (CCAAT/enhancer binding protein alpha), which tempers the final step in adipocyte maturity and capacity to synthesize leptin, and the TATA motif controlling leptin synthesis. Previous studies report that increased methylation in this region is correlated to decreased gene expression, suggesting tissue-specific methylation variation at this region ( Melzner et al. 2002 ). We hypothesized that evidence of nutritional epigenetic programming would be identified through variation in patterns of DNA methylation and that functional relevance of that variation among populations would be identified through biomarkers that reflect leptin's metabolic signals: serum leptin levels, lipoproteins of the lipid transport system, and anthropometric measures. In phase 1, our combined analyses of 313 individuals documented a distinct and consistent overall pattern of differential DNA methylation across seven CpG sites of LEP core promoter in all ethnicities and both sexes. This pattern replicates those identified in previous studies, suggesting a conserved core promoter region across populations. Phase 2 analyses of two of the four populations (n = 239), correlating methylation at the C/EBPα transcription binding site (TBS) with metabolic and anthropometric biomarkers reflecting LEP roles, showed that stature, which reflects bone growth and remodeling, was significantly and inversely correlated with the percentage of DNA methylation at this site in both sexes. We suggest that variation in DNA methylation along the LEP core promoter plays a substantial role in energy signals affecting both adipogenesis and bone metabolism.
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Della Puppa, Alessandro; De Pellegrin, Serena; d'Avella, Elena; Gioffrè, Giorgio; Munari, Marina; Saladini, Marina; Salillas, Elena; Scienza, Renato; Semenza, Carlo
2013-11-01
The role of parietal areas in number processing is well known. The significance of intraoperative functional mapping of these areas has been only partially explored, however, and only a few discordant data are available in the surgical literature with regard to the right parietal lobe. The purpose of this study was to evaluate the clinical impact of simple calculation in cortical electrostimulation of right-handed patients affected by a right parietal brain tumor. Calculation mapping in awake surgery was performed in 3 right-handed patients affected by high-grade gliomas located in the right parietal lobe. Preoperatively, none of the patients presented with calculation deficits. In all 3 cases, after sensorimotor and language mapping, cortical and intraparietal sulcus areas involved in single-digit multiplication and addition calculations were mapped using bipolar electrostimulation. In all patients, different sites of the right parietal cortex, mainly in the inferior lobule, were detected as being specifically related to calculation (multiplication or addition). In 2 patients the intraparietal sulcus was functionally specific for multiplication. No functional sites for language were detected. All sites functional for calculation were spared during tumor resection, which was complete in all cases without postoperative neurological deficits. These findings provide intraoperative data in support of an anatomofunctional organization for multiplication and addition within the right parietal area. Furthermore, the study shows the potential clinical relevance of intraoperative mapping of calculation in patients undergoing surgery in the right parietal area. Further and larger studies are needed to confirm these data and assess whether mapped areas are effectively essential for function.
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Ma, Jihong; Zou, Chunbin; Guo, Lida; Seneviratne, Danushka S.; Tan, Xinping; Kwon, Yong-Kook; An, Jiyan; Bowser, Robert; DeFrances, Marie C.; Zarnegar, Reza
2013-01-01
Met, the transmembrane tyrosine kinase receptor for hepatocyte growth factor (HGF) is known to function as a potent anti-apoptotic mediator in normal and neoplastic cells. Herein we report that intracellular cytoplasmic tail of Met has evolved to harbor a tandem pair of Caspase-3 cleavage sites, which bait, trap and disable the active site of Caspase-3, thereby blocking the execution of apoptosis. We call this Caspase-3 cleavage motif the ‘Death Defying Domain’ (DDD). This site consists of the following sequence: DNAD-DEVD-T (where the hyphens denote caspase cleavage sites). Through functional and mechanistic studies, we show that upon DDD cleavage by Caspase-3, the resulting DEVD-T peptide acts as a competitive inhibitor and entraps the active site of Caspase-3 akin to DEVD-CHO, which is a potent, synthetic inhibitor of Caspase-3 activity. By gain and loss-of-function studies using restoration of DDD expression in DDD deficient hepatocytic cells, we found that both Caspase-3 sites in DDD are necessary for inhibition of Caspase-3 and promotion of cell survival. Employing mutagenesis studies, we show that DDD could operate independently of Met’s enzymatic activity as determined by using kinase-dead human Met mutant constructs. Studies of both human liver cancer tissues and cell lines uncovered that DDD cleavage and entrapment of Caspase-3 by DDD occur in vivo, further proving that this site has physiological and pathophysiological relevance. Conclusion Our findings show that Met can directly inhibit Caspase-3 via a novel mechanism and promote hepato-cyte survival. Results presented here will further our understanding of the mechanisms that control not only normal tissue homeostasis but also abnormal tissue growth such as cancer and degenerative diseases in which apoptotic caspases are at play. PMID:24122846
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Determinants of cation transport selectivity: Equilibrium binding and transport kinetics
2015-01-01
The crystal structures of channels and transporters reveal the chemical nature of ion-binding sites and, thereby, constrain mechanistic models for their transport processes. However, these structures, in and of themselves, do not reveal equilibrium selectivity or transport preferences, which can be discerned only from various functional assays. In this Review, I explore the relationship between cation transport protein structures, equilibrium binding measurements, and ion transport selectivity. The primary focus is on K+-selective channels and nonselective cation channels because they have been extensively studied both functionally and structurally, but the principles discussed are relevant to other transport proteins and molecules. PMID:26078056
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Hasatsri, Sukhontha; Angspatt, Apichai
2015-01-01
We developed the novel silk fibroin-based bilayered wound dressing for the treatment of partial thickness wounds. And it showed relevant characteristics and accelerated the healing of full-thickness wounds in a rat model. This study is the clinical evaluation of the bilayered wound dressing to confirm its safety and efficacy for the treatment of split-thickness skin donor sites. The safety test was performed using a patch model and no evidence of marked and severe cutaneous reactions was found. The efficacy test of the bilayered wound dressing was conducted on 23 patients with 30 split-thickness skin graft donor sites to evaluate healing time, pain score, skin barrier function, and systemic reaction in comparison to Bactigras. We found that the healing time of donor site wounds treated with the bilayered wound dressing (11 ± 6 days) was significantly faster than those treated with Bactigras (14 ± 6 days) (p = 10−6). The wound sites treated with the bilayered wound dressing showed significantly less pain and more rapid skin functional barrier recovery than those treated with Bactigras (p = 10−5). Therefore, these results confirmed the clinical safety and efficacy of the bilayered wound dressing for the treatment of split-thickness skin graft donor sites. PMID:26221170
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Measuring interactivity on tobacco control websites.
Freeman, Becky; Chapman, Simon
2012-08-01
With the increased reach of Web 2.0, Internet users expect webpages to be interactive. No studies have been conducted to assess whether tobacco control-relevant sites have implemented these features. The authors conducted an analysis of an international sample of tobacco control-relevant websites to determine their level of interactivity. The sample included 68 unique websites selected from Google searches in 5 countries, on each country's Google site, using the term smoking. The 68 sites were analyzed for 10 categories of interactive tools. The most common type of interactive content found on 46 (68%) of sites was for multimedia featuring content that was not primarily text based, such as photo galleries, videos, or podcasts. Only 11 (16%) websites-outside of media sites-allowed people to interact and engage with the site owners and other users by allowing posting comments on content and/or hosting forums/discussions. Linkages to social networking sites were low: 17 pages (25%) linked to Twitter, 15 (22%) to Facebook, and 11 (16%) to YouTube. Interactivity and connectedness to online social media appears to still be in its infancy among tobacco control-relevant sites.
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Costanzo, Maria C.; Crawford, Matthew E.; Hirschman, Jodi E.; Kranz, Janice E.; Olsen, Philip; Robertson, Laura S.; Skrzypek, Marek S.; Braun, Burkhard R.; Hopkins, Kelley Lennon; Kondu, Pinar; Lengieza, Carey; Lew-Smith, Jodi E.; Tillberg, Michael; Garrels, James I.
2001-01-01
The BioKnowledge Library is a relational database and web site (http://www.proteome.com) composed of protein-specific information collected from the scientific literature. Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant phenotype and genetic interactions, regulation, domains and motifs, interactions with other proteins and other relevant data. This report describes four species-specific volumes of the BioKnowledge Library, concerned with the model organisms Saccharomyces cerevisiae (YPD), Schizosaccharomyces pombe (PombePD) and Caenorhabditis elegans (WormPD), and with the fungal pathogen Candida albicans (CalPD™). Protein Reports of each species are unified in format, easily searchable and extensively cross-referenced between species. The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins involved in disease. PMID:11125054
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Chialvo, Ariel A; Simonson, J Michael
2010-01-01
We analyzed the solvation behavior of aqueous lithium, nickel, and ytterbium sulfates at ambient conditions in terms of the relevant radial distributions functions and the corresponding first-order difference of the sulfur-site neutronweighted distribution functions generated by isothermal-isobaric molecular dynamics simulation. We determined of the partial contributions to the neutronweighted distribution functions, to identify the main peaks, and the effect of the contact ion-pair configuration on the resulting H ! S coordination number. Finally, we assessed the extent of the ion-pair formation according to Poirier- DeLap formalism and highlighted the significant increase of the ion-pair association exhibited by these salts withmore » cation charge.« less
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Pliotas, Christos; Grayer, Samuel C; Ekkerman, Silvia; Chan, Anthony K N; Healy, Jess; Marius, Phedra; Bartlett, Wendy; Khan, Amjad; Cortopassi, Wilian A; Chandler, Shane A; Rasmussen, Tim; Benesch, Justin L P; Paton, Robert S; Claridge, Timothy D W; Miller, Samantha; Booth, Ian R; Naismith, James H; Conway, Stuart J
2017-08-15
Ligand binding is one of the most fundamental properties of proteins. Ligand functions fall into three basic types: substrates, regulatory molecules, and cofactors essential to protein stability, reactivity, or enzyme-substrate complex formation. The regulation of potassium ion movement in bacteria is predominantly under the control of regulatory ligands that gate the relevant channels and transporters, which possess subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that adenosine monophosphate (AMP) is bound to both RFs of the dimeric bacterial Kef potassium efflux system (Kef), where it plays a structural role. We conclude that AMP binds with high affinity, ensuring that the site is fully occupied at all times in the cell. Loss of the ability to bind AMP, we demonstrate, causes protein, and likely dimer, instability and consequent loss of function. Kef system function is regulated via the reversible binding of comparatively low-affinity glutathione-based ligands at the interface between the dimer subunits. We propose this interfacial binding site is itself stabilized, at least in part, by AMP binding.
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2017-01-01
Ligand binding is one of the most fundamental properties of proteins. Ligand functions fall into three basic types: substrates, regulatory molecules, and cofactors essential to protein stability, reactivity, or enzyme–substrate complex formation. The regulation of potassium ion movement in bacteria is predominantly under the control of regulatory ligands that gate the relevant channels and transporters, which possess subunits or domains that contain Rossmann folds (RFs). Here we demonstrate that adenosine monophosphate (AMP) is bound to both RFs of the dimeric bacterial Kef potassium efflux system (Kef), where it plays a structural role. We conclude that AMP binds with high affinity, ensuring that the site is fully occupied at all times in the cell. Loss of the ability to bind AMP, we demonstrate, causes protein, and likely dimer, instability and consequent loss of function. Kef system function is regulated via the reversible binding of comparatively low-affinity glutathione-based ligands at the interface between the dimer subunits. We propose this interfacial binding site is itself stabilized, at least in part, by AMP binding. PMID:28656748
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LIBRA-WA: a web application for ligand binding site detection and protein function recognition.
Toti, Daniele; Viet Hung, Le; Tortosa, Valentina; Brandi, Valentina; Polticelli, Fabio
2018-03-01
Recently, LIBRA, a tool for active/ligand binding site prediction, was described. LIBRA's effectiveness was comparable to similar state-of-the-art tools; however, its scoring scheme, output presentation, dependence on local resources and overall convenience were amenable to improvements. To solve these issues, LIBRA-WA, a web application based on an improved LIBRA engine, has been developed, featuring a novel scoring scheme consistently improving LIBRA's performance, and a refined algorithm that can identify binding sites hosted at the interface between different subunits. LIBRA-WA also sports additional functionalities like ligand clustering and a completely redesigned interface for an easier analysis of the output. Extensive tests on 373 apoprotein structures indicate that LIBRA-WA is able to identify the biologically relevant ligand/ligand binding site in 357 cases (∼96%), with the correct prediction ranking first in 349 cases (∼98% of the latter, ∼94% of the total). The earlier stand-alone tool has also been updated and dubbed LIBRA+, by integrating LIBRA-WA's improved engine for cross-compatibility purposes. LIBRA-WA and LIBRA+ are available at: http://www.computationalbiology.it/software.html. polticel@uniroma3.it. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Go, Eden P; Moon, Hee-Jung; Mure, Minae; Desaire, Heather
2018-05-04
Human lysyl oxidase-like 2 (hLOXL2), a glycoprotein implicated in tumor progression and organ fibrosis, is a molecular target for anticancer and antifibrosis treatment. This glycoprotein contains three predicted N-linked glycosylation sites; one is near the protein's active site, and at least one more is known to facilitate the protein's secretion. Because the glycosylation impacts the protein's biology, we sought to characterize the native, mammalian glycosylation profile and to determine how closely this profile is recapitulated when the protein is expressed in insect cells. All three glycosylation sites on the protein, expressed in human embryonic kidney (HEK) cells, were characterized individually using a mass spectrometry-based glycopeptide analysis workflow. These data were compared to the glycosylation profile of the same protein expressed in insect cells. We found that the producer cell type imparts a substantial influence on the glycosylation of this important protein. The more-relevant version, expressed in HEK cells, contains large, acidic glycoforms; these glycans are not generated in insect cells. The glycosylation differences likely have structural and functional consequences, and these data should be considered when generating protein for functional studies or for high-throughput screening campaigns.
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Wang, Han; Harrison, Sandy P; Prentice, Iain C; Yang, Yanzheng; Bai, Fan; Togashi, Henrique F; Wang, Meng; Zhou, Shuangxi; Ni, Jian
2018-02-01
Plant functional traits provide information about adaptations to climate and environmental conditions, and can be used to explore the existence of alternative plant strategies within ecosystems. Trait data are also increasingly being used to provide parameter estimates for vegetation models. Here we present a new database of plant functional traits from China. Most global climate and vegetation types can be found in China, and thus the database is relevant for global modeling. The China Plant Trait Database contains information on morphometric, physical, chemical, and photosynthetic traits from 122 sites spanning the range from boreal to tropical, and from deserts and steppes through woodlands and forests, including montane vegetation. Data collection at each site was based either on sampling the dominant species or on a stratified sampling of each ecosystem layer. The database contains information on 1,215 unique species, though many species have been sampled at multiple sites. The original field identifications have been taxonomically standardized to the Flora of China. Similarly, derived photosynthetic traits, such as electron-transport and carboxylation capacities, were calculated using a standardized method. To facilitate trait-environment analyses, the database also contains detailed climate and vegetation information for each site. The data set is released under a Creative Commons BY license. When using the data set, we kindly request that you cite this article, recognizing the hard work that went into collecting the data and the authors' willingness to make it publicly available. © 2017 by the Ecological Society of America.
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Sexual Selection Halts the Relaxation of Protamine 2 among Rodents
Lüke, Lena; Vicens, Alberto; Serra, Francois; Luque-Larena, Juan Jose; Dopazo, Hernán; Roldan, Eduardo R. S.; Gomendio, Montserrat
2011-01-01
Sexual selection has been proposed as the driving force promoting the rapid evolutionary changes observed in some reproductive genes including protamines. We test this hypothesis in a group of rodents which show marked differences in the intensity of sexual selection. Levels of sperm competition were not associated with the evolutionary rates of protamine 1 but, contrary to expectations, were negatively related to the evolutionary rate of cleaved- and mature-protamine 2. Since both domains were found to be under relaxation, our findings reveal an unforeseen role of sexual selection: to halt the degree of degeneration that proteins within families may experience due to functional redundancy. The degree of relaxation of protamine 2 in this group of rodents is such that in some species it has become dysfunctional and it is not expressed in mature spermatozoa. In contrast, protamine 1 is functionally conserved but shows directed positive selection on specific sites which are functionally relevant such as DNA-anchoring domains and phosphorylation sites. We conclude that in rodents protamine 2 is under relaxation and that sexual selection removes deleterious mutations among species with high levels of sperm competition to maintain the protein functional and the spermatozoa competitive. PMID:22216223
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Thiol–ene click hydrogels for therapeutic delivery
Kharkar, Prathamesh M.; Rehmann, Matthew S.; Skeens, Kelsi M.; Maverakis, Emanual; Kloxin, April M.
2016-01-01
Hydrogels are of growing interest for the delivery of therapeutics to specific sites in the body. For use as a delivery vehicle, hydrophilic precursors are usually laden with bioactive moieties and then directly injected to the site of interest for in situ gel formation and controlled release dictated by precursor design. Hydrogels formed by thiol–ene click reactions are attractive for local controlled release of therapeutics owing to their rapid reaction rate and efficiency under mild aqueous conditions, enabling in situ formation of gels with tunable properties often responsive to environmental cues. Herein, we will review the wide range of applications for thiol–ene hydrogels, from the prolonged release of anti-inflammatory drugs in the spine to the release of protein-based therapeutics in response to cell-secreted enzymes, with a focus on their clinical relevance. We will also provide a brief overview of thiol–ene click chemistry and discuss the available alkene chemistries pertinent to macromolecule functionalization and hydrogel formation. These chemistries include functional groups susceptible to Michael type reactions relevant for injection and radically-mediated reactions for greater temporal control of formation at sites of interest using light. Additionally, mechanisms for the encapsulation and controlled release of therapeutic cargoes are reviewed, including i) tuning the mesh size of the hydrogel initially and temporally for cargo entrapment and release and ii) covalent tethering of the cargo with degradable linkers or affinity binding sequences to mediate release. Finally, myriad thiol–ene hydrogels and their specific applications also are discussed to give a sampling of the current and future utilization of this chemistry for delivery of therapeutics, such as small molecule drugs, peptides, and biologics. PMID:28361125
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Kirkby, Nicholas S; Sampaio, Walkyria; Etelvino, Gisele; Alves, Daniele T; Anders, Katie L; Temponi, Rafael; Shala, Fisnik; Nair, Anitha S; Ahmetaj-Shala, Blerina; Jiao, Jing; Herschman, Harvey R; Xiaomeng, Wang; Wahli, Walter; Santos, Robson A; Mitchell, Jane A
2018-02-01
Cyclooxygenase-2 (COX-2) is an inducible enzyme expressed in inflammation and cancer targeted by nonsteroidal anti-inflammatory drugs. COX-2 is also expressed constitutively in discreet locations where its inhibition drives gastrointestinal and cardiovascular/renal side effects. Constitutive COX-2 expression in the kidney regulates renal function and blood flow; however, the global relevance of the kidney versus other tissues to COX-2-dependent blood flow regulation is not known. Here, we used a microsphere deposition technique and pharmacological COX-2 inhibition to map the contribution of COX-2 to regional blood flow in mice and compared this to COX-2 expression patterns using luciferase reporter mice. Across all tissues studied, COX-2 inhibition altered blood flow predominantly in the kidney, with some effects also seen in the spleen, adipose, and testes. Of these sites, only the kidney displayed appreciable local COX-2 expression. As the main site where COX-2 regulates blood flow, we next analyzed the pathways involved in kidney vascular responses using a novel technique of video imaging small arteries in living tissue slices. We found that the protective effect of COX-2 on renal vascular function was associated with prostacyclin signaling through PPARβ/δ (peroxisome proliferator-activated receptor-β/δ). These data demonstrate the kidney as the principle site in the body where local COX-2 controls blood flow and identifies a previously unreported PPARβ/δ-mediated renal vasodilator pathway as the mechanism. These findings have direct relevance to the renal and cardiovascular side effects of drugs that inhibit COX-2, as well as the potential of the COX-2/prostacyclin/PPARβ/δ axis as a therapeutic target in renal disease. © 2018 The Authors.
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Statistical functions and relevant correlation coefficients of clearness index
NASA Astrophysics Data System (ADS)
Pavanello, Diego; Zaaiman, Willem; Colli, Alessandra; Heiser, John; Smith, Scott
2015-08-01
This article presents a statistical analysis of the sky conditions, during years from 2010 to 2012, for three different locations: the Joint Research Centre site in Ispra (Italy, European Solar Test Installation - ESTI laboratories), the site of National Renewable Energy Laboratory in Golden (Colorado, USA) and the site of Brookhaven National Laboratories in Upton (New York, USA). The key parameter is the clearness index kT, a dimensionless expression of the global irradiance impinging upon a horizontal surface at a given instant of time. In the first part, the sky conditions are characterized using daily averages, giving a general overview of the three sites. In the second part the analysis is performed using data sets with a short-term resolution of 1 sample per minute, demonstrating remarkable properties of the statistical distributions of the clearness index, reinforced by a proof using fuzzy logic methods. Successively some time-dependent correlations between different meteorological variables are presented in terms of Pearson and Spearman correlation coefficients, and introducing a new one.
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Rangarajan, Srinivas; Mavrikakis, Manos
2016-04-07
The adsorption of 20 nitrogen-/sulfur-containing and hydrocarbon compounds on the sulfur edge of cobalt-promoted molybdenum sulfide (CoMoS) catalyst was studied using density functional theory, accounting for van der Waals interactions, to elicit comparative structure–property trends across different classes of molecules relevant to hydrotreating. Unhindered organosulfur compounds preferentially adsorb on a “CUS-like” site formed by the dimerization of two neighboring sulfur atoms on the edge to create a vacancy. Nitrogen-containing compounds and 4,6-dimethyldibenzothiophene, however, prefer the brim sites. Binding energy trends indicate that nitrogen-containing compounds will inhibit hydrodesulfurization on the brim sites and, relatively weakly, on the CUS-like sites. Edge vacanciesmore » are,thus, likely to be essential for hydrodesulfurization of unhindered organosulfur compounds. Furthermore, van der Waals forces contribute significantly to the binding energy of compounds (up to 1.0 eV for large compounds such as alkyl-substituted acridines) on CoMoS.« less
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Structural basis for the interaction of antibiotics with peptidyl transferase center in eubacteria
DOE Office of Scientific and Technical Information (OSTI.GOV)
Schlunzen, Frank; Zarivach, Raz; Harms, Jörg
2009-10-07
Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate the structural basis of ribosome-antibiotic interactions, we determined the high-resolution X-ray structures of the 50S ribosomal subunit of the eubacterium Deinococcus radiodurans, complexed with the clinically relevant antibiotics chloramphenicol, clindamycin and the three macrolides erythromycin, clarithromycin and roxithromycin. We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavitymore » and do not involve any interaction of the drugs with ribosomal proteins. Here we report the details of antibiotic interactions with the components of their binding sites. Our results also show the importance of putative Mg{sup +2} ions for the binding of some drugs. This structural analysis should facilitate rational drug design.« less
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Xia, Jun Hong; Li, Hong Lian; Zhang, Yong; Meng, Zi Ning; Lin, Hao Ran
2018-05-01
Fish species inhabitating seawater (SW) or freshwater (FW) habitats have to develop genetic adaptations to alternative environment factors, especially salinity. Functional consequences of the protein variations associated with habitat environments in fish mitochondrial genomes have not yet received much attention. We analyzed 829 complete fish mitochondrial genomes and compared the amino acid differences of 13 mitochondrial protein families between FW and SW fish groups. We identified 47 specificity determining sites (SDS) that associated with FW or SW environments from 12 mitochondrial protein families. Thirty-two (68%) of the SDS sites are hydrophobic, 13 (28%) are neutral, and the remaining sites are acidic or basic. Seven of those SDS from ND1, ND2 and ND5 were scored as probably damaging to the protein structures. Furthermore, phylogenetic tree based Bayes Empirical Bayes analysis also detected 63 positive sites associated with alternative habitat environments across ten mtDNA proteins. These signatures could be important for studying mitochondrial genetic variation relevant to fish physiology and ecology.
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Ruhi, Albert; Dong, Xiaoli; McDaniel, Courtney H; Batzer, Darold P; Sabo, John L
2018-04-17
Novel flow regimes resulting from dam operations and overallocation of freshwater resources are an emerging consequence of global change. Yet, anticipating how freshwater biodiversity will respond to surging flow regime alteration requires overcoming two challenges in environmental flow science: shifting from local to riverscape-level understanding of biodiversity dynamics, and from static to time-varying characterizations of the flow regime. Here, we used time-series methods (wavelets and multivariate autoregressive models) to quantify flow-regime alteration and to link time-varying flow regimes to the dynamics of multiple local communities potentially connected by dispersal (i.e., a metacommunity). We studied the Chattahoochee River below Buford dam (Georgia, U.S.A.), and asked how flow regime alteration by a large hydropower dam may control the long-term functional trajectory of the downstream invertebrate metacommunity. We found that seasonal variation in hydropeaking synchronized temporal fluctuations in trait abundance among the flow-altered sites. Three biological trait states describing adaptation to fast flows benefitted from flow management for hydropower, but did not compensate for declines in 16 "loser" traits. Accordingly, metacommunity-wide functional diversity responded negatively to hydropeaking intensity, and stochastic simulations showed that the risk of functional diversity collapse within the next 4 years would decrease by 17% if hydropeaking was ameliorated, or by 9% if it was applied every other season. Finally, an analysis of 97 reference and 23 dam-affected river sites across the U.S. Southeast suggested that flow variation at extraneous, human-relevant scales (12-hr, 24-hr, 1-week) is relatively common in rivers affected by hydropower dams. This study advances the notion that novel flow regimes are widespread, and simplify the functional structure of riverine communities by filtering out taxa with nonadaptive traits and by spatially synchronizing their dynamics. This is relevant in the light of ongoing and future hydrologic alteration due to climate non-stationarity and the new wave of dams planned globally. © 2018 John Wiley & Sons Ltd.
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ECOLOGICALLY-RELEVANT QUANTIFICATION OF STREAMFLOW REGIMES IN WESTERN STREAMS
This report describes the rationale for and application of a protocol for estimation of ecologically-relevant streamflow metrics that quantify streamflow regime for ungaged sites subject to a range of human impact. The analysis presented here is focused on sites sampled by the U....
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NASA Astrophysics Data System (ADS)
Thorslund, Josefin; Jarsjö, Jerker; Destouni, Georgia
2017-04-01
Wetlands are often considered as nature-based solutions that can provide a multitude of services of great social, economic and environmental value to humankind. The services may include recreation, greenhouse gas sequestration, contaminant retention, coastal protection, groundwater level and soil moisture regulation, flood regulation and biodiversity support. Changes in land-use, water use and climate can all impact wetland functions and occur at scales extending well beyond the local scale of an individual wetland. However, in practical applications, management decisions usually regard and focus on individual wetland sites and local conditions. To understand the potential usefulness and services of wetlands as larger-scale nature-based solutions, e.g. for mitigating negative impacts from large-scale change pressures, one needs to understand the combined function multiple wetlands at the relevant large scales. We here systematically investigate if and to what extent research so far has addressed the large-scale dynamics of landscape systems with multiple wetlands, which are likely to be relevant for understanding impacts of regional to global change. Our investigation regards key changes and impacts of relevance for nature-based solutions, such as large-scale nutrient and pollution retention, flow regulation and coastal protection. Although such large-scale knowledge is still limited, evidence suggests that the aggregated functions and effects of multiple wetlands in the landscape can differ considerably from those observed at individual wetlands. Such scale differences may have important implications for wetland function-effect predictability and management under large-scale change pressures and impacts, such as those of climate change.
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Overview of Seismic Noise and it’s Relevance to Personnel Detection
2008-04-01
production sites. Young et al. (1996) measured seismic noise with seismometers at the surface and within boreholes at three sites, and generated...ER D C/ CR R EL T R -0 8 -5 Overview of Seismic Noise and its Relevance to Personnel Detection Lindamae Peck April 2008 C ol d R...April 2008 Overview of Seismic Noise and its Relevance to Personnel Detection Lindamae Peck Cold Regions Research and Engineering Laboratory
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The Functional Impact of the Intestinal Microbiome on Mucosal Immunity and Systemic Autoimmunity
Longman, Randy S.; Littman, Dan R.
2016-01-01
Purpose of Review This review will highlight recent advances functionally linking the gut microbiome with mucosal and systemic immune cell activation potentially underlying autoimmunity. Recent Findings Dynamic interactions between the gut microbiome and environmental cues (including diet and medicines) shape the effector potential of the microbial organ. Key bacteria and viruses have emerged, that, in defined microenvironments, play a critical role in regulating effector lymphocyte functions. The coordinated interactions between these different microbial kingdoms—including bacteria, helminths, and viruses (termed transkingdom interactions)—play a critical role in shaping immunity. Emerging strategies to identify immunologically-relevant microbes with the potential to regulate immune cell functions both at mucosal sites and systemically will likely define key diagnostic and therapeutic targets. Summary The microbiome constitutes a critical microbial organ with coordinated interactions that shape host immunity. PMID:26002030
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Wang, ShaoPeng; Zhang, Yu-Hang; Huang, GuoHua; Chen, Lei; Cai, Yu-Dong
2017-01-01
Myristoylation is an important hydrophobic post-translational modification that is covalently bound to the amino group of Gly residues on the N-terminus of proteins. The many diverse functions of myristoylation on proteins, such as membrane targeting, signal pathway regulation and apoptosis, are largely due to the lipid modification, whereas abnormal or irregular myristoylation on proteins can lead to several pathological changes in the cell. To better understand the function of myristoylated sites and to correctly identify them in protein sequences, this study conducted a novel computational investigation on identifying myristoylation sites in protein sequences. A training dataset with 196 positive and 84 negative peptide segments were obtained. Four types of features derived from the peptide segments following the myristoylation sites were used to specify myristoylatedand non-myristoylated sites. Then, feature selection methods including maximum relevance and minimum redundancy (mRMR), incremental feature selection (IFS), and a machine learning algorithm (extreme learning machine method) were adopted to extract optimal features for the algorithm to identify myristoylation sites in protein sequences, thereby building an optimal prediction model. As a result, 41 key features were extracted and used to build an optimal prediction model. The effectiveness of the optimal prediction model was further validated by its performance on a test dataset. Furthermore, detailed analyses were also performed on the extracted 41 features to gain insight into the mechanism of myristoylation modification. This study provided a new computational method for identifying myristoylation sites in protein sequences. We believe that it can be a useful tool to predict myristoylation sites from protein sequences. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
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NASA Astrophysics Data System (ADS)
Gadeken, K.; Dorgan, K. M.; Moore, J.; Berke, S. K.
2016-02-01
Evolutionary relationships may shed light on observed patterns of diversity and functional traits when viewed through the lens of phylogeny. The potential for phylogenetic information to be used to explain patterns in community structure, such as niche partitioning and responses to stress, is extensive. Differential distribution of related species with similar functional traits suggests niche partitioning, and local redundancy in functional traits may indicate the potential for interspecific competition. In this study, we investigated phylogenetic and functional diversity as a function of habitat for sites with varying levels of oil contamination in the Northern Gulf of Mexico. Our study was conducted in a shallow benthic community at the Chandeleur Islands, a group of uninhabited barrier islands. Infauna were sampled from seagrass (Halodule wrightii) and bare sediment at three sites along the island chain that experienced variable levels of oil impact from the Deepwater Horizon oil spill. Individuals were preserved and 18S and COI genes sequenced, and a phylogenetic tree was constructed of the local community using maximum likelihood. Phylogenetic diversity and evenness were quantified. Ecologically important functional traits were then compiled into respective distance matrices, evaluated through different functional diversity indices, and assessed for correlation with the phylogeny. This integration of functional and phylogenetic diversity has the potential to provide greater insight into factors driving community structure than either metric alone. Determining relevant metrics of diversity is critical to understanding the ecological effects of major disturbances such as oil spills.
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Ripley, Jennifer; Iwanowicz, Luke; Blazer, Vicki; Foran, Christy
2008-08-01
The Shenandoah River (VA, USA), the largest tributary of the Potomac River (MD, USA) and an important source of drinking water, has been the site of extensive fish kills since 2004. Previous investigations indicate environmental stressors may be adversely modulating the immune system of smallmouth bass (Micropterus dolomieu) and other species. Anterior kidney (AK) tissue, the major site of blood cell production in fish, was collected from smallmouth bass at three sites along the Shenandoah River. The tissue was divided for immune function and proteomics analyses. Bactericidal activity and respiratory burst were significantly different between North Fork and mainstem Shenandoah River smallmouth bass, whereas South Fork AK tissue did not significantly differ in either of these measures compared with the other sites. Cytotoxic cell activity was highest among South Fork and lowest among North Fork AK leukocytes. The composite two-dimension gels of the North Fork and mainstem smallmouth bass AK tissues contained 584 and 591 spots, respectively. South Fork smallmouth bass AK expressed only 335 proteins. Nineteen of 50 proteins analyzed by matrix-assisted laser desorption ionization-time of flight were successfully identified. Three of the four identified proteins with increased expression in South Fork AK tissue were involved in metabolism. Seven proteins exclusive to mainstem and North Fork smallmouth bass AK and expressed at comparable abundances serve immune and stress response functions. The proteomics data indicate these fish differ in metabolic capacity of AK tissue and in the ability to produce functional leukocytes. The variable responses of the immune function assays further indicate disruption to the immune system. Our results allow us to hypothesize underlying physiological changes that may relate to fish kills and suggest relevant contaminants known to produce similar physiological disruption.
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Ripley, J.; Iwanowicz, L.; Blazer, V.; Foran, C.
2008-01-01
The Shenandoah River (VA, USA), the largest tributary of the Potomac River (MD, USA) and an important source of drinking water, has been the site of extensive fish kills since 2004. Previous investigations indicate environmental stressors may be adversely modulating the immune system of smallmouth bass (Micropterus dolomieu) and other species. Anterior kidney (AK) tissue, the major site of blood cell production in fish, was collected from smallmouth bass at three sites along the Shenandoah River. The tissue was divided for immune function and proteomics analyses. Bactericidal activity and respiratory burst were significantly different between North Fork and mainstem Shenandoah River smallmouth bass, whereas South Fork AK tissue did not significantly differ in either of these measures compared with the other sites. Cytotoxic cell activity was highest among South Fork and lowest among North Fork AK leukocytes. The composite two-dimension gels of the North Fork and mainstem smallmouth bass AK tissues contained 584 and 591 spots, respectively. South Fork smallmouth bass AK expressed only 335 proteins. Nineteen of 50 proteins analyzed by matrix-assisted laser desorption ionization-time of flight were successfully identified. Three of the four identified proteins with increased expression in South Fork AK tissue were involved in metabolism. Seven proteins exclusive to mainstem and North Fork smallmouth bass AK and expressed at comparable abundances serve immune and stress response functions. The proteomics data indicate these fish differ in metabolic capacity of AK tissue and in the ability to produce functional leukocytes. The variable responses of the immune function assays further indicate disruption to the immune system. Our results allow us to hypothesize underlying physiological changes that may relate to fish kills and suggest relevant contaminants known to produce similar physiological disruption. ?? 2008 SETAC.
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Monsky, Wayne L; Mouta Carreira, Carla; Tsuzuki, Yoshikazu; Gohongi, Takeshi; Fukumura, Dai; Jain, Rakesh K
2002-04-01
The host microenvironment differs between primary and metastatic sites, affecting gene expression and various physiological functions. Here we show the differences in the physiological parameters between orthotopic primary and metastatic breast tumor xenografts using intravital microscopy and reveal the relationship between angiogenic gene expression and microvascular functions in vivo. ZR75-1, a human estrogen-dependent mammary carcinoma, was implanted into the mammary fat pad (primary site) of ovariectomized SCID female mice carrying estrogen pellets. The same tumor line was also grown in the cranial window (metastasis site). When tumors reached the diameter of 2.5 mm, angiogenesis, hemodynamics, and vascular permeability were measured by intravital microscopy, and expression of angiogenic growth factors was determined by quantitative reverse transcription-PCR. ZR75-1 tumors grown in the mammary fat pad had higher microvascular permeability but lower vascular density than the same tumors grown in the cranial window (2.5- and 0.7-fold, respectively). There was no significant difference in RBC velocity, vessel diameter, blood flow rate, and shear rate between two sites. The levels of vascular endothelial growth factor (VEGF), its receptors VEGFR1 and VEGFR2, and angiopoietin-1 mRNA tended to be higher in the mammary fat pad tumors than in the cranial tumors (1.5-, 1.5-, 3-, and 2-fold, respectively). The primary breast cancer exhibited higher vascular permeability, but the cranial tumor showed more angiogenesis, suggesting that the cranial environment is leakage resistant but proangiogenic. Collectively, host microenvironment is an important determinant of tumor gene expression and microvascular functions, and, thus, orthotopic breast tumor models should be useful for obtaining clinically relevant information.
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Dendritic spine dysgenesis in Autism Related Disorders
Phillips, Mary; Pozzo-Miller, Lucas
2015-01-01
The activity-dependent structural and functional plasticity of dendritic spines has led to the long-standing belief that these neuronal compartments are the subcellular sites of learning and memory. Of relevance to human health, central neurons in several neuropsychiatric illnesses, including autism related disorders, have atypical numbers and morphologies of dendritic spines. These so-called dendritic spine dysgeneses found in individuals with autism related disorders are consistently replicated in experimental mouse models. Dendritic spine dysgenesis reflects the underlying synaptopathology that drives clinically relevant behavioral deficits in experimental mouse models, providing a platform for testing new therapeutic approaches. By examining molecular signaling pathways, synaptic deficits, and spine dysgenesis in experimental mouse models of autism related disorders we find strong evidence for mTOR to be a critical point of convergence and promising therapeutic target. PMID:25578949
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Sentiment Analysis of Web Sites Related to Vaginal Mesh Use in Pelvic Reconstructive Surgery.
Hobson, Deslyn T G; Meriwether, Kate V; Francis, Sean L; Kinman, Casey L; Stewart, J Ryan
2018-05-02
The purpose of this study was to utilize sentiment analysis to describe online opinions toward vaginal mesh. We hypothesized that sentiment in legal Web sites would be more negative than that in medical and reference Web sites. We generated a list of relevant key words related to vaginal mesh and searched Web sites using the Google search engine. Each unique uniform resource locator (URL) was sorted into 1 of 6 categories: "medical", "legal", "news/media", "patient generated", "reference", or "unrelated". Sentiment of relevant Web sites, the primary outcome, was scored on a scale of -1 to +1, and mean sentiment was compared across all categories using 1-way analysis of variance. Tukey test evaluated differences between category pairs. Google searches of 464 unique key words resulted in 11,405 URLs. Sentiment analysis was performed on 8029 relevant URLs (3472 legal, 1625 "medical", 1774 "reference", 666 "news media", 492 "patient generated"). The mean sentiment for all relevant Web sites was +0.01 ± 0.16; analysis of variance revealed significant differences between categories (P < 0.001). Web sites categorized as "legal" and "news/media" had a slightly negative mean sentiment, whereas those categorized as "medical," "reference," and "patient generated" had slightly positive mean sentiments. Tukey test showed differences between all category pairs except the "medical" versus "reference" in comparison with the largest mean difference (-0.13) seen in the "legal" versus "reference" comparison. Web sites related to vaginal mesh have an overall mean neutral sentiment, and Web sites categorized as "medical," "reference," and "patient generated" have significantly higher sentiment scores than related Web sites in "legal" and "news/media" categories.
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Solution of effective Hamiltonian of impurity hopping between two sites in a metal
NASA Astrophysics Data System (ADS)
Ye, Jinwu
1998-03-01
We analyze in detail all the possible fixed points of the effective Hamiltonian of a non-magnetic impurity hopping between two sites in a metal obtained by Moustakas and Fisher(MF). We find a line of non-fermi liquid fixed points which continuously interpolates between the 2-channel Kondo fixed point(2CK) and the one channel, two impurity Kondo (2IK) fixed point. There is one relevant direction with scaling dimension 1/2 and one leading irrelevant operator with dimension 3/2. There is also one marginal operator in the spin sector moving along this line. The additional non-fermi liquid fixed point found by MF has the same symmetry as the 2IK, it has two relevant directions with scaling dimension 1/2, therefore also unstable. The system is shown to flow to a line of fermi-liquid fixed points which continuously interpolates between the non-interacting fixed point and the 2 channel spin-flavor Kondo fixed point (2CSFK) discussed by the author previously. The effect of particle-hole symmetry breaking is discussed. The effective Hamiltonian in the external magnetic field is analysed. The scaling functions for the physical measurable quantities are derived in the different regimes; their predictions for the experiments are given. Finally the implications are given for a non-magnetic impurity hopping around three sites with triangular symmetry discussed by MF.
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Cistrome of the aldosterone-activated mineralocorticoid receptor in human renal cells.
Le Billan, Florian; Khan, Junaid A; Lamribet, Khadija; Viengchareun, Say; Bouligand, Jérôme; Fagart, Jérôme; Lombès, Marc
2015-09-01
Aldosterone exerts its effects mainly by activating the mineralocorticoid receptor (MR), a transcription factor that regulates gene expression through complex and dynamic interactions with coregulators and transcriptional machinery, leading to fine-tuned control of vectorial ionic transport in the distal nephron. To identify genome-wide aldosterone-regulated MR targets in human renal cells, we set up a chromatin immunoprecipitation (ChIP) assay by using a specific anti-MR antibody in a differentiated human renal cell line expressing green fluorescent protein (GFP)-MR. This approach, coupled with high-throughput sequencing, allowed identification of 974 genomic MR targets. Computational analysis identified an MR response element (MRE) including single or multiple half-sites and palindromic motifs in which the AGtACAgxatGTtCt sequence was the most prevalent motif. Most genomic MR-binding sites (MBSs) are located >10 kb from the transcriptional start sites of target genes (84%). Specific aldosterone-induced recruitment of MR on the first most relevant genomic sequences was further validated by ChIP-quantitative (q)PCR and correlated with concomitant and positive aldosterone-activated transcriptional regulation of the corresponding gene, as assayed by RT-qPCR. It was notable that most MBSs lacked MREs but harbored DNA recognition motifs for other transcription factors (FOX, EGR1, AP1, PAX5) suggesting functional interaction. This work provides new insights into aldosterone MR-mediated renal signaling and opens relevant perspectives for mineralocorticoid-related pathophysiology. © FASEB.
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Metal Transport across Biomembranes: Emerging Models for a Distinct Chemistry*
Argüello, José M.; Raimunda, Daniel; González-Guerrero, Manuel
2012-01-01
Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models. PMID:22389499
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Metal transport across biomembranes: emerging models for a distinct chemistry.
Argüello, José M; Raimunda, Daniel; González-Guerrero, Manuel
2012-04-20
Transition metals are essential components of important biomolecules, and their homeostasis is central to many life processes. Transmembrane transporters are key elements controlling the distribution of metals in various compartments. However, due to their chemical properties, transition elements require transporters with different structural-functional characteristics from those of alkali and alkali earth ions. Emerging structural information and functional studies have revealed distinctive features of metal transport. Among these are the relevance of multifaceted events involving metal transfer among participating proteins, the importance of coordination geometry at transmembrane transport sites, and the presence of the largely irreversible steps associated with vectorial transport. Here, we discuss how these characteristics shape novel transition metal ion transport models.
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Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B
2018-01-01
Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of the enzyme's active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modeling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.
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NASA Astrophysics Data System (ADS)
Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.
2018-04-01
Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modelling techniques offer an alternative route to study the enzyme’s reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modelling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modelling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789 and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modelling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of the enzyme’s active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modelling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.
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NMR resolved multiple anesthetic binding sites in the TM domains of the α4β2 nAChR
Bondarenko, Vasyl; Mowrey, David; Liu, Lu Tian; Xu, Yan; Tang, Pei
2012-01-01
The α4β2 nicotinic acetylcholine receptor (nAChR) has significant roles in nervous system function and disease. It is also a molecular target of general anesthetics. Anesthetics inhibit the α4β2 nAChR at clinically relevant concentrations, but their binding sites in α4β2 remain unclear. The recently determined NMR structures of the α4β2 nAChR transmembrane (TM) domains provide valuable frameworks for identifying the binding sites. In this study, we performed solution NMR experiments on the α4β2 TM domains in the absence and presence of halothane and ketamine. Both anesthetics were found in an intra-subunit cavity near the extracellular end of the 2 transmembrane helices, homologous to a common anesthetic binding site observed in X-ray structures of anesthetic-bound GLIC (Nury, et. al. 2011). Halothane, but not ketamine, was also found in cavities adjacent to the common anesthetic site at the interface of α4 and β2. In addition, both anesthetics bound to cavities near the ion selectivity filter at the intracellular end of the TM domains. Anesthetic binding induced profound changes in protein conformational exchanges. A number of residues, close to or remote from the binding sites, showed resonance signal splitting from single to double peaks, signifying that anesthetics decreased conformation exchange rates. It was also evident that anesthetics shifted population of two conformations. Altogether, the study comprehensively resolved anesthetic binding sites in the α4β2 nAChR. Furthermore, the study provided compelling experimental evidence of anesthetic-induced changes in protein dynamics, especially near regions of the hydrophobic gate and ion selectivity filter that directly regulate channel functions. PMID:23000369
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NMR resolved multiple anesthetic binding sites in the TM domains of the α4β2 nAChR.
Bondarenko, Vasyl; Mowrey, David; Liu, Lu Tian; Xu, Yan; Tang, Pei
2013-02-01
The α4β2 nicotinic acetylcholine receptor (nAChR) has significant roles in nervous system function and disease. It is also a molecular target of general anesthetics. Anesthetics inhibit the α4β2 nAChR at clinically relevant concentrations, but their binding sites in α4β2 remain unclear. The recently determined NMR structures of the α4β2 nAChR transmembrane (TM) domains provide valuable frameworks for identifying the binding sites. In this study, we performed solution NMR experiments on the α4β2 TM domains in the absence and presence of halothane and ketamine. Both anesthetics were found in an intra-subunit cavity near the extracellular end of the β2 transmembrane helices, homologous to a common anesthetic binding site observed in X-ray structures of anesthetic-bound GLIC (Nury et al., [32]). Halothane, but not ketamine, was also found in cavities adjacent to the common anesthetic site at the interface of α4 and β2. In addition, both anesthetics bound to cavities near the ion selectivity filter at the intracellular end of the TM domains. Anesthetic binding induced profound changes in protein conformational exchanges. A number of residues, close to or remote from the binding sites, showed resonance signal splitting from single to double peaks, signifying that anesthetics decreased conformation exchange rates. It was also evident that anesthetics shifted population of two conformations. Altogether, the study comprehensively resolved anesthetic binding sites in the α4β2 nAChR. Furthermore, the study provided compelling experimental evidence of anesthetic-induced changes in protein dynamics, especially near regions of the hydrophobic gate and ion selectivity filter that directly regulate channel functions. Copyright © 2012 Elsevier B.V. All rights reserved.
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Deforges, Jules; de Breyne, Sylvain; Ameur, Melissa; Ulryck, Nathalie; Chamond, Nathalie; Saaidi, Afaf; Ponty, Yann; Ohlmann, Theophile; Sargueil, Bruno
2017-07-07
In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been described with little rationale for their multiplicity. The Gag-IRES has the singularity to be located within Gag ORF and to directly interact with ribosomal 40S. Aiming at elucidating the specificity and the relevance of this interaction, we probed HIV-1 Gag-IRES structure and developed an innovative integrative modelling strategy to take into account all the gathered information. We propose a novel Gag-IRES secondary structure strongly supported by all experimental data. We further demonstrate the presence of two regions within Gag-IRES that independently and directly interact with the ribosome. Importantly, these binding sites are functionally relevant to Gag translation both in vitro and ex vivo. This work provides insight into the Gag-IRES molecular mechanism and gives compelling evidence for its physiological importance. It allows us to propose original hypotheses about the IRES physiological role and conservation among primate lentiviruses. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
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Elovic, Elie P; Simone, Lisa K; Zafonte, Ross
2004-01-01
The objective of this article was to (1) review the engineering and medical literature to structure the available information concerning the assessment of spasticity in the neurological population; (2) to discuss the strengths and weaknesses of the different methods currently in use in spasticity assessment; and (3) make recommendations for future efforts in spasticity outcome assessment. Spasticity textbooks, Web sites, and OVID, IEEE, and Medline searches from 1966 through 2003 of spasticity, quantitative measure, or outcome assessment in the rehabilitation population were used as data sources. Over 500 articles were reviewed. Articles that discussed outcome measures used to assess interventions and evaluation of spasticity were included. Authors reviewed the articles looking at inclusion criteria, data collection, methodology, assessment methods, and conclusions for validity and relevance to this article. Issues such as clinical relevance, real-world function and lack of objectivity, and time consumed during performance are important issues for spasticity assessment. Some measures such as the Ashworth Scale remain in common use secondary to ease of use despite their obvious functional limitations. More functional outcome goals are plagued by being more time consuming and a general inability to demonstrate changes after an intervention. This may be secondary to the other factors that combine with spasticity to cause dysfunction at that level. Quantitative metrics can provide more objective measurements but their clinical relevance is sometimes problematic. The assessment of spasticity outcome is still somewhat problematic. Further work is necessary to develop measures that have real-world functional significance to both the individuals being treated and the clinicians. A lack of objectivity is still a problem. In the future it is important for clinicians and the engineers to work together in the development of better outcome measures.
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Boareto, Marcelo; Yamagishi, Michel E B; Caticha, Nestor; Leite, Vitor B P
2012-10-01
In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them. Copyright © 2012 Elsevier Ltd. All rights reserved.
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Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen
2014-01-01
Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of microbial processes in contaminated soils. PMID:24376192
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MO-E-18C-01: Open Access Web-Based Peer-To-Peer Training and Education in Radiotherapy
DOE Office of Scientific and Technical Information (OSTI.GOV)
Pawlicki, T; Brown, D; Dunscombe, P
Purpose: Current training and education delivery models have limitations which result in gaps in clinical proficiency with equipment, procedures, and techniques. Educational and training opportunities offered by vendors and professional societies are by their nature not available at point of need or for the life of clinical systems. The objective of this work is to leverage modern communications technology to provide peer-to-peer training and education for radiotherapy professionals, in the clinic and on demand, as they undertake their clinical duties. Methods: We have developed a free of charge web site ( https://i.treatsafely.org ) using the Google App Engine and datastoremore » (NDB, GQL), Python with AJAX-RPC, and Javascript. The site is a radiotherapy-specific hosting service to which user-created videos illustrating clinical or physics processes and other relevant educational material can be uploaded. Efficient navigation to the material of interest is provided through several RT specific search tools and videos can be scored by users, thus providing comprehensive peer review of the site content. The site also supports multilingual narration\\translation of videos, a quiz function for competence assessment and a library function allowing groups or institutions to define their standard operating procedures based on the video content. Results: The website went live in August 2013 and currently has over 680 registered users from 55 countries; 27.2% from the United States, 9.8% from India, 8.3% from the United Kingdom, 7.3% from Brazil, and 47.5% from other countries. The users include physicists (57.4%), Oncologists (12.5%), therapists (8.2%) and dosimetrists (4.8%). There are 75 videos to date including English, Portuguese, Mandarin, and Thai. Conclusion: Based on the initial acceptance of the site, we conclude that this open access web-based peer-to-peer tool is fulfilling an important need in radiotherapy training and education. Site functionality should expand in the future to include document sharing and continuing education credits.« less
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Submolecular Gates Self-Assemble for Hot-Electron Transfer in Proteins.
Filip-Granit, Neta; Goldberg, Eran; Samish, Ilan; Ashur, Idan; van der Boom, Milko E; Cohen, Hagai; Scherz, Avigdor
2017-07-27
Redox reactions play key roles in fundamental biological processes. The related spatial organization of donors and acceptors is assumed to undergo evolutionary optimization facilitating charge mobilization within the relevant biological context. Experimental information from submolecular functional sites is needed to understand the organization strategies and driving forces involved in the self-development of structure-function relationships. Here we exploit chemically resolved electrical measurements (CREM) to probe the atom-specific electrostatic potentials (ESPs) in artificial arrays of bacteriochlorophyll (BChl) derivatives that provide model systems for photoexcited (hot) electron donation and withdrawal. On the basis of computations we show that native BChl's in the photosynthetic reaction center (RC) self-assemble at their ground-state as aligned gates for functional charge transfer. The combined computational and experimental results further reveal how site-specific polarizability perpendicular to the molecular plane enhances the hot-electron transport. Maximal transport efficiency is predicted for a specific, ∼5 Å, distance above the center of the metalized BChl, which is in remarkably close agreement with the distance and mutual orientation of corresponding native cofactors. These findings provide new metrics and guidelines for analysis of biological redox centers and for designing charge mobilizing machines such as artificial photosynthesis.
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Dendritic spine dysgenesis in autism related disorders.
Phillips, Mary; Pozzo-Miller, Lucas
2015-08-05
The activity-dependent structural and functional plasticity of dendritic spines has led to the long-standing belief that these neuronal compartments are the subcellular sites of learning and memory. Of relevance to human health, central neurons in several neuropsychiatric illnesses, including autism related disorders, have atypical numbers and morphologies of dendritic spines. These so-called dendritic spine dysgeneses found in individuals with autism related disorders are consistently replicated in experimental mouse models. Dendritic spine dysgenesis reflects the underlying synaptopathology that drives clinically relevant behavioral deficits in experimental mouse models, providing a platform for testing new therapeutic approaches. By examining molecular signaling pathways, synaptic deficits, and spine dysgenesis in experimental mouse models of autism related disorders we find strong evidence for mTOR to be a critical point of convergence and promising therapeutic target. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
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Groppe, Sarah E; Gossen, Anna; Rademacher, Lena; Hahn, Alexa; Westphal, Luzie; Gründer, Gerhard; Spreckelmeyer, Katja N
2013-08-01
Evidence accumulates that the neuropeptide oxytocin plays an important role in mediating social interaction among humans and that a dysfunction in oxytocin-modulated brain mechanisms might lie at the core of disturbed social behavior in neuropsychiatric disease. Explanatory models suggest that oxytocin guides social approach and avoidance by modulating the perceived salience of socially meaningful cues. Animal data point toward the ventral tegmental area (VTA) as the brain site where this modulation takes place. We used functional magnetic resonance imaging and a social incentive delay task to test the hypothesis that oxytocin modulates the neural processing of socially relevant cues in the VTA, hereby facilitating behavioral response. Twenty-eight nulliparous women (not taking any hormones) received intranasal oxytocin or placebo in a double-blind randomized clinical trial with a parallel-group design. Oxytocin significantly enhanced VTA activation in response to cues signaling social reward (friendly face) or social punishment (angry face). Oxytocin effects on behavioral performance were modulated by individual differences in sociability with enhanced performance in women scoring low but decreased performance in women scoring high on self-reported measures of agreeableness. Our data provide evidence that the VTA is the human brain site where oxytocin attaches salience to socially relevant cues. This mechanism might play an important role in triggering motivation to react at the prospect of social reward or punishment. Copyright © 2013 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.
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Walz, Yvonne; Wegmann, Martin; Leutner, Benjamin; Dech, Stefan; Vounatsou, Penelope; N'Goran, Eliézer K; Raso, Giovanna; Utzinger, Jürg
2015-11-30
Schistosomiasis is a widespread water-based disease that puts close to 800 million people at risk of infection with more than 250 million infected, mainly in sub-Saharan Africa. Transmission is governed by the spatial distribution of specific freshwater snails that act as intermediate hosts and the frequency, duration and extent of human bodies exposed to infested water sources during human water contact. Remote sensing data have been utilized for spatially explicit risk profiling of schistosomiasis. Since schistosomiasis risk profiling based on remote sensing data inherits a conceptual drawback if school-based disease prevalence data are directly related to the remote sensing measurements extracted at the location of the school, because the disease transmission usually does not exactly occur at the school, we took the local environment around the schools into account by explicitly linking ecologically relevant environmental information of potential disease transmission sites to survey measurements of disease prevalence. Our models were validated at two sites with different landscapes in Côte d'Ivoire using high- and moderate-resolution remote sensing data based on random forest and partial least squares regression. We found that the ecologically relevant modelling approach explained up to 70% of the variation in Schistosoma infection prevalence and performed better compared to a purely pixel-based modelling approach. Furthermore, our study showed that model performance increased as a function of enlarging the school catchment area, confirming the hypothesis that suitable environments for schistosomiasis transmission rarely occur at the location of survey measurements.
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Maugeri, Pearson T; Griese, Julia J; Branca, Rui M; Miller, Effie K; Smith, Zachary R; Eirich, Jürgen; Högbom, Martin; Shafaat, Hannah S
2018-01-31
The heterobimetallic R2lox protein binds both manganese and iron ions in a site-selective fashion and activates oxygen, ultimately performing C-H bond oxidation to generate a tyrosine-valine cross-link near the active site. In this work, we demonstrate that, following assembly, R2lox undergoes photoinduced changes to the active site geometry and metal coordination motif. Through spectroscopic, structural, and mass spectrometric characterization, the photoconverted species is found to consist of a tyrosinate-bound iron center following light-induced decarboxylation of a coordinating glutamate residue and cleavage of the tyrosine-valine cross-link. This process occurs with high quantum efficiencies (Φ = 3%) using violet and near-ultraviolet light, suggesting that the photodecarboxylation is initiated via ligand-to-metal charge transfer excitation. Site-directed mutagenesis and structural analysis suggest that the cross-linked tyrosine-162 is the coordinating residue. One primary product is observed following irradiation, indicating potential use of this class of proteins, which contains a putative substrate channel, for controlled photoinduced decarboxylation processes, with relevance for in vivo functionality of R2lox as well as application in environmental remediation.
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Protective Mechanism of STAT3-siRNA on Cerebral Ischemia Injury
NASA Astrophysics Data System (ADS)
He, Jinting; Yang, Le; Liang, Wenzhao
2018-01-01
Nerve cells in ischemic brain injury will occur a series of complex signal transduction pathway changes and produce the corresponding biological function, thus affecting the central nervous system functionally different cells in the ischemic brain injury metabolism, division, Differentiation and death process, while changes in signal pathways also play an important role in the repair process of the post-ischemic nervous system. JAK/STAT pathway and vascular lesions have some relevance, but its exact mechanism after cerebral ischemia is not yet fully understood. This study is intended to further explore the JAK / STAT pathway in the functional site of STAT3 in neuronal ischemia Hypoxic injury and related molecular mechanisms, targeting these targets design intervention strategies to block the signal pathway, in order to provide a theoretical basis for the treatment of ischemic brain damage in this pathway.
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Bogart, Justin A; Lewis, Andrew J; Schelter, Eric J
2015-01-19
Rare-earth metal cations have recently been demonstrated to be essential co-factors for the growth of the methanotrophic bacterium Methylacidiphilum fumariolicum SolV. A crystal structure of the rare-earth-dependent methanol dehydrogenase (MDH) includes a cerium cation in the active site. Herein, the Ce-MDH active site has been analyzed through DFT calculations. The results show the stability of the Ce(III)-pyrroloquinoline quinone (PQQ) semiquinone configuration. Calculations on the active oxidized form of this complex indicate a 0.81 eV stabilization of the PQQ(0) LUMO at cerium versus calcium, supporting the observation that the cerium cation in the active site confers a competitive advantage to Methylacidiphilum fumariolicum SolV. Using reported aqueous electrochemical data, a semi-empirical correlation was established based on cerium(IV/III) redox potentials. The correlation allowed estimation of the cerium oxidation potential of +1.35 V versus saturated calomel electrode (SCE) in the active site. The results are expected to guide the design of functional model complexes and alcohol-oxidation catalysts based on lanthanide complexes of biologically relevant quinones. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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NASA Astrophysics Data System (ADS)
Zanzoni, Serena; Ceccon, Alberto; Assfalg, Michael; Singh, Rajesh K.; Fushman, David; D'Onofrio, Mariapina
2015-04-01
The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with 15N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways.The use of nanoparticles (NPs) in biomedical applications requires an in-depth understanding of the mechanisms by which NPs interact with biomolecules. NPs associating with proteins may interfere with protein-protein interactions and affect cellular communication pathways, however the impact of NPs on biomolecular recognition remains poorly characterized. In this respect, particularly relevant is the study of NP-induced functional perturbations of proteins implicated in the regulation of key biochemical pathways. Ubiquitin (Ub) is a prototypical protein post-translational modifier playing a central role in numerous essential biological processes. To contribute to the understanding of the interactions between this universally distributed biomacromolecule and NPs, we investigated the adsorption of polyhydroxylated [60]fullerene on monomeric Ub and on a minimal polyubiquitin chain in vitro at atomic resolution. Site-resolved chemical shift and intensity perturbations of Ub's NMR signals, together with 15N spin relaxation rate changes, exchange saturation transfer effects, and fluorescence quenching data were consistent with the reversible formation of soluble aggregates incorporating fullerenol clusters. The specific interaction epitopes were identified, coincident with functional recognition sites in a monomeric and lysine48-linked dimeric Ub. Fullerenol appeared to target the open state of the dynamic structure of a dimeric Ub according to a conformational selection mechanism. Importantly, the protein-NP association prevented the enzyme-catalyzed synthesis of polyubiquitin chains. Our findings provide an experiment-based insight into protein/fullerenol recognition, with implications in functional biomolecular communication, including regulatory protein turnover, and for the opportunity of therapeutic intervention in Ub-dependent cellular pathways. Electronic supplementary information (ESI) available: Experimental details. Fig. S1. Characterization of fullerenol by dynamic light scattering. Fig. S2. Size-exclusion chromatography. Fig. S3. 15N R1 spin relaxation rates of Ub and Ub2 upon subsequent additions of fullerenol. See DOI: 10.1039/c5nr00539f
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Relevant Telecomputing Activities.
ERIC Educational Resources Information Center
Ross, Patricia
1995-01-01
Discusses the use of telecomputing in classrooms. Topics include telecomputing goals; use of the Internet; language arts and music FTP (file transfer protocol) sites; social studies FTP sites; science Telnet sites; social studies Telnet sites; skill building and learning processes; and instructional design. (LRW)
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NASA Astrophysics Data System (ADS)
Yang, Yi-Chen E.; Cai, Ximing; Herricks, Edwin E.
2008-04-01
This paper develops a new approach to identify hydrologic indicators related to fish community and generate a quantitative function between an ecological target index and the identified hydrologic indicators. The approach is based on genetic programming (GP), a data mining method. Using the Shannon Index (a fish community diversity index) or the number of individuals (total abundance) of a fish community, as an ecological target, the GP identified the most ecologically relevant hydrologic indicators (ERHIs) from 32 indicators of hydrologic alteration, for the case study site, the upper Illinois River. Robustness analysis showed that different GP runs found a similar set of ERHIs; each of the identified ERHI from different GP runs had a consistent relationship with the target index. By comparing the GP results with those from principal component analysis and autecology matrix, the three approaches identified a small number (six) of common ERHIs. Particularly, the timing of low flow (Dmin) seems to be more relevant to the diversity of the fish community, while the magnitude of the low flow (Qb) is more relevant to the total fish abundance; large rising rates result in a significant improvement of fish diversity, which is counterintuitive and against previous findings. The quantitative function developed by GP was further used to construct an indicator impact matrix (IIM), which was demonstrated as a potentially useful tool for streamflow restoration design.
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Linking plant and ecosystem functional biogeography.
Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D; Kattge, Jens; Baldocchi, Dennis D
2014-09-23
Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere-atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches.
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Linking plant and ecosystem functional biogeography
Reichstein, Markus; Bahn, Michael; Mahecha, Miguel D.; Kattge, Jens; Baldocchi, Dennis D.
2014-01-01
Classical biogeographical observations suggest that ecosystems are strongly shaped by climatic constraints in terms of their structure and function. On the other hand, vegetation function feeds back on the climate system via biosphere–atmosphere exchange of matter and energy. Ecosystem-level observations of this exchange reveal very large functional biogeographical variation of climate-relevant ecosystem functional properties related to carbon and water cycles. This variation is explained insufficiently by climate control and a classical plant functional type classification approach. For example, correlations between seasonal carbon-use efficiency and climate or environmental variables remain below 0.6, leaving almost 70% of variance unexplained. We suggest that a substantial part of this unexplained variation of ecosystem functional properties is related to variations in plant and microbial traits. Therefore, to progress with global functional biogeography, we should seek to understand the link between organismic traits and flux-derived ecosystem properties at ecosystem observation sites and the spatial variation of vegetation traits given geoecological covariates. This understanding can be fostered by synergistic use of both data-driven and theory-driven ecological as well as biophysical approaches. PMID:25225392
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Lokhandwala, Jameela; Silverman Y de la Vega, Rafael I; Hopkins, Hilary C; Britton, Collin W; Rodriguez-Iglesias, Aroa; Bogomolni, Roberto; Schmoll, Monika; Zoltowski, Brian D
2016-07-08
Light-oxygen-voltage (LOV) domain-containing proteins function as small light-activated modules capable of imparting blue light control of biological processes. Their small modular nature has made them model proteins for allosteric signal transduction and optogenetic devices. Despite intense research, key aspects of their signal transduction mechanisms and photochemistry remain poorly understood. In particular, ordered water has been identified as a possible key mediator of photocycle kinetics, despite the lack of ordered water in the LOV active site. Herein, we use recent crystal structures of a fungal LOV protein ENVOY to interrogate the role of Thr(101) in recruiting water to the flavin active site where it can function as an intrinsic base to accelerate photocycle kinetics. Kinetic and molecular dynamic simulations confirm a role in solvent recruitment to the active site and identify structural changes that correlate with solvent recruitment. In vivo analysis of T101I indicates a direct role of the Thr(101) position in mediating adaptation to osmotic stress, thereby verifying biological relevance of ordered water in LOV signaling. The combined studies identify position 101 as a mediator of both allostery and photocycle catalysis that can impact organism physiology. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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Lesne, Annick; Bécavin, Christophe; Victor, Jean-Marc
2012-02-01
Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.
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NASA Astrophysics Data System (ADS)
Lesne, Annick; Bécavin, Christophe; Victor, Jean–Marc
2012-02-01
Allostery is a key concept of molecular biology which refers to the control of an enzyme activity by an effector molecule binding the enzyme at another site rather than the active site (allos = other in Greek). We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for spacetime coordination of gene expression at all scales from DNA to the whole chromosome. We further suggest that this functional architecture is provided by the chromatin fiber itself. The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or nonspecific) effectors to specific (or nonspecific) active sites. Mechanical constraints can travel along the fiber all the better since the fiber is more compact and regular, which speaks in favor of the actual existence of the (so-called 30 nm) chromatin fiber. Chromatin fiber allostery reconciles both the physical and biochemical approaches of chromatin. We illustrate this view with two supporting specific examples. Moreover, from a methodological point of view, we suggest that the notion of chromatin fiber allostery is particularly relevant for systemic approaches. Finally we discuss the evolutionary power of allostery in the context of chromatin and its relation to modularity.
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Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.
Cohen, Sarah; Tirindelli, Joëlle; Gomez-Chiarri, Marta; Nacci, Diane
2006-12-01
Recently, there has been a dramatic expansion of studies of major histocompatibility complex (MHC) variation aimed at discovering functional differences in immunity across wild populations of diverse vertebrate species. Some species with relatively low genetic diversity or under strong directional selection by pathogens have revealed fascinating cases of MHC allelic disease linkage. More generally in genetically diverse species, however, these linkages may be hard to find. In this paper, we review approaches for assessing functional variation in MHC and discuss their potential use for discovering smaller-scale intraspecific spatial and temporal patterns of MHC variation. Then, we describe and illustrate an approach using the structural model to produce a population composite of variation in antigen-binding regions by mapping population-specific substitutions onto functional regions of the molecule. We are producing models of variation in major histocompatibility (MH) loci for populations of non-migratory fish (killifish, Fundulus heteroclitus) resident at sites that vary dramatically in environmental quality. We discuss the goal of relating MH population variation to functional differences in disease susceptibility such as those inferred by observations of parasitic infection and direct measurement of bacterial challenges in the laboratory. Our study has focused on relatively well-studied killifish populations, including those resident in a highly disturbed, chemically contaminated estuary and nearby less contaminated sites. Population-specific genetic changes at MHC antigen-binding loci are described, and evidence relevant to functional implications of these changes is reviewed. Population-specific patterns of variation in antigen-binding regions in combination with a range of assessments of immune function will provide a powerful new approach to reveal functional changes in MHC.
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NASA Astrophysics Data System (ADS)
Bochet, Esther; García-Fayos, Patricio; José Molina, Maria; Moreno de las Heras, Mariano; Espigares, Tíscar; Nicolau, Jose Manuel; Monleon, Vicente
2017-04-01
Theoretical models predict that drylands are particularly prone to suffer critical transitions with abrupt non-linear changes in their structure and functions as a result of the existing complex interactions between climatic fluctuations and human disturbances. However, so far, few studies provide empirical data to validate these models. We aim at determining how holm oak (Quercus ilex) woodlands undergo changes in their functions in response to human disturbance along an aridity gradient (from semi-arid to sub-humid conditions), in eastern Spain. For that purpose, we used (a) remote-sensing estimations of precipitation-use-efficiency (PUE) from enhanced vegetation index (EVI) observations performed in 231x231 m plots of the Moderate Resolution Imaging Spectroradiometer (MODIS); (b) biological and chemical soil parameter determinations (extracellular soil enzyme activity, soil respiration, nutrient cycling processes) from soil sampled in the same plots; (c) vegetation parameter determinations (ratio of functional groups) from vegetation surveys performed in the same plots. We analyzed and compared the shape of the functional change (in terms of PUE and soil and vegetation parameters) in response to human disturbance intensity for our holm oak sites along the aridity gradient. Overall, our results evidenced important differences in the shape of the functional change in response to human disturbance between climatic conditions. Semi-arid areas experienced a more accelerated non-linear decrease with an increasing disturbance intensity than sub-humid ones. The proportion of functional groups (herbaceous vs. woody cover) played a relevant role in the shape of the functional response of the holm oak sites to human disturbance.
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Larrabee, James A; Schenk, Gerhard; Mitić, Nataša; Riley, Mark J
2015-09-01
Magnetic circular dichroism (MCD) is a convenient technique for providing structural and mechanistic insight into enzymatic systems in solution. The focus of this review is on aspects of geometric and electronic structure that can be determined by MCD, and how this method can further our understanding of enzymatic mechanisms. Dinuclear Co(II) systems that catalyse hydrolytic reactions were selected to illustrate the approach. These systems all contain active sites with similar structures consisting of two Co(II) ions bridged by one or two carboxylates and a water or hydroxide. In most of these active sites one Co(II) is five-coordinate and one is six-coordinate, with differing binding affinities. It is shown how MCD can be used to determine which binding site--five or six-coordinate--has the greater affinity. Importantly, zero-field-splitting data and magnetic exchange coupling constants may be determined from the temperature and field dependence of MCD data. The relevance of these data to the function of the enzymatic systems is discussed.
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Meng, Jingbo; Martinez, Lourdes; Holmstrom, Amanda; Chung, Minwoong; Cox, Jeff
2017-01-01
The article presents a narrative review of scholarship on social support through social networking sites (SNSs) published from 2004 to 2015. By searching keywords related to social support and SNSs in major databases for social sciences, we identified and content analyzed directly relevant articles (N = 88). The article summarizes the prevalence of theory usage; the function of theory usage (e.g., testing a theory, developing a theory); major theories referenced; and methodologies, including research designs, measurement, and the roles of social support and SNS examined in this literature. It also reports four themes identified across the studies, indicating the trends in the current research. Based on the review, the article presents a discussion about study sites, conceptualization of social support, theoretical coherence, the role of social networks, and the dynamic relationships between SNS use and social support, which points out potential avenues for shaping a future research agenda.
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ADP Regulates SNF1, the Saccharomyces cerevisiae Homolog of AMP-Activated Protein Kinase
Mayer, Faith V.; Heath, Richard; Underwood, Elizabeth; Sanders, Matthew J.; Carmena, David; McCartney, Rhonda R.; Leiper, Fiona C.; Xiao, Bing; Jing, Chun; Walker, Philip A.; Haire, Lesley F.; Ogrodowicz, Roksana; Martin, Stephen R.; Schmidt, Martin C.; Gamblin, Steven J.; Carling, David
2011-01-01
Summary The SNF1 protein kinase complex plays an essential role in regulating gene expression in response to the level of extracellular glucose in budding yeast. SNF1 shares structural and functional similarities with mammalian AMP-activated protein kinase. Both kinases are activated by phosphorylation on a threonine residue within the activation loop segment of the catalytic subunit. Here we show that ADP is the long-sought metabolite that activates SNF1 in response to glucose limitation by protecting the enzyme against dephosphorylation by Glc7, its physiologically relevant protein phosphatase. We also show that the regulatory subunit of SNF1 has two ADP binding sites. The tighter site binds AMP, ADP, and ATP competitively with NADH, whereas the weaker site does not bind NADH, but is responsible for mediating the protective effect of ADP on dephosphorylation. Mutagenesis experiments suggest that the general mechanism by which ADP protects against dephosphorylation is strongly conserved between SNF1 and AMPK. PMID:22019086
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Jha, Santosh Kumar; Ji, Minbiao; Gaffney, Kelly J; Boxer, Steven G
2011-10-04
Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.
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Jha, Santosh Kumar; Ji, Minbiao; Gaffney, Kelly J.; Boxer, Steven G.
2011-01-01
Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ5-3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields. PMID:21949360
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Site-preference and valency for rare-earth sites in (R-Ce)2Fe14B magnets
DOE Office of Scientific and Technical Information (OSTI.GOV)
Alam, Aftab; Khan, Mahmud; McCallum, R. W.
2013-01-28
Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two R-sites (Wyckoff 4f and 4g, with four-fold multiplicity) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1-xCex)2Fe14B [R=La,Nd] using density functional theory (DFT) methods—including a DFT+U scheme to treat localized 4f-electrons. Fe moments compare well with neutron data—almost unaffected by Hubbard U, and weakly affected by spin-orbit coupling.more » In La2Fe14B, Ce alloys for 0 ≤ x ≤ 1 and prefers smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas, in Nd2Fe14B, Ce is predicted to have limited alloying (x ≤ 0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. The Curie temperatures versus x for (Nd,Ce) were predicted for a typical sample processing and verified experimentally.« less
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Pedrana, Alisa E; Stoove, Mark A; Chang, Shanton; Howard, Steve; Asselin, Jason; Ilic, Olivia; Batrouney, Colin; Hellard, Margaret E
2012-01-01
Online social networking sites offer a novel setting for the delivery of health promotion interventions due to their potential to reach a large population and the possibility for two-way engagement. However, few have attempted to host interventions on these sites, or to use the range of interactive functions available to enhance the delivery of health-related messages. This paper presents lessons learnt from “The FaceSpace Project”, a sexual health promotion intervention using social networking sites targeting two key at-risk groups. Based on our experience, we make recommendations for developing and implementing health promotion interventions on these sites. Elements crucial for developing interventions include establishing a multidisciplinary team, allowing adequate time for obtaining approvals, securing sufficient resources for building and maintaining an online presence, and developing an integrated process and impact evaluation framework. With two-way interaction an important and novel feature of health promotion interventions in this medium, we also present strategies trialled to generate interest and engagement in our intervention. Social networking sites are now an established part of the online environment; our experience in developing and implementing a health promotion intervention using this medium are of direct relevance and utility for all health organizations creating a presence in this new environment. PMID:22374589
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Spielberg, Jeffrey M.; Miller, Gregory A.; Engels, Anna S.; Herrington, John D.; Sutton, Bradley P.; Banich, Marie T.; Heller, Wendy
2010-01-01
Motivation and executive function are both necessary for the completion of goal-directed behavior. Research investigating the manner in which these processes interact is beginning to emerge and has implicated middle frontal gyrus (MFG) as a site of interaction for relevant neural mechanisms. However, this research has focused on state motivation, and it has not examined functional lateralization. The present study examined the impact of trait levels of approach and avoidance motivation on neural processes associated with executive function. Functional magnetic resonance imaging was conducted while participants performed a color-word Stroop task. Analyses identified brain regions in which trait approach and avoidance motivation (measured by questionnaires) moderated activation associated with executive control. Approach was hypothesized to be associated with left-lateralized MFG activation, whereas avoidance was hypothesized to be associated with right-lateralized MFG activation. Results supported both hypotheses. Present findings implicate areas of middle frontal gyrus in top-down control to guide behavior in accordance with motivational goals. PMID:20728552
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Spielberg, Jeffrey M; Miller, Gregory A; Engels, Anna S; Herrington, John D; Sutton, Bradley P; Banich, Marie T; Heller, Wendy
2011-01-01
Motivation and executive function are both necessary for the completion of goal-directed behavior. Research investigating the manner in which these processes interact is beginning to emerge and has implicated middle frontal gyrus (MFG) as a site of interaction for relevant neural mechanisms. However, this research has focused on state motivation, and it has not examined functional lateralization. The present study examined the impact of trait levels of approach and avoidance motivation on neural processes associated with executive function. Functional magnetic resonance imaging was conducted while participants performed a color-word Stroop task. Analyses identified brain regions in which trait approach and avoidance motivation (measured by questionnaires) moderated activation associated with executive control. Approach was hypothesized to be associated with left-lateralized MFG activation, whereas avoidance was hypothesized to be associated with right-lateralized MFG activation. Results supported both hypotheses. Present findings implicate areas of middle frontal gyrus in top-down control to guide behavior in accordance with motivational goals. Copyright © 2010 Elsevier Inc. All rights reserved.
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Conceptual Model of Iodine Behavior in the Subsurface at the Hanford Site
DOE Office of Scientific and Technical Information (OSTI.GOV)
Truex, Michael J.; Lee, Brady D.; Johnson, Christian D.
The fate and transport of 129I in the environment and potential remediation technologies are currently being studied as part of environmental remediation activities at the Hanford Site. A conceptual model describing the nature and extent of subsurface contamination, factors that control plume behavior, and factors relevant to potential remediation processes is needed to support environmental remedy decisions. Because 129I is an uncommon contaminant, relevant remediation experience and scientific literature are limited. Thus, the conceptual model also needs to both describe known contaminant and biogeochemical process information and to identify aspects about which additional information needed to effectively support remedy decisions.more » this document summarizes the conceptual model of iodine behavior relevant to iodine in the subsurface environment at the Hanford site.« less
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An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis.
Arribas-Hernández, Laura; Bressendorff, Simon; Hansen, Mathias Henning; Poulsen, Christian; Erdmann, Susanne; Brodersen, Peter
2018-04-11
Methylation of N6-adenosine (m6A) in mRNA is an important post-transcriptional gene regulatory mechanism in eukaryotes. m6A provides a binding site for effector proteins ("readers") that influence pre-mRNA splicing, mRNA degradation or translational efficiency. YT521-B homology (YTH) domain proteins are important m6A readers with established functions in animals. Plants contain more YTH domain proteins than other eukaryotes, but their biological importance remains unknown. Here, we show that the cytoplasmic Arabidopsis thaliana YTH domain proteins EVOLUTIONARILY CONSERVED C-TERMINAL REGION2/3 (ECT2/3) are required for the correct timing of leaf formation and for normal leaf morphology. These functions depend fully on intact m6A binding sites of ECT2 and ECT3, indicating that they function as m6A readers. Mutation of the close ECT2 homolog, ECT4, enhances the delayed leaf emergence and leaf morphology defects of ect2/ect3 mutants, and all three ECT proteins are expressed at leaf formation sites in the shoot apex of young seedlings and in the division zone of developing leaves. ECT2 and ECT3 are also highly expressed at early stages of trichome development and are required for trichome morphology, as previously reported for m6A itself. Overall, our study establishes the relevance of a cytoplasmic m6A-YTH regulatory module in the timing and execution of plant organogenesis. © 2018 American Society of Plant Biologists. All rights reserved.
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Xu, Xiang; Zhao, Jingyue; Xu, Zhen; Peng, Baozhen; Huang, Qiuhua; Arnold, Eddy; Ding, Jianping
2004-08-06
Isocitrate dehydrogenases (IDHs) catalyze the oxidative decarboxylation of isocitrate to alpha-ketoglutarate, and regulation of the enzymatic activity of IDHs is crucial for their biological functions. Bacterial IDHs are reversibly regulated by phosphorylation of a strictly conserved serine residue at the active site. Eukaryotic NADP-dependent IDHs (NADP-IDHs) have been shown to have diverse important biological functions; however, their regulatory mechanism remains unclear. Structural studies of human cytosolic NADP-IDH (HcIDH) in complex with NADP and in complex with NADP, isocitrate, and Ca2+ reveal three biologically relevant conformational states of the enzyme that differ substantially in the structure of the active site and in the overall structure. A structural segment at the active site that forms a conserved alpha-helix in all known NADP-IDH structures assumes a loop conformation in the open, inactive form of HcIDH; a partially unraveled alpha-helix in the semi-open, intermediate form; and an alpha-helix in the closed, active form. The side chain of Asp279 of this segment occupies the isocitrate-binding site and forms hydrogen bonds with Ser94 (the equivalent of the phosphorylation site in bacterial IDHs) in the inactive form and chelates the metal ion in the active form. The structural data led us to propose a novel self-regulatory mechanism for HcIDH that mimics the phosphorylation mechanism used by the bacterial homologs, consistent with biochemical and biological data. This mechanism might be applicable to other eukaryotic NADP-IDHs. The results also provide insights into the recognition and specificity of substrate and cofactor by eukaryotic NADP-IDHs.
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Long-term electrical resistivity monitoring of recharge-induced contaminant plume behavior.
Gasperikova, Erika; Hubbard, Susan S; Watson, David B; Baker, Gregory S; Peterson, John E; Kowalsky, Michael B; Smith, Meagan; Brooks, Scott
2012-11-01
Geophysical measurements, and electrical resistivity tomography (ERT) data in particular, are sensitive to properties that are related (directly or indirectly) to hydrological processes. The challenge is in extracting information from geophysical data at a relevant scale that can be used to gain insight about subsurface behavior and to parameterize or validate flow and transport models. Here, we consider the use of ERT data for examining the impact of recharge on subsurface contamination at the S-3 ponds of the Oak Ridge Integrated Field Research Challenge (IFRC) site in Tennessee. A large dataset of time-lapse cross-well and surface ERT data, collected at the site over a period of 12 months, is used to study time variations in resistivity due to changes in total dissolved solids (primarily nitrate). The electrical resistivity distributions recovered from cross-well and surface ERT data agrees well, and both of these datasets can be used to interpret spatiotemporal variations in subsurface nitrate concentrations due to rainfall, although the sensitivity of the electrical resistivity response to dilution varies with nitrate concentration. Using the time-lapse surface ERT data interpreted in terms of nitrate concentrations, we find that the subsurface nitrate concentration at this site varies as a function of spatial position, episodic heavy rainstorms (versus seasonal and annual fluctuations), and antecedent rainfall history. These results suggest that the surface ERT monitoring approach is potentially useful for examining subsurface plume responses to recharge over field-relevant scales. Published by Elsevier B.V.
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González-Plaza, Juan J.; Šimatović, Ana; Milaković, Milena; Bielen, Ana; Wichmann, Fabienne; Udiković-Kolić, Nikolina
2018-01-01
Environments polluted by direct discharges of effluents from antibiotic manufacturing are important reservoirs for antibiotic resistance genes (ARGs), which could potentially be transferred to human pathogens. However, our knowledge about the identity and diversity of ARGs in such polluted environments remains limited. We applied functional metagenomics to explore the resistome of two Croatian antibiotic manufacturing effluents and sediments collected upstream of and at the effluent discharge sites. Metagenomic libraries built from an azithromycin-production site were screened for resistance to macrolide antibiotics, whereas the libraries from a site producing veterinary antibiotics were screened for resistance to sulfonamides, tetracyclines, trimethoprim, and beta-lactams. Functional analysis of eight libraries identified a total of 82 unique, often clinically relevant ARGs, which were frequently found in clusters and flanked by mobile genetic elements. The majority of macrolide resistance genes identified from matrices exposed to high levels of macrolides were similar to known genes encoding ribosomal protection proteins, macrolide phosphotransferases, and transporters. Potentially novel macrolide resistance genes included one most similar to a 23S rRNA methyltransferase from Clostridium and another, derived from upstream unpolluted sediment, to a GTPase HflX from Emergencia. In libraries deriving from sediments exposed to lower levels of veterinary antibiotics, we found 8 potentially novel ARGs, including dihydrofolate reductases and beta-lactamases from classes A, B, and D. In addition, we detected 7 potentially novel ARGs in upstream sediment, including thymidylate synthases, dihydrofolate reductases, and class D beta-lactamase. Taken together, in addition to finding known gene types, we report the discovery of novel and diverse ARGs in antibiotic-polluted industrial effluents and sediments, providing a qualitative basis for monitoring the dispersal of ARGs from environmental hotspots such as discharge sites of pharmaceutical effluents. PMID:29387045
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kumari, Sangeeta; Saradhi, Mallampati; Rana, Manjul
2015-01-15
Nuclear receptor PXR is predominantly expressed in liver and intestine. Expression of PXR is observed to be dysregulated in various metabolic disorders indicating its involvement in disease development. However, information available on mechanisms of PXR self-regulation is fragmentary. The present investigation identifies some of the regulatory elements responsible for its tight regulation and low cellular expression. Here, we report that the PXR-promoter is a target for some key transcription factors like PU.1/Ets-1, Pax5, LEF-1 and c-Jun. Interestingly, we observed that PXR-promoter responsiveness to Pax5, LEF-1 and c-Jun, is considerably enhanced by Ets transcription factors (PU.1 and Ets-1). Co-transfection of cellsmore » with Ets-1, LEF-1 and c-Jun increased PXR-promoter activity by 5-fold and also induced expression of endogenous human PXR. Site-directed mutagenesis and transfection studies revealed that two Ets binding sites and two of the three LEF binding sites in the PXR-promoter are functional and have a positive effect on PXR transcription. Results suggest that expression of Ets family members, in conjunction with Pax5, LEF-1 and c-Jun, lead to coordinated up-regulation of PXR gene transcription. Insights obtained on the regulation of PXR gene have relevance in offering important cues towards normal functioning as well as development of several metabolic disorders via PXR signaling. - Highlights: • The study identified cis-regulatory elements in the nuclear receptor PXR promoter. • Several trans-acting factors modulating the PXR-promoter have been identified. • PU.1/Ets-1, Pax5, LEF-1, c-Jun, LyF-VI and NF-1 act as modulators of the PXR-promoter. • Ets-1 in conjunction with LEF-1 and c-Jun exhibit 5-fold activation of the PXR-promoter. • Insights into PXR-regulation have relevance in normal and pathological conditions.« less
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Understanding bimolecular machines: Theoretical and experimental approaches
NASA Astrophysics Data System (ADS)
Goler, Adam Scott
This dissertation concerns the study of two classes of molecular machines from a physical perspective: enzymes and membrane proteins. Though the functions of these classes of proteins are different, they each represent important test-beds from which new understanding can be developed by the application of different techniques. HIV1 Reverse Transcriptase is an enzyme that performs multiple functions, including reverse transcription of RNA into an RNA/DNA duplex, RNA degradation by the RNaseH domain, and synthesis of dsDNA. These functions allow for the incorporation of the retroviral genes into the host genome. Its catalytic cycle requires repeated large-scale conformational changes fundamental to its mechanism. Motivated by experimental work, these motions were studied theoretically by the application of normal mode analysis. It was observed that the lowest order modes correlate with largest amplitude (low-frequency) motion, which are most likely to be catalytically relevant. Comparisons between normal modes obtained via an elastic network model to those calculated from the essential dynamics of a series of all-atom molecular dynamics simulations show the self-consistency between these calculations. That similar conformational motions are seen between independent theoretical methods reinforces the importance of large-scale subdomain motion for the biochemical action of DNA polymerases in general. Moreover, it was observed that the major subunits of HIV1 Reverse Transcriptase interact quasi-harmonically. The 5HT3A Serotonin receptor and P2X1 receptor, by contrast, are trans-membrane proteins that function as ligand gated ion channels. Such proteins feature a central pore, which allows for the transit of ions necessary for cellular function across a membrane. The pore is opened by the ligation of binding sites on the extracellular portion of different protein subunits. In an attempt to resolve the individual subunits of these membrane proteins beyond the diffraction limit, a super-localization microscope capable of reconstructing super-resolution images was constructed. This novel setup allows for the study of discrete state kinetic mechanisms with spatial resolution good enough to distinguish individual binding sites of these membrane proteins. Further use of this technique may allow for the study of allostery and subunit specific stoichiometry in the presence of agonist or antagonist ligands relevant to pharmacology.
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Grundeken, Maik J; White, Roseann M; Hernandez, John B; Dudek, Dariusz; Cequier, Angel; Haude, Michael; van Boven, Adrianus J; Piek, Jan J; Helqvist, Steffen; Sabate, Manel; Baumbach, Andreas; Suwannasom, Pannipa; Ishibashi, Yuki; Staehr, Peter; Veldhof, Susan; Cheong, Wai-Fung; de Winter, Robbert J; Garcia-Garcia, Hector M; Wykrzykowska, Joanna J; Onuma, Yoshinobu; Serruys, Patrick W; Chevalier, Bernard
2016-04-01
In the ABSORB II trial, comparing Absorb™ bioresorbable vascular scaffold with metallic XIENCE™ everolimus-eluting stent (EES), a difference was found in site-reported new or worsening angina using adverse event (AE) reporting. However, the clinical relevance of this site-reported angina is unclear. The aim of the present study was therefore to investigate the clinical relevance of site-reported angina by evaluating its relation with cardiac endpoints, cardiovascular resource utilization (including diagnostics and treatment), positive exercise stress tolerance tests (ETTs), and Seattle Angina Questionnaire (SAQ). Site-reported new or worsening angina was captured on cardiac AE forms. There was a wide variation in the total number of days with site-reported angina (overall interquartile range 35-279 days). Patients with site-reported angina showed higher rates of cardiovascular events [including the patient-oriented composite endpoint of all deaths, all myocardial infarctions (MI), or all revascularizations (21.1 vs. 4.2%, P < 0.0001), all MIs (2.3 vs. 0%, P = 0.03), and all revascularizations (21.1 vs. 0.7%, P < 0.0001)], cardiovascular resource utilization (including stress tests, anti-anginal medication, diagnostic angiographies, and hospitalization), and positive ETTs (51.9 vs. 14.9%, P < 0.001), compared with those without site-reported angina. Furthermore, an event-based analysis of the SAQ showed that patients with ongoing angina within the recall period of 4 weeks prior to the SAQ assessment have clinically and statistically significant decrements of >14 points in SAQ scores compared with those with no reported angina. We showed that the site-reported angina through AE reporting may be clinically relevant because of their relation with cardiovascular events (mostly repeat revascularizations), cardiovascular resource utilization, ETT, and SAQ. https://clinicaltrials.gov/ct2/show/NCT01425281; Unique identifier: NCT01425281.
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Henríquez, C.; Riquelme, T. T.; Vera, D.; Julio-Kalajzić, F.; Ehrenfeld, P.; Melvin, J. E.; Figueroa, C. D.; Sarmiento, J.; Flores, C. A.
2017-01-01
Aim Neutrophils are the first cells to arrive at sites of injury. Nevertheless, many inflammatory diseases are characterized by an uncontrolled infiltration and action of these cells. Cell migration depends on volume changes that are governed by ion channel activity, but potassium channels in neutrophil have not been clearly identified. We aim to test whether KCa3.1 participates in neutrophil migration and other relevant functions of the cell. Methods Cytometer and confocal measurements to determine changes in cell volume were used. Cells isolated from human, mouse and horse were tested for KCa3.1-dependent chemotaxis. Chemokinetics, calcium handling and release of reactive oxygen species were measured to determine the role of KCa3.1 in those processes. A mouse model was used to test for neutrophil recruitment after acute lung injury in vivo. Results We show for the first time that KCa3.1 is expressed in mammalian neutrophils. When the channel is inhibited by a pharmacological blocker or by genetic silencing, it profoundly affects cell volume regulation, and chemotactic and chemokinetic properties of the cells. We also demonstrated that pharmacological inhibition of KCa3.1 did not affect calcium entry or reactive oxygen species production in neutrophils. Using a mouse model of acute lung injury, we observed that Kca3.1−/− mice are significantly less effective at recruiting neutrophils into the site of inflammation. Conclusions These results demonstrate that KCa3.1 channels are key actors in the migration capacity of neutrophils, and its inhibition did not affect other relevant cellular functions. PMID:26138196
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GPR 120: The Potential Target for Obesity Treatment.
Tanagho, Peter A; Shohdy, Kyrillus S
2016-01-01
G protein coupled receptor 120 (GPR120) is a class of receptors in the gastrointestinal tract (GIT) that is implicated in nutrient sensing and body weight regulation. Functions of GPR120 are thought to be mediated by the release of a group of hormones known as incretins, such as glucagon like peptide 1 (GLP-1) and gastric inhibitory polypeptide (GIP). We have searched PubMed with the keywords "GPR120","GLP-1" and "obesity". Relevant studies were retrieved and included in the review. Recently, many exogenous compounds have been investigated in their role in the release of GLP-1 and in causing weight loss in obese rats. However, some results question the putative role of GPR120 in metabolic homeostasis. Herein, we evaluate the potential use of GPR120 as a target receptor in obesity and found it to be ubiquitous throughout the GIT, with various functions in each site. In order to find the optimal drug, the role of GPR120 in each site needs to be defined and selectivity of the potential drug needs to be studied to ensure the success of this growing line of obesity management.
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Münze, Ronald; Orlinskiy, Polina; Gunold, Roman; Paschke, Albrecht; Kaske, Oliver; Beketov, Mikhail A; Hundt, Matthias; Bauer, Coretta; Schüürmann, Gerrit; Möder, Monika; Liess, Matthias
2015-12-15
Pesticides negatively affect biodiversity and ecosystem function in aquatic environments. In the present study, we investigated the effects of pesticides on stream macroinvertebrates at 19 sites in a rural area dominated by forest cover and arable land in Central Germany. Pesticide exposure was quantified with Chemcatcher® passive samplers equipped with a diffusion-limiting membrane. Ecological effects on macroinvertebrate communities and on the ecosystem function detritus breakdown were identified using the indicator system SPEARpesticides and the leaf litter degradation rates, respectively. A decrease in the abundance of pesticide-vulnerable taxa and a reduction in leaf litter decomposition rates were observed at sites contaminated with the banned insecticide Carbofuran (Toxic Units≥-2.8), confirming the effect thresholds from previous studies. The results show that Chemcatcher® passive samplers with a diffusion-limiting membrane reliably detect ecologically relevant pesticide pollution, and we suggest Chemcatcher® passive samplers and SPEARpesticides as a promising combination to assess pesticide exposure and effects in rivers and streams. Copyright © 2015 Elsevier B.V. All rights reserved.
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Muñoz-Quiles, Cintia; Santos-Benito, Fernando F.; Llamusí, M. Beatriz; Ramón-Cueto, Almudena
2009-01-01
Olfactory bulb ensheathing glia (OB-OEG) promote repair of spinal cord injury (SCI) in rats after transplantation at acute or subacute (up to 45 days) stages. The most relevant clinical scenario in humans, however, is chronic SCI, in which no more major cellular or molecular changes occur at the injury site; this occurs after the third month in rodents. Whether adult OB-OEG grafts promote repair of severe chronic SCI has not been previously addressed. Rats with complete SCI that were transplanted with OB-OEG 4 months after injury exhibited progressive improvement in motor function and axonal regeneration from different brainstem nuclei across and beyond the SCI site. A positive correlation between motor outcome and axonal regeneration suggested a role for brainstem neurons in the recovery. Functional and histological outcomes did not differ at subacute or chronic stages. Thus, autologous transplantation is a feasible approach as there is time for patient stabilization and OEG preparation in human chronic SCI; the healing effects of OB-OEG on established injuries may offer new therapeutic opportunities for chronic SCI patients. PMID:19915486
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ATAD2 is an epigenetic reader of newly synthesized histone marks during DNA replication.
Koo, Seong Joo; Fernández-Montalván, Amaury E; Badock, Volker; Ott, Christopher J; Holton, Simon J; von Ahsen, Oliver; Toedling, Joern; Vittori, Sarah; Bradner, James E; Gorjánácz, Mátyás
2016-10-25
ATAD2 (ATPase family AAA domain-containing protein 2) is a chromatin regulator harboring an AAA+ ATPase domain and a bromodomain, previously proposed to function as an oncogenic transcription co-factor. Here we suggest that ATAD2 is also required for DNA replication. ATAD2 is co-expressed with genes involved in DNA replication in various cancer types and predominantly expressed in S phase cells where it localized on nascent chromatin (replication sites). Our extensive biochemical and cellular analyses revealed that ATAD2 is recruited to replication sites through a direct interaction with di-acetylated histone H4 at K5 and K12, indicative of newly synthesized histones during replication-coupled chromatin reassembly. Similar to ATAD2-depletion, ectopic expression of ATAD2 mutants that are deficient in binding to these di-acetylation marks resulted in reduced DNA replication and impaired loading of PCNA onto chromatin, suggesting relevance of ATAD2 in DNA replication. Taken together, our data show a novel function of ATAD2 in cancer and for the first time identify a reader of newly synthesized histone di-acetylation-marks during replication.
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A Pictet-Spengler ligation for protein chemical modification
Agarwal, Paresh; van der Weijden, Joep; Sletten, Ellen M.; Rabuka, David; Bertozzi, Carolyn R.
2013-01-01
Aldehyde- and ketone-functionalized proteins are appealing substrates for the development of chemically modified biotherapeutics and protein-based materials. Their reactive carbonyl groups are typically conjugated with α-effect nucleophiles, such as substituted hydrazines and alkoxyamines, to generate hydrazones and oximes, respectively. However, the resulting C=N linkages are susceptible to hydrolysis under physiologically relevant conditions, which limits the utility of such conjugates in biological systems. Here we introduce a Pictet-Spengler ligation that is based on the classic Pictet-Spengler reaction of aldehydes and tryptamine nucleophiles. The ligation exploits the bioorthogonal reaction of aldehydes and alkoxyamines to form an intermediate oxyiminium ion; this intermediate undergoes intramolecular C–C bond formation with an indole nucleophile to form an oxacarboline product that is hydrolytically stable. We used the reaction for site-specific chemical modification of glyoxyl- and formylglycine-functionalized proteins, including an aldehyde-tagged variant of the therapeutic monoclonal antibody Herceptin. In conjunction with techniques for site-specific introduction of aldehydes into proteins, the Pictet-Spengler ligation offers a means to generate stable bioconjugates for medical and materials applications. PMID:23237853
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Functional advantages of dynamic protein disorder.
Berlow, Rebecca B; Dyson, H Jane; Wright, Peter E
2015-09-14
Intrinsically disordered proteins participate in many important cellular regulatory processes. The absence of a well-defined structure in the free state of a disordered domain, and even on occasion when it is bound to physiological partners, is fundamental to its function. Disordered domains are frequently the location of multiple sites for post-translational modification, the key element of metabolic control in the cell. When a disordered domain folds upon binding to a partner, the resulting complex buries a far greater surface area than in an interaction of comparably-sized folded proteins, thus maximizing specificity at modest protein size. Disorder also maintains accessibility of sites for post-translational modification. Because of their inherent plasticity, disordered domains frequently adopt entirely different structures when bound to different partners, increasing the repertoire of available interactions without the necessity for expression of many different proteins. This feature also adds to the faithfulness of cellular regulation, as the availability of a given disordered domain depends on competition between various partners relevant to different cellular processes. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
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Herbicide volatilization trumps runoff losses, a multi-year investigation
USDA-ARS?s Scientific Manuscript database
Surface runoff and volatilization are two processes critical to herbicide off-site transport. To determine the relevance of these off-site transport mechanisms, runoff and turbulent vapor fluxes were simultaneously monitored on the same site for eight years. Site location, herbicide formulations, ...
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Quero, Grazia Marina; Cassin, Daniele; Botter, Margherita; Perini, Laura; Luna, Gian Marco
2015-01-01
Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea), which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea), is a chronically polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to contaminant bioremediation actions. PMID:26528247
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Like mother, like offspring: maternal and offspring wound healing correlate in snakes.
Hopkins, Brittney C; Chin, Stephanie Y; Willson, John D; Hopkins, William A
2013-07-15
Immune function early in life can be influenced by parental effects and the environment, but it remains unclear how these two factors may interact to influence immunocompetence. We evaluated maternal and environmental contributions to offspring healing ability in a viviparous reptile, the northern watersnake (Nerodia sipedon). We measured wound healing rates, a highly integrative and biologically relevant measure of innate immunity, of females and their offspring collected from sites contaminated with a toxic heavy metal and compared them with those of individuals from reference sites. We found that female watersnakes that healed the fastest produced offspring that also exhibited faster healing rates. However, we detected no influence of environmental pollution on maternal or offspring healing rates. To our knowledge, our study is the first to correlate maternal and offspring wound healing ability in a wild vertebrate.
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Climate Change Projection for the Department of Energy's Savannah River Site
NASA Astrophysics Data System (ADS)
Werth, D. W.
2014-12-01
As per recent Department of Energy (DOE) sustainability requirements, the Savannah River National Laboratory (SRNL) is developing a climate projection for the DOE's Savannah River Site (SRS) near Aiken, SC. This will comprise data from both a statistical and a dynamic downscaling process, each interpolated to the SRS. We require variables most relevant to operational activities at the site (such as the US Forest Service's forest management program), and select temperature, precipitation, wind, and humidity as being most relevant to energy and water resource requirements, fire and forest ecology, and facility and worker safety. We then develop projections of the means and extremes of these variables, estimate the effect on site operations, and develop long-term mitigation strategies. For example, given that outdoor work while wearing protective gear is a daily facet of site operations, heat stress is of primary importance to work planning, and we use the downscaled data to estimate changes in the occurrence of high temperatures. For the statistical downscaling, we use global climate model (GCM) data from the Climate Model Intercomparison Project, version 5 (CMIP-5), which was used in the IPCC Fifth Assessment Report (AR5). GCM data from five research groups was selected, and two climate change scenarios - RCP 4.5 and RCP 8.5 - are used with observed data from site instruments and other databases to produce the downscaled projections. We apply a quantile regression downscaling method, which involves the use of the observed cumulative distribution function to correct that of the GCM. This produces a downscaled projection with an interannual variability closer to that of the observed data and allows for more extreme values in the projections, which are often absent in GCM data. The statistically downscaled data is complemented with dynamically downscaled data from the NARCCAP database, which comprises output from regional climate models forced with GCM output from the CMIP-3 database of GCM simulations. Applications of the downscaled climate projections to some of the unique operational needs of a large DOE weapons complex site are described.
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Joshi, Shilpa M.; Mastrangelo, Ashley N.; Magarian, Elise M.; Fleming, Braden C.; Murray, Martha M.
2010-01-01
Background The anterior cruciate ligament (ACL) fails to heal after traumatic rupture. Furthermore, large-animal models have recently shown that 1-month functional ACL healing is augmented after suture repair when a bioactive scaffold is placed in the tear site. Hypothesis At the time of suture repair, placement of a bioactive scaffold in the ACL wound site would improve the structural properties of the tissue. Study Design Controlled laboratory study. Methods Twenty-seven knees in immature pigs underwent ACL transection and suture repair. A collagen-platelet composite (CPC) was used to supplement the repair in 14 knees. Knees were harvested at 4 weeks, 6 weeks, and 3 months. Mechanical testing and histologic analysis were performed. Results The addition of a CPC to a suture repair resulted in improvements in yield load and linear stiffness of the repair tissue at 3 months, as well as a significant increase in cell density. A reduction in yield load and stiffness occurred at the 6-week time point in both groups, a phase when revascularization was noted. Conclusion The addition of a CPC to a suture repair enhanced the structural properties of the ACL, and the improvement was associated with increased cellularity within the healing ligament. Clinical Relevance The addition of a bioactive scaffold to the wound site improved the functional healing of the ACL after suture repair. The decreased repair strength during revascularization may indicate a need to protect the repair site through this period. PMID:19940313
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Martin, David P; Blachly, Patrick G; Marts, Amy R; Woodruff, Tessa M; de Oliveira, César A F; McCammon, J Andrew; Tierney, David L; Cohen, Seth M
2014-04-09
The binding of three closely related chelators: 5-hydroxy-2-methyl-4H-pyran-4-thione (allothiomaltol, ATM), 3-hydroxy-2-methyl-4H-pyran-4-thione (thiomaltol, TM), and 3-hydroxy-4H-pyran-4-thione (thiopyromeconic acid, TPMA) to the active site of human carbonic anhydrase II (hCAII) has been investigated. Two of these ligands display a monodentate mode of coordination to the active site Zn(2+) ion in hCAII that is not recapitulated in model complexes of the enzyme active site. This unprecedented binding mode in the hCAII-thiomaltol complex has been characterized by both X-ray crystallography and X-ray spectroscopy. In addition, the steric restrictions of the active site force the ligands into a 'flattened' mode of coordination compared with inorganic model complexes. This change in geometry has been shown by density functional computations to significantly decrease the strength of the metal-ligand binding. Collectively, these data demonstrate that the mode of binding by small metal-binding groups can be significantly influenced by the protein active site. Diminishing the strength of the metal-ligand bond results in unconventional modes of metal coordination not found in typical coordination compounds or even carefully engineered active site models, and understanding these effects is critical to the rational design of inhibitors that target clinically relevant metalloproteins.
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Sabooh, M Fazli; Iqbal, Nadeem; Khan, Mukhtaj; Khan, Muslim; Maqbool, H F
2018-05-01
This study examines accurate and efficient computational method for identification of 5-methylcytosine sites in RNA modification. The occurrence of 5-methylcytosine (m 5 C) plays a vital role in a number of biological processes. For better comprehension of the biological functions and mechanism it is necessary to recognize m 5 C sites in RNA precisely. The laboratory techniques and procedures are available to identify m 5 C sites in RNA, but these procedures require a lot of time and resources. This study develops a new computational method for extracting the features of RNA sequence. In this method, first the RNA sequence is encoded via composite feature vector, then, for the selection of discriminate features, the minimum-redundancy-maximum-relevance algorithm was used. Secondly, the classification method used has been based on a support vector machine by using jackknife cross validation test. The suggested method efficiently identifies m 5 C sites from non- m 5 C sites and the outcome of the suggested algorithm is 93.33% with sensitivity of 90.0 and specificity of 96.66 on bench mark datasets. The result exhibits that proposed algorithm shown significant identification performance compared to the existing computational techniques. This study extends the knowledge about the occurrence sites of RNA modification which paves the way for better comprehension of the biological uses and mechanism. Copyright © 2018 Elsevier Ltd. All rights reserved.
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SF Box--a tool for evaluating the effects on soil functions in remediation projects.
Volchko, Yevheniya; Norrman, Jenny; Rosén, Lars; Norberg, Tommy
2014-10-01
Although remediation is usually aimed at reducing the risks posed by contaminants to human health and the environment, it is also desirable that the remediated soil within future green spaces is capable of providing relevant ecological functions, e.g., basis for primary production. Yet while addressing a contamination problem by reducing contaminant concentration and/or amounts in the soil, the remedial action itself can lead to soil structure disturbances, decline in organic matter and nutrient deficiencies, and in turn affect a soil's capacity to carry out its ecological soil functions. This article presents the Soil Function Box (SF Box) tool that is aimed to facilitate integration of information from suggested soil quality indicators (SQIs) into a management process in remediation using a scoring method. The scored SQIs are integrated into a soil quality index corresponding to 1 of 5 classes. SF Box is applied to 2 cases from Sweden (Kvillebäcken and Hexion), explicitly taking into consideration uncertainties in the results by means of Monte Carlo simulations. At both sites the generated soil quality indices corresponded to a medium soil performance (soil class 3) with a high certainty. The main soil constraints at both Kvillebäcken and Hexion were associated with biological activity in the soil, as soil organisms were unable to supply plant-available N. At the Kvillebäcken site the top layer had a content of coarse fragment (ø > 2 mm) higher than 35%, indicating plant rooting limitations. At the Hexion site, the soil had limited amount of organic matter, thus poor aggregate stability and nutrient cycling potential. In contrast, the soil at Kvillebäcken was rich in organic matter. The soils at both sites were capable of storing a sufficient amount of water for soil organisms between precipitation events. © 2014 SETAC.
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NASA Astrophysics Data System (ADS)
Mattson, E.; Versteeg, R.; Ankeny, M.; Stormberg, G.
2005-12-01
Long term performance monitoring has been identified by DOE, DOD and EPA as one of the most challenging and costly elements of contaminated site remedial efforts. Such monitoring should provide timely and actionable information relevant to a multitude of stakeholder needs. This information should be obtained in a manner which is auditable, cost effective and transparent. Over the last several years INL staff has designed and implemented a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition from diverse sensors (geophysical, geochemical and hydrological) with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic javascript and html/css) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This system has been implemented and is operational for several sites, including the Ruby Gulch Waste Rock Repository (a capped mine waste rock dump on the Gilt Edge Mine Superfund Site), the INL Vadoze Zone Research Park and an alternative cover landfill. Implementations for other vadoze zone sites are currently in progress. These systems allow for autonomous performance monitoring through automated data analysis and report generation. This performance monitoring has allowed users to obtain insights into system dynamics, regulatory compliance and residence times of water. Our system uses modular components for data selection and graphing and WSDL compliant webservices for external functions such as statistical analyses and model invocations. Thus, implementing this system for novel sites and extending functionality (e.g. adding novel models) is relatively straightforward. As system access requires a standard webbrowser and uses intuitive functionality, stakeholders with diverse degrees of technical insight can use this system with little or no training.
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Markunas, Christina A; Johnson, Eric O; Hancock, Dana B
2017-07-01
Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p < 5×10 -8 ) from the NHGRI-EBI Catalog across seven disease/trait categories: cancer, cardiovascular disease, diabetes, autoimmune disease, psychiatric disease, neurological disease, and anthropometric traits. SNPs were annotated using HaploReg for the eight functional elements across any tissue: DNase sites, expression quantitative trait loci (eQTL), sequence conservation, enhancers, promoters, missense variants, sequence motifs, and protein binding sites. In addition, tissue-specific annotations were considered for brain vs. blood. Disease/trait SNPs were compared to a control set of 4809 SNPs matched to the GWAS SNPs (N = 1639) on allele frequency, gene density, distance to nearest gene, and linkage disequilibrium at ~3:1 ratio. Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference = 1.28 × 10 -6 vs. enhancers P TissueDifference = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.
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Wang, Xiaoyang; Barrett, Matthew; Sondek, John; Harden, T. Kendall; Zhang, Qisheng
2013-01-01
The capacity to monitor spatiotemporal activity of phospholipase C (PLC) isozymes with a PLC-selective sensor would dramatically enhance understanding of the physiological function and disease relevance of these signaling proteins. Previous structural and biochemical studies defined critical roles for several of the functional groups of the endogenous substrate of PLC isozymes, phosphatidylinositol 4,5-bisphosphate (PIP2), indicating that these sites cannot be readily modified without compromising interactions with the lipase active site. However, the role of the 6-hydroxy group of PIP2 for interaction and hydrolysis by PLC has not been explored, possibly due to challenges in synthesizing 6-hydroxy derivatives. Here, we describe an efficient route for the synthesis of novel, fluorescent PIP2 derivatives modified at the 6-hydroxy group. Two of these derivatives were used in assays of PLC activity in which the fluorescent PIP2 substrates were separated from their diacylglycerol products and reaction rates quantified by fluorescence. Both PIP2 analogues effectively function as substrates of PLC-δ1, and the KM and Vmax values obtained with one of these are similar to those observed with native PIP2 substrate. These results indicate that the 6-hydroxy group can be modified to develop functional substrates for PLC isozymes, thereby serving as the foundation for further development of PLC-selective sensors. PMID:22703043
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Connectivity constraints on cortical reorganization of neural circuits involved in object naming.
Papagno, Costanza; Gallucci, Marcello; Casarotti, Alessandra; Castellano, Antonella; Falini, Andrea; Fava, Enrica; Giussani, Carlo; Carrabba, Giorgio; Bello, Lorenzo; Caramazza, Alfonso
2011-04-01
The brain's plasticity in response to sensory deprivation and other perturbations is well established. While the functional properties of the reorganized areas are under vigorous investigation, the factors that constrain cortical reorganization remain poorly understood. One factor constraining such reorganization may be long-distance subcortical connectivity between relevant cortical regions-reorganization attempts to preserve the functionality of subcortical connections. Here we provide human neurophysiological evidence for the role of the subcortical connections in shaping cortical reorganization of the networks involved in object naming following perturbation of normal function. We used direct electrical stimulation (DES) during surgical removal of gliomas to identify the sites that are involved in naming different categories of objects. The sites that were selectively inhibited in naming either living or non-living objects were displaced relative to those observed with other subject populations, possibly reflecting cortical reorganization due to slowly evolving brain damage. Subcortical DES applied to the white matter underlying these regions also led to category-specific naming deficits. The existence of these subcortical fiber pathways was confirmed using diffusion tensor tractography. These results constitute the first neurophysiological evidence for the critical role of subcortical pathways as part of the neural circuits that are involved in object naming; they also highlight the importance of subcortical connectivity in shaping cortical reorganization following perturbations of normal function. Copyright © 2011 Elsevier Inc. All rights reserved.
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Hu, Gang; Wu, Zhonghua
2017-01-01
Some of the intrinsically disordered proteins and protein regions are promiscuous interactors that are involved in one-to-many and many-to-one binding. Several studies have analyzed enrichment of intrinsic disorder among the promiscuous hub proteins. We extended these works by providing a detailed functional characterization of the disorder-enriched hub protein-protein interactions (PPIs), including both hubs and their interactors, and by analyzing their enrichment among disease-associated proteins. We focused on the human interactome, given its high degree of completeness and relevance to the analysis of the disease-linked proteins. We quantified and investigated numerous functional and structural characteristics of the disorder-enriched hub PPIs, including protein binding, structural stability, evolutionary conservation, several categories of functional sites, and presence of over twenty types of posttranslational modifications (PTMs). We showed that the disorder-enriched hub PPIs have a significantly enlarged number of disordered protein binding regions and long intrinsically disordered regions. They also include high numbers of targeting, catalytic, and many types of PTM sites. We empirically demonstrated that these hub PPIs are significantly enriched among 11 out of 18 considered classes of human diseases that are associated with at least 100 human proteins. Finally, we also illustrated how over a dozen specific human hubs utilize intrinsic disorder for their promiscuous PPIs. PMID:29257115
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Goldman-Rakic, P S
1996-10-29
The functional architecture of prefrontal cortex is central to our understanding of human mentation and cognitive prowess. This region of the brain is often treated as an undifferentiated structure, on the one hand, or as a mosaic of psychological faculties, on the other. This paper focuses on the working memory processor as a specialization of prefrontal cortex and argues that the different areas within prefrontal cortex represent iterations of this function for different information domains, including spatial cognition, object cognition and additionally, in humans, semantic processing. According to this parallel processing architecture, the 'central executive' could be considered an emergent property of multiple domain-specific processors operating interactively. These processors are specializations of different prefrontal cortical areas, each interconnected both with the domain-relevant long-term storage sites in posterior regions of the cortex and with appropriate output pathways.
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Howard, Rebecca J; Trudell, James R; Harris, R Adron
2014-01-01
Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.
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Worm Algorithm simulations of the hole dynamics in the t-J model
NASA Astrophysics Data System (ADS)
Prokof'ev, Nikolai; Ruebenacker, Oliver
2001-03-01
In the limit of small J << t, relevant for HTSC materials and Mott-Hubbard systems, computer simulations have to be performed for large systems and at low temperatures. Despite convincing evidence against spin-charge separation obtained by various methods for J > 0.4t there is an ongoing argument that at smaller J spin-charge separation is still possible. Worm algorithm Monte Carlo simulations of the hole Green function for 0.1 < J/t < 0.4 were performed on lattices with up to 32x32 sites, and at temperature J/T = 40 (for the largest size). Spectral analysis reveals a single, delta-function sharp quasiparticle peak at the lowest edge of the spectrum and two distinct peaks above it at all studied J. We rule out the possibility of spin-charge separation in this parameter range, and present, apparently, the hole spectral function in the thermodynamic limit.
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Engineered TAL Effector modulators for the large-scale gain-of-function screening
Zhang, Hanshuo; Li, Juan; Hou, Sha; Wang, Gancheng; Jiang, Mingjun; Sun, Changhong; Hu, Xiongbing; Zhuang, Fengfeng; Dai, Zhifei; Dai, Junbiao; Xi, Jianzhong Jeff
2014-01-01
Recent effective use of TAL Effectors (TALEs) has provided an important approach to the design and synthesis of sequence-specific DNA-binding proteins. However, it is still a challenging task to design and manufacture effective TALE modulators because of the limited knowledge of TALE–DNA interactions. Here we synthesized more than 200 TALE modulators and identified two determining factors of transcription activity in vivo: chromatin accessibility and the distance from the transcription start site. The implementation of these modulators in a gain-of-function screen was successfully demonstrated for four cell lines in migration/invasion assays and thus has broad relevance in this field. Furthermore, a novel TALE–TALE modulator was developed to transcriptionally inhibit target genes. Together, these findings underscore the huge potential of these TALE modulators in the study of gene function, reprogramming of cellular behaviors, and even clinical investigation. PMID:24939900
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Trudell, James R.; Harris, R. Adron
2014-01-01
Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646
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Role of the Environment in the Transmission of Antimicrobial Resistance to Humans: A Review.
Huijbers, Patricia M C; Blaak, Hetty; de Jong, Mart C M; Graat, Elisabeth A M; Vandenbroucke-Grauls, Christina M J E; de Roda Husman, Ana Maria
2015-10-20
To establish a possible role for the natural environment in the transmission of clinically relevant AMR bacteria to humans, a literature review was conducted to systematically collect and categorize evidence for human exposure to extended-spectrum β-lactamase-producing Enterobacteriaceae, methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus spp. in the environment. In total, 239 datasets adhered to inclusion criteria. AMR bacteria were detected at exposure-relevant sites (35/38), including recreational areas, drinking water, ambient air, and shellfish, and in fresh produce (8/16). More datasets were available for environmental compartments (139/157), including wildlife, water, soil, and air/dust. Quantitative data from exposure-relevant sites (6/35) and environmental compartments (11/139) were scarce. AMR bacteria were detected in the contamination sources (66/66) wastewater and manure, and molecular data supporting their transmission from wastewater to the environment (1/66) were found. The abundance of AMR bacteria at exposure-relevant sites suggests risk for human exposure. Of publications pertaining to both environmental and human isolates, however, only one compared isolates from samples that had a clear spatial and temporal relationship, and no direct evidence was found for transmission to humans through the environment. To what extent the environment, compared to the clinical and veterinary domains, contributes to human exposure needs to be quantified. AMR bacteria in the environment, including sites relevant for human exposure, originate from contamination sources. Intervention strategies targeted at these sources could therefore limit emission of AMR bacteria to the environment.
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Prediction of lysine glutarylation sites by maximum relevance minimum redundancy feature selection.
Ju, Zhe; He, Jian-Jun
2018-06-01
Lysine glutarylation is new type of protein acylation modification in both prokaryotes and eukaryotes. To better understand the molecular mechanism of glutarylation, it is important to identify glutarylated substrates and their corresponding glutarylation sites accurately. In this study, a novel bioinformatics tool named GlutPred is developed to predict glutarylation sites by using multiple feature extraction and maximum relevance minimum redundancy feature selection. On the one hand, amino acid factors, binary encoding, and the composition of k-spaced amino acid pairs features are incorporated to encode glutarylation sites. And the maximum relevance minimum redundancy method and the incremental feature selection algorithm are adopted to remove the redundant features. On the other hand, a biased support vector machine algorithm is used to handle the imbalanced problem in glutarylation sites training dataset. As illustrated by 10-fold cross-validation, the performance of GlutPred achieves a satisfactory performance with a Sensitivity of 64.80%, a Specificity of 76.60%, an Accuracy of 74.90% and a Matthew's correlation coefficient of 0.3194. Feature analysis shows that some k-spaced amino acid pair features play the most important roles in the prediction of glutarylation sites. The conclusions derived from this study might provide some clues for understanding the molecular mechanisms of glutarylation. Copyright © 2018 Elsevier Inc. All rights reserved.
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The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers
Lueders, Tillmann
2017-01-01
Abstract The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. PMID:27810873
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"Urban geosites" as an alternative geotourism destination - evidence from Belgrade
NASA Astrophysics Data System (ADS)
Petrović, Marko D.; Lukić, Dobrila M.; Radovanović, Milan; Vujko, Aleksandra; Gajić, Tamara; Vuković, Darko
2017-10-01
The research aimed at testing the combination of GAM/M-GAM models (Geosite Assessment Model/Modified Geosite Assessment Model) on selected geoheritage sites (geosites) of great scientific significance and geotourism potential. Testing was done on eight sites in the City of Belgrade (Serbian capital), an area which has significant potential for geotourism development in typical urban conditions. For this purpose, an assessment scale was used to highlight differences and similarities between main and additional values of the observed geosites. The modification of the original GAM model is based on the inclusion of visitors' opinions regarding the importance of indicators in the assessment process. The assessment was done by using both GAM/M-GAM and its results were analyzed and compared afterwards. The analysis has successfully identified locations and features of geosites that require action for maintaining or increasing their overall value and function. Moreover, the principal aim of the paper was to analyze the relevance of each sub-indicator for the assessment process by introducing the importance factor in the modified model. The authors were able to point out those values of principal importance for geosite visitors, as well as to attach a different relevance to sub-indicators, which can influence the position of the geosites in the GAM/M-GAM matrices.
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[Perioperative onset of sarcoidosis : Rare differential diagnosis of a difficult airway].
Jansen, G; Nowak, A
2018-05-01
Sarcoidosis is a rare multisystemic chronic inflammatory condition. Typically, there is a big discrepancy between the patient's subjectively perceived symptoms and the presence of clinical signs. Due to the high number of potential sites of onset (e. g. larynx, lungs, heart, liver, kidneys) the affected organs may show functional restrictions that are relevant for decisions related to anesthesia. Therefore, an anesthetists working in a clinical setting should be familiar with the special needs of this patient collective. This article describes the onset of sarcoidosis in a case of an unexpected difficult airway.
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Linnemann, Birgit; Thalhammer, Axel; Wolf, Zsuzsanna; Tirneci, Vanessa; Vogl, Thomas J; Edelgard Lindhoff-Last, And
2012-03-01
Late peripheral arterial stent thrombosis usually occurs due to haemodynamically relevant in-stent restenosis. However, late stent thrombosis may be multicausal. We report here the well-documented case of a 69-year-old man with acute thrombosis of the stented superficial femoral artery after a long-distance bicycle tour. Catheter-directed thrombolysis revealed a residual stenosis located at a stent fracture site. In addition, platelet function tests revealed an inadequate platelet response to clopidogrel. In conclusion, stent fracture, strenuous exercise and hyporesponsiveness to clopidogrel may have contributed to the development of late peripheral stent thrombosis.
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Connecting Projects to Complete the In Situ Resource Utilization Paradigm
NASA Technical Reports Server (NTRS)
Linne, Diane L.; Sanders, Gerald B.
2017-01-01
Terrain Identify specifics such as slope, rockiness, traction parameters Identify what part of ISRU needs each Physical Geotechnical Hardness, density, cohesion, etc. Identify what part of ISRU needs each (e.g., excavation needs to know hardness, density; soil processing needs to know density, cohesion; etc.)Mineral Identify specifics Identify what part of ISRU needs each Volatile Identify specifics Identify what part of ISRU needs each Atmosphere Identify specifics Identify what part of ISRU needs each Environment Identify specifics Identify what part of ISRU needs each Resource Characterization What: Develop an instrument suite to locate and evaluate the physical, mineral, and volatile resources at the lunar poles Neutron Spectrometer Near Infrared (IR) to locate subsurface hydrogen surface water Near IR for mineral identification Auger drill for sample removal down to 1 m Oven with Gas Chromatograph Mass Spectrometer to quantify volatiles present ISRU relevance: Water volatile resource characterization and subsurface material access removal Site Evaluation Resource Mapping What: Develop and utilize new data products and tools for evaluating potential exploration sites for selection and overlay mission data to map terrain, environment, and resource information e.g., New techniques applied to generate Digital Elevation Map (DEMs) at native scale of images (1mpxl)ISRU relevance: Resource mapping and estimation with terrain and environment information is needed for extraction planning Mission Planning and Operations What: Develop and utilize tools and procedures for planning mission operations and real time changes Planning tools include detailed engineering models (e.g., power and data) of surface segment systems allows evaluation of designs ISRU relevance: Allows for iterative engineering as a function of environment and hardware performance.
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de Dianous, Valérie; Fiévez, Cécile
2006-03-31
Over the last two decades a growing interest for risk analysis has been noted in the industries. The ARAMIS project has defined a methodology for risk assessment. This methodology has been built to help the industrialist to demonstrate that they have a sufficient risk control on their site. Risk analysis consists first in the identification of all the major accidents, assuming that safety functions in place are inefficient. This step of identification of the major accidents uses bow-tie diagrams. Secondly, the safety barriers really implemented on the site are taken into account. The barriers are identified on the bow-ties. An evaluation of their performance (response time, efficiency, and level of confidence) is performed to validate that they are relevant for the expected safety function. At last, the evaluation of their probability of failure enables to assess the frequency of occurrence of the accident. The demonstration of the risk control based on a couple gravity/frequency of occurrence is also possible for all the accident scenarios. During the risk analysis, a practical tool called risk graph is used to assess if the number and the reliability of the safety functions for a given cause are sufficient to reach a good risk control.
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De Filippis, Vincenzo; Acquasaliente, Laura; Pontarollo, Giulia; Peterle, Daniele
2018-01-01
The advent of recombinant DNA technology allowed to site-specifically insert, delete, or mutate almost any amino acid in a given protein, significantly improving our knowledge of protein structure, stability, and function. Nevertheless, a quantitative description of the physical and chemical basis that makes a polypeptide chain to efficiently fold into a stable and functionally active conformation is still elusive. This mainly originates from the fact that nature combined, in a yet unknown manner, different properties (i.e., hydrophobicity, conformational propensity, polarizability, and hydrogen bonding capability) into the 20 standard natural amino acids, thus making difficult, if not impossible, to univocally relate the change in protein stability or function to the alteration of physicochemical properties caused by amino acid exchange(s). In this view, incorporation of noncoded amino acids with tailored side chains, allowing to finely tune the structure at a protein site, would facilitate to dissect the effects of a given mutation in terms of one or a few physicochemical properties, thus much expanding the scope of physical organic chemistry in the study of proteins. In this review, relevant applications from our laboratory will be presented on the use of noncoded amino acids in structure-activity relationships studies of hirudin binding to thrombin. © 2017 International Union of Biochemistry and Molecular Biology, Inc.
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Improving Web Searches: Case Study of Quit-Smoking Web Sites for Teenagers
Skinner, Harvey
2003-01-01
Background The Web has become an important and influential source of health information. With the vast number of Web sites on the Internet, users often resort to popular search sites when searching for information. However, little is known about the characteristics of Web sites returned by simple Web searches for information about smoking cessation for teenagers. Objective To determine the characteristics of Web sites retrieved by search engines about smoking cessation for teenagers and how information quality correlates with the search ranking. Methods The top 30 sites returned by 4 popular search sites in response to the search terms "teen quit smoking" were examined. The information relevance and quality characteristics of these sites were evaluated by 2 raters. Objective site characteristics were obtained using a page-analysis Web site. Results Only 14 of the 30 Web sites are of direct relevance to smoking cessation for teenagers. The readability of about two-thirds of the 14 sites is below an eighth-grade school level and they ranked significantly higher (Kendall rank correlation, tau = -0.39, P= .05) in search-site results than sites with readability above or equal to that grade level. Sites that ranked higher were significantly associated with the presence of e-mail address for contact (tau = -0.46, P= .01), annotated hyperlinks to external sites (tau = -0.39, P= .04), and the presence of meta description tag (tau = -0.48, P= .002). The median link density (number of external sites that have a link to that site) of the Web pages was 6 and the maximum was 735. A higher link density was significantly associated with a higher rank (tau = -0.58, P= .02). Conclusions Using simple search terms on popular search sites to look for information on smoking cessation for teenagers resulted in less than half of the sites being of direct relevance. To improve search efficiency, users could supplement results obtained from simple Web searches with human-maintained Web directories and learn to refine their searches with more advanced search syntax. PMID:14713656
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NASA Astrophysics Data System (ADS)
Pan, Patricia Wang; Dickson, Russell J.; Gordon, Heather L.; Rothstein, Stuart M.; Tanaka, Shigenori
2005-01-01
Functionally relevant motion of proteins has been associated with a number of atoms moving in a concerted fashion along so-called "collective coordinates." We present an approach to extract collective coordinates from conformations obtained from molecular dynamics simulations. The power of this technique for differentiating local structural fuctuations between classes of conformers obtained by clustering is illustrated by analyzing nanosecond-long trajectories for the response regulator protein Spo0F of Bacillus subtilis, generated both in vacuo and using an implicit-solvent representation. Conformational clustering is performed using automated histogram filtering of the inter-Cα distances. Orthogonal (varimax) rotation of the vectors obtained by principal component analysis of these interresidue distances for the members of individual clusters is key to the interpretation of collective coordinates dominating each conformational class. The rotated loadings plots isolate significant variation in interresidue distances, and these are associated with entire mobile secondary structure elements. From this we infer concerted motions of these structural elements. For the Spo0F simulations employing an implicit-solvent representation, collective coordinates obtained in this fashion are consistent with the location of the protein's known active sites and experimentally determined mobile regions.
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Insights into Structural and Mechanistic Features of Viral IRES Elements
Martinez-Salas, Encarnacion; Francisco-Velilla, Rosario; Fernandez-Chamorro, Javier; Embarek, Azman M.
2018-01-01
Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of protein synthesis using cap-independent mechanisms. However, distinct types of IRES elements present in the genome of various RNA viruses perform the same function despite lacking conservation of sequence and secondary RNA structure. Likewise, IRES elements differ in host factor requirement to recruit the ribosomal subunits. In spite of this diversity, evolutionarily conserved motifs in each family of RNA viruses preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES activity. Indeed, IRES elements adopting remarkable different structural organizations contain RNA structural motifs that play an essential role in recruiting ribosomes, initiation factors and/or RNA-binding proteins using different mechanisms. Therefore, given that a universal IRES motif remains elusive, it is critical to understand how diverse structural motifs deliver functions relevant for IRES activity. This will be useful for understanding the molecular mechanisms beyond cap-independent translation, as well as the evolutionary history of these regulatory elements. Moreover, it could improve the accuracy to predict IRES-like motifs hidden in genome sequences. This review summarizes recent advances on the diversity and biological relevance of RNA structural motifs for viral IRES elements. PMID:29354113
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Scott, J E
1991-06-01
Electron histochemical investigations of mammalian and echinoderm tissues, using cupromeronic blue to stain proteoglycans (PGs) specifically in critical electrolyte concentration methods, showed that collagen fibrils are associated with keratan sulphate and chondroitin (dermatan) sulphate ('tadpole') PGs at the a, c, d and e bands on the fibril surface, giving rise to the 'one proteoglycan: one binding site' hypothesis. Intra-fibrillar PGs have been observed, distributed in a regular way which suggests that collagen fibrils are aggregates of 'protofibrils', some of which carry PGs at their surfaces. A scheme for remodelling of collagen fibrils, based on recycling of these protofibrils, is outlined. The choice of which tadpole PG to use to carry out a given function is decided to a considerable extent by the availability of oxygen to the relevant tissue element.
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Small-Molecule Inhibitors of Urea Transporters
Verkman, Alan S.; Esteva-Font, Cristina; Cil, Onur; Anderson, Marc O.; Li, Fei; Li, Min; Lei, Tianluo; Ren, Huiwen; Yang, Baoxue
2015-01-01
Urea transporter (UT) proteins, which include isoforms of UT-A in kidney tubule epithelia and UT-B in vasa recta endothelia and erythrocytes, facilitate urinary concentrating function. Inhibitors of urea transporter function have potential clinical applications as sodium-sparing diuretics, or ‘urearetics,’ in edema from different etiologies, such as congestive heart failure and cirrhosis, as well as in syndrome of inappropriate antidiuretic hormone (SIADH). High-throughput screening of drug-like small molecules has identified UT-A and UT-B inhibitors with nanomolar potency. Inhibitors have been identified with different UT-A versus UT-B selectivity profiles and putative binding sites on UT proteins. Studies in rodent models support the utility of UT inhibitors in reducing urinary concentration, though testing in clinically relevant animal models of edema has not yet been done. PMID:25298345
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Linking microbiota and respiratory disease.
Hauptmann, Matthias; Schaible, Ulrich E
2016-11-01
An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions. © 2016 Federation of European Biochemical Societies.
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Code of Federal Regulations, 2011 CFR
2011-07-01
... through a Web Site. Web Site is a site located on the World Wide Web that can be located by an end user... transmitted over the Internet during the relevant period to all end users within the United States from all...
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Code of Federal Regulations, 2014 CFR
2014-07-01
... through a Web Site. Web Site is a site located on the World Wide Web that can be located by an end user... transmitted over the Internet during the relevant period to all end users within the United States from all...
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Resources for Functional Genomics Studies in Drosophila melanogaster
Mohr, Stephanie E.; Hu, Yanhui; Kim, Kevin; Housden, Benjamin E.; Perrimon, Norbert
2014-01-01
Drosophila melanogaster has become a system of choice for functional genomic studies. Many resources, including online databases and software tools, are now available to support design or identification of relevant fly stocks and reagents or analysis and mining of existing functional genomic, transcriptomic, proteomic, etc. datasets. These include large community collections of fly stocks and plasmid clones, “meta” information sites like FlyBase and FlyMine, and an increasing number of more specialized reagents, databases, and online tools. Here, we introduce key resources useful to plan large-scale functional genomics studies in Drosophila and to analyze, integrate, and mine the results of those studies in ways that facilitate identification of highest-confidence results and generation of new hypotheses. We also discuss ways in which existing resources can be used and might be improved and suggest a few areas of future development that would further support large- and small-scale studies in Drosophila and facilitate use of Drosophila information by the research community more generally. PMID:24653003
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NASA Astrophysics Data System (ADS)
Manzke, R.; Bornstedt, A.; Lutz, A.; Schenderlein, M.; Hombach, V.; Binner, L.; Rasche, V.
2010-02-01
Various multi-center trials have shown that cardiac resynchronization therapy (CRT) is an effective procedure for patients with end-stage drug invariable heart failure (HF). Despite the encouraging results of CRT, at least 30% of patients do not respond to the treatment. Detailed knowledge of the cardiac anatomy (coronary venous tree, left ventricle), functional parameters (i.e. ventricular synchronicity) is supposed to improve CRT patient selection and interventional lead placement for reduction of the number of non-responders. As a pre-interventional imaging modality, cardiac magnetic resonance (CMR) imaging has the potential to provide all relevant information. With functional information from CMR optimal implantation target sites may be better identified. Pre-operative CMR could also help to determine whether useful vein target segments are available for lead placement. Fused with X-ray, the mainstay interventional modality, improved interventional guidance for lead-placement could further help to increase procedure outcome. In this contribution, we present novel and practicable methods for a) pre-operative functional and anatomical imaging of relevant cardiac structures to CRT using CMR, b) 2D-3D registration of CMR anatomy and functional meshes with X-ray vein angiograms and c) real-time capable breathing motion compensation for improved fluoroscopy mesh overlay during the intervention based on right ventricular pacer lead tracking. With these methods, enhanced interventional guidance for left ventricular lead placement is provided.
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Surface states and annihilation characteristics of positrons trapped at the oxidized Cu(100) surface
NASA Astrophysics Data System (ADS)
Fazleev, N. G.; Weiss, A. H.
2013-06-01
In this work we present the results of theoretical studies of positron surface and bulk states and annihilation probabilities of surface-trapped positrons with relevant core electrons at the oxidized Cu(100) surface under conditions of high oxygen coverage. Oxidation of the Cu(100) surface has been studied by performing an ab-initio investigation of the stability and electronic structure of the Cu(100) missing row reconstructed surface at various on-surface and subsurface oxygen coverages ranging from 0.5 to 1.5 monolayers using density functional theory (DFT). All studied structures have been found to be energetically more favorable as compared to structures formed by purely on-surface oxygen adsorption. The observed decrease in the positron work function when oxygen atoms occupy on-surface and subsurface sites has been attributed to a significant charge redistribution within the first two layers, buckling effects within each layer and an interlayer expansion. The computed positron binding energy, positron surface state wave function, and annihilation probabilities of the surface trapped positrons with relevant core electrons demonstrate their sensitivity to oxygen coverage, atomic structure of the topmost layers of surfaces, and charge transfer effects. Theoretical results are compared with experimental data obtained from studies of oxidation of the Cu(100) surface using positron annihilation induced Auger electron spectroscopy (PAES). The results presented provide an explanation for the changes observed in the probability of annihilation of surface trapped positrons with Cu 3p core-level electrons as a function of annealing temperature.
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Volume transmission-mediated encephalopathies: a possible new concept?
Hartung, Hans-Peter; Dihné, Marcel
2012-03-01
There is strong evidence that the composition of cerebrospinal fluid (CSF) influences brain development, neurogenesis, and behavior. The bidirectional exchange of CSF and interstitial fluid (ISF) across the ependymal and pia-glial membranes is required for these phenomena to occur. Because ISF surrounds the parenchymal compartment, neuroactive substances in the CSF and ISF can influence neuronal activity. Functionally important neuroactive substances are distributed to distant sites of the central nervous system by the convection and diffusion of CSF and ISF, a process known as volume transmission. It has recently been shown that pathologically altered CSF from patients with acute traumatic brain injury suppresses in vitro neuronal network activity (ivNNA) recorded by multielectrode arrays measuring synchronously bursting neural populations. Functionally relevant substances in pathologically altered CSF have been biochemically identified, and ivNNA has been partially recovered by pharmacologic intervention. It remains unclear whether the in vivo parenchymal compartment remains unaffected by pathologically altered CSF that significantly impairs ivNNA. We hypothesize that pathologic CSF alterations are not just passive indicators of brain diseases but that they actively and directly evoke functional disturbances in global brain activity through the distribution of neuroactive substances, for instance, secondary to focal neurologic disease. For this mechanism, we propose the new term volume transmission-mediated encephalopathies (VTE). Recording ivNNA in the presence of pure human CSF could help to identify and monitor functionally relevant CSF alterations that directly result in VTEs, and the collected data might point to therapeutic ways to antagonize these alterations.
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Tortorella, Stephanie; Karagiannis, Tom C
2014-01-01
Anticancer therapeutic research aims to improve clinical management of the disease through the development of strategies that involve currently-relevant treatment options and targeted delivery. Tumour-specific and -targeted delivery of compounds to the site of malignancy allows for enhanced cellular uptake, increased therapeutic benefit with high intratumoural drug concentrations, and decreased systemic exposure. Due to the upregulation of transferrin receptor expression in a wide variety of cancers, its function and its highly efficient recycling pathway, strategies involving the selective targeting of the receptor are well documented. Direct conjugation and immunotoxin studies using the transferrin peptide or anti-transferrin receptor antibodies as the targeting moiety have established the capacity to enhance cellular uptake, cross the blood brain barrier, limit systemic toxicity and reverse multi-drug resistance. Limitations in direct conjugation, including the difficulty in linking an adequate amount of therapeutic compound to the ligand or antibody have identified the requirement to develop novel delivery methods. The application of nanoparticulate theory in the development of functional drug delivery systems has proven to be most promising, with the ability to selectively modify size-dependent properties and surface chemistry. The transferrin modification on a range of nanoparticle formulations enhances selective cellular uptake through transferrin-mediated processes, and increases therapeutic benefit through the ability to encapsulate high concentrations of relevant drug to the tumour site. Although ineffective in crossing the blood brain barrier in its free form, chemotherapeutic compounds including doxorubicin, may be loaded into transferrin-conjugated nanocarriers and impart cytotoxic effects in glioma cells in vitro and in vivo. Additionally, transferrin-targeted nanoparticles may be used in selective diagnostic applications with enhanced selectivity and sensitivity. Four transferrin-modified nano-based drug delivery systems are currently in early phases of human clinical trials. Despite the collective promise, inconsistencies in some studies have exposed some limitations in current formulations and the difficulty in translating preliminary studies into clinically-relevant therapeutic options. The main objective of this review is to investigate the development of transferrin targeted nano-based drug delivery systems in order to establish the use of transferrin as a cancer-targeted moiety, and to ultimately evaluate the progression of cancer therapeutic strategies for future research.
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Parmanto, Bambang
2004-01-01
Background The World Wide Web (WWW) has become an increasingly essential resource for health information consumers. The ability to obtain accurate medical information online quickly, conveniently and privately provides health consumers with the opportunity to make informed decisions and participate actively in their personal care. Little is known, however, about whether the content of this online health information is equally accessible to people with disabilities who must rely on special devices or technologies to process online information due to their visual, hearing, mobility, or cognitive limitations. Objective To construct a framework for an automated Web accessibility evaluation; to evaluate the state of accessibility of consumer health information Web sites; and to investigate the possible relationships between accessibility and other features of the Web sites, including function, popularity and importance. Methods We carried out a cross-sectional study of the state of accessibility of health information Web sites to people with disabilities. We selected 108 consumer health information Web sites from the directory service of a Web search engine. A measurement framework was constructed to automatically measure the level of Web Accessibility Barriers (WAB) of Web sites following Web accessibility specifications. We investigated whether there was a difference between WAB scores across various functional categories of the Web sites, and also evaluated the correlation between the WAB and Alexa traffic rank and Google Page Rank of the Web sites. Results We found that none of the Web sites we looked at are completely accessible to people with disabilities, i.e., there were no sites that had no violation of Web accessibility rules. However, governmental and educational health information Web sites do exhibit better Web accessibility than the other categories of Web sites (P < 0.001). We also found that the correlation between the WAB score and the popularity of a Web site is statistically significant (r = 0.28, P < 0.05), although there is no correlation between the WAB score and the importance of the Web sites (r = 0.15, P = 0.111). Conclusions Evaluation of health information Web sites shows that no Web site scrupulously abides by Web accessibility specifications, even for entities mandated under relevant laws and regulations. Government and education Web sites show better performance than Web sites among other categories. Accessibility of a Web site may have a positive impact on its popularity in general. However, the Web accessibility of a Web site may not have a significant relationship with its importance on the Web. PMID:15249268
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Preparation for a first-in-man lentivirus trial in patients with cystic fibrosis
Alton, Eric W F W; Beekman, Jeffery M; Boyd, A Christopher; Brand, June; Carlon, Marianne S; Connolly, Mary M; Chan, Mario; Conlon, Sinead; Davidson, Heather E; Davies, Jane C; Davies, Lee A; Dekkers, Johanna F; Doherty, Ann; Gea-Sorli, Sabrina; Gill, Deborah R; Griesenbach, Uta; Hasegawa, Mamoru; Higgins, Tracy E; Hironaka, Takashi; Hyndman, Laura; McLachlan, Gerry; Inoue, Makoto; Hyde, Stephen C; Innes, J Alastair; Maher, Toby M; Moran, Caroline; Meng, Cuixiang; Paul-Smith, Michael C; Pringle, Ian A; Pytel, Kamila M; Rodriguez-Martinez, Andrea; Schmidt, Alexander C; Stevenson, Barbara J; Sumner-Jones, Stephanie G; Toshner, Richard; Tsugumine, Shu; Wasowicz, Marguerite W; Zhu, Jie
2017-01-01
We have recently shown that non-viral gene therapy can stabilise the decline of lung function in patients with cystic fibrosis (CF). However, the effect was modest, and more potent gene transfer agents are still required. Fuson protein (F)/Hemagglutinin/Neuraminidase protein (HN)-pseudotyped lentiviral vectors are more efficient for lung gene transfer than non-viral vectors in preclinical models. In preparation for a first-in-man CF trial using the lentiviral vector, we have undertaken key translational preclinical studies. Regulatory-compliant vectors carrying a range of promoter/enhancer elements were assessed in mice and human air–liquid interface (ALI) cultures to select the lead candidate; cystic fibrosis transmembrane conductance receptor (CFTR) expression and function were assessed in CF models using this lead candidate vector. Toxicity was assessed and ‘benchmarked’ against the leading non-viral formulation recently used in a Phase IIb clinical trial. Integration site profiles were mapped and transduction efficiency determined to inform clinical trial dose-ranging. The impact of pre-existing and acquired immunity against the vector and vector stability in several clinically relevant delivery devices was assessed. A hybrid promoter hybrid cytosine guanine dinucleotide (CpG)- free CMV enhancer/elongation factor 1 alpha promoter (hCEF) consisting of the elongation factor 1α promoter and the cytomegalovirus enhancer was most efficacious in both murine lungs and human ALI cultures (both at least 2-log orders above background). The efficacy (at least 14% of airway cells transduced), toxicity and integration site profile supports further progression towards clinical trial and pre-existing and acquired immune responses do not interfere with vector efficacy. The lead rSIV.F/HN candidate expresses functional CFTR and the vector retains 90–100% transduction efficiency in clinically relevant delivery devices. The data support the progression of the F/HN-pseudotyped lentiviral vector into a first-in-man CF trial in 2017. PMID:27852956
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Resonant inelastic X-ray scattering on synthetic nickel compounds and Ni-Fe hydrogenase protein
NASA Astrophysics Data System (ADS)
Sanganas, Oliver; Löscher, Simone; Pfirrmann, Stefan; Marinos, Nicolas; Glatzel, Pieter; Weng, Tsu-Chien; Limberg, Christian; Driess, Matthias; Dau, Holger; Haumann, Michael
2009-11-01
Ni-Fe hydrogenases are proteins catalyzing the oxidative cleavage of dihydrogen (H2) and proton reduction to H2 at high turnover rates. Their active site is a heterobimetallic center comprising one Ni and one Fe atom. To understand the function of the site, well resolved structural and electronic information is required. Such information is expected to become accessible by high resolution X-ray absorption and emission techniques, which are rapidly developing at third generation synchrotron radiation sources. We studied a number of synthetic Ni compounds, which mimic relevant features of the Ni site in hydrogenases, and the Ni site in the soluble, NAD-reducing hydrogenase (SH) from the bacterium Ralstonia eutropha by resonant inelastic X-ray scattering (RIXS) using a Rowland-type spectrometer at the ESRF. The SH is particularly interesting because its H2-cleavage reaction is highly resistant against inhibition by O2. Kα-fluorescence detected RIXS planes in the 1s→3d region of the X-ray absorption spectrum were recorded on the protein which allow to extract L3-edge type spectra Spectral features of the protein are compared to those of the model compounds.
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Applicable or Relevant and Appropriate Requirements (ARARs)
On-site remedial actions must attain or waive the Applicable or Relevant and Appropriate Requirements (ARARs) upon completion. The following links provide information about identifying, attaining and waiving these requirements.
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Dehouck, Yves; Kwasigroch, Jean Marc; Gilis, Dimitri; Rooman, Marianne
2011-05-13
The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level. PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability. The freely available PoPMuSiC-2.1 web server is highly useful for identifying very rapidly a list of possibly relevant mutations with the desired stability properties, on which subsequent experimental studies can be focused. It can also be used to detect sequence regions corresponding to structural weaknesses, which could be functionally important or structurally delicate regions, with obvious applications in rational protein design.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1998-06-01
Topics addressed include the following: Regulatory Summary (Role and Definition of Applicable or Relevant and Appropriate Requirements); Types of ARARs; Extent of ARARs: On-Site vs. Off-Site Management; Remedial vs. Removal Actions; To-Be-Considered Guidelines and Other Controls; ARAR Identification (ARAR Identification Process); Federal ARARs: RCRA, CAA, CWA, SDWA, TSCA; State and Local ARARs and ARAR Waivers; and Module Summary.
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Zimmermann, Michael T; Oberg, Ann L; Grill, Diane E; Ovsyannikova, Inna G; Haralambieva, Iana H; Kennedy, Richard B; Poland, Gregory A
2016-01-01
Failure to achieve a protected state after influenza vaccination is poorly understood but occurs commonly among aged populations experiencing greater immunosenescence. In order to better understand immune response in the elderly, we studied epigenetic and transcriptomic profiles and humoral immune response outcomes in 50-74 year old healthy participants. Associations between DNA methylation and gene expression reveal a system-wide regulation of immune-relevant functions, likely playing a role in regulating a participant's propensity to respond to vaccination. Our findings show that sites of methylation regulation associated with humoral response to vaccination impact known cellular differentiation signaling and antigen presentation pathways. We performed our analysis using per-site and regionally average methylation levels, in addition to continuous or dichotomized outcome measures. The genes and molecular functions implicated by each analysis were compared, highlighting different aspects of the biologic mechanisms of immune response affected by differential methylation. Both cis-acting (within the gene or promoter) and trans-acting (enhancers and transcription factor binding sites) sites show significant associations with measures of humoral immunity. Specifically, we identified a group of CpGs that, when coordinately hypo-methylated, are associated with lower humoral immune response, and methylated with higher response. Additionally, CpGs that individually predict humoral immune responses are enriched for polycomb-group and FOXP2 transcription factor binding sites. The most robust associations implicate differential methylation affecting gene expression levels of genes with known roles in immunity (e.g. HLA-B and HLA-DQB2) and immunosenescence. We believe our data and analysis strategy highlight new and interesting epigenetic trends affecting humoral response to vaccination against influenza; one of the most common and impactful viral pathogens.
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Protein Conformational Populations and Functionally Relevant Sub-states
DOE Office of Scientific and Technical Information (OSTI.GOV)
Agarwal, Pratul K; Burger, Virginia; Savol, Andrej
2013-01-01
Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of themore » protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.« less
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Site-preference and valency for rare-earth sites in (R-Ce)(2)Fe14B magnets
DOE Office of Scientific and Technical Information (OSTI.GOV)
Alam, A; Khan, M; McCallum, RW
2013-01-28
Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two R-sites (Wyckoff 4f and 4g, with four-fold multiplicity) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1-xCex)(2)Fe14B [R = La, Nd] using density functional theory (DFT) methods-including a DFT+U scheme to treat localized 4f-electrons. Fe moments compare well with neutron data-almost unaffected by Hubbard U, and weakly affectedmore » by spin-orbit coupling. In La2Fe14B, Ce alloys for 0 <= x <= 1 and prefers smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas, in Nd2Fe14B, Ce is predicted to have limited alloying (x <= 0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. The Curie temperatures versus x for (Nd, Ce) were predicted for a typical sample processing and verified experimentally. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4789527]« less
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Carreón-Diazconti, Concepción; Santamaría, Johanna; Berkompas, Justin; Field, James A.; Brusseau, Mark L.
2010-01-01
Isotopic analysis and molecular-based bioassay methods were used in conjunction with geochemical data to assess intrinsic reductive dechlorination processes for a chlorinated-solvent contaminated site in Tucson, Arizona. Groundwater samples were obtained from monitoring wells within a contaminant plume comprising tetrachloroethene and its metabolites trichloroethene, cis-1,2-dichloroethene, vinyl chloride, and ethene, as well as compounds associated with free-phase diesel present at the site. Compound specific isotope (CSI) analysis was performed to characterize biotransformation processes influencing the transport and fate of the chlorinated contaminants. PCR analysis was used to assess the presence of indigenous reductive dechlorinators. The target regions employed were the 16s rRNA gene sequences of Dehalococcoides sp. and Desulfuromonas sp., and DNA sequences of genes pceA, tceA, bvcA, and vcrA, which encode reductive dehalogenases. The results of the analyses indicate that relevant microbial populations are present and that reductive dechlorination is presently occurring at the site. The results further show that potential degrader populations as well as biotransformation activity is non-uniformly distributed within the site. The results of laboratory microcosm studies conducted using groundwater collected from the field site confirmed the reductive dechlorination of tetrachloroethene to dichloroethene. This study illustrates the use of an integrated, multiple-method approach for assessing natural attenuation at a complex chlorinated-solvent contaminated site. PMID:19603638
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Zhang, Emma Xuxiao; Yang, Yinping; Di Shang, Richard; Simons, Joseph John Pyne; Quek, Boon Kiat; Yin, Xiao Feng; See, Wanhan; Oh, Olivia Seen Huey; Nandar, Khine Sein Tun; Ling, Vivienne Ruo Yun; Chan, Pei Pei; Wang, Zhaoxia; Goh, Rick Siow Mong; James, Lyn; Tey, Jeannie Su Hui
2015-01-01
We conducted in-depth analysis on the use of a popular Chinese social networking and microblogging site, Sina Weibo, to monitor an avian influenza A(H7N9) outbreak in China and to assess the value of social networking sites in the surveillance of disease outbreaks that occur overseas. Two data sets were employed for our analysis: a line listing of confirmed cases obtained from conventional public health information channels and case information from Weibo posts. Our findings showed that the level of activity on Weibo corresponded with the number of new cases reported. In addition, the reporting of new cases on Weibo was significantly faster than those of conventional reporting sites and non-local news media. A qualitative review of the functions of Weibo also revealed that Weibo enabled timely monitoring of other outbreak-relevant information, provided access to additional crowd-sourced epidemiological information and was leveraged by the local government as an interactive platform for risk communication and monitoring public sentiment on the policy response. Our analysis demonstrated the potential for social networking sites to be used by public health agencies to enhance traditional communicable disease surveillance systems for the global surveillance of overseas public health threats. Social networking sites also can be used by governments for calibration of response policies and measures and for risk communication.
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Zhang, Emma Xuxiao; Yang, Yinping; Di Shang, Richard; Simons, Joseph John Pyne; Quek, Boon Kiat; Yin, Xiao Feng; See, Wanhan; Oh, Olivia Seen Huey; Nandar, Khine Sein Tun; Ling, Vivienne Ruo Yun; Chan, Pei Pei; Wang, Zhaoxia; Goh, Rick Siow Mong; James, Lyn
2015-01-01
We conducted in-depth analysis on the use of a popular Chinese social networking and microblogging site, Sina Weibo, to monitor an avian influenza A(H7N9) outbreak in China and to assess the value of social networking sites in the surveillance of disease outbreaks that occur overseas. Two data sets were employed for our analysis: a line listing of confirmed cases obtained from conventional public health information channels and case information from Weibo posts. Our findings showed that the level of activity on Weibo corresponded with the number of new cases reported. In addition, the reporting of new cases on Weibo was significantly faster than those of conventional reporting sites and non-local news media. A qualitative review of the functions of Weibo also revealed that Weibo enabled timely monitoring of other outbreak-relevant information, provided access to additional crowd-sourced epidemiological information and was leveraged by the local government as an interactive platform for risk communication and monitoring public sentiment on the policy response. Our analysis demonstrated the potential for social networking sites to be used by public health agencies to enhance traditional communicable disease surveillance systems for the global surveillance of overseas public health threats. Social networking sites also can be used by governments for calibration of response policies and measures and for risk communication. PMID:26306219
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Hod, Idan; Sampson, Matthew D.; Deria, Pravas; ...
2015-09-18
Realization of heterogeneous electrochemical CO 2-to-fuel conversion via molecular catalysis under high-flux conditions requires the assembly of large quantities of reactant-accessible catalysts on conductive surfaces. As a proof of principle, we demonstrate that electrophoretic deposition of thin films of an appropriately chosen metal–organic framework (MOF) material is an effective method for immobilizing the needed quantity of catalyst. For electrocatalytic CO 2 reduction, we used a material that contains functionalized Fe-porphyrins as catalytically competent, redox-conductive linkers. The approach yields a high effective surface coverage of electrochemically addressable catalytic sites (~10 15 sites/cm 2). The chemical products of the reduction, obtained withmore » ~100% Faradaic efficiency, are mixtures of CO and H 2. The results validate the strategy of using MOF chemistry to obtain porous, electrode-immobilized, networks of molecular catalysts having competency for energy-relevant electrochemical reactions.« less
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Pediatric thermal injury: acute care and reconstruction update.
Armour, Alexis D; Billmire, David A
2009-07-01
The acute and reconstructive care of each pediatric burn patient presents unique challenges to the plastic surgeon and the burn care team. : The purpose of this review article is to highlight the interdependence between the acute and reconstructive needs of pediatric burn patients as it pertains to each anatomical site. Relevant principles of acute pediatric burn care and burn reconstruction are outlined, based on the authors' experience and review of the literature. The need for late reconstruction in pediatric burn survivors is significantly influenced by the acute surgical and rehabilitative treatments. With their vulnerability to airway swelling, hypothermia, pulmonary edema, and ischemia-reperfusion injury, pediatric patients with large burns require precise, life-saving treatment in the acute phase. Decision-making in pediatric burn reconstruction must take into account the patient's future growth, maturity, and often lack of suitable donor sites. Appropriately selected reconstructive techniques are essential to optimize function, appearance, and quality of life in pediatric burn survivors.
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Distinct bone marrow blood vessels differentially regulate haematopoiesis.
Itkin, Tomer; Gur-Cohen, Shiri; Spencer, Joel A; Schajnovitz, Amir; Ramasamy, Saravana K; Kusumbe, Anjali P; Ledergor, Guy; Jung, Yookyung; Milo, Idan; Poulos, Michael G; Kalinkovich, Alexander; Ludin, Aya; Kollet, Orit; Shakhar, Guy; Butler, Jason M; Rafii, Shahin; Adams, Ralf H; Scadden, David T; Lin, Charles P; Lapidot, Tsvee
2016-04-21
Bone marrow endothelial cells (BMECs) form a network of blood vessels that regulate both leukocyte trafficking and haematopoietic stem and progenitor cell (HSPC) maintenance. However, it is not clear how BMECs balance these dual roles, and whether these events occur at the same vascular site. We found that mammalian bone marrow stem cell maintenance and leukocyte trafficking are regulated by distinct blood vessel types with different permeability properties. Less permeable arterial blood vessels maintain haematopoietic stem cells in a low reactive oxygen species (ROS) state, whereas the more permeable sinusoids promote HSPC activation and are the exclusive site for immature and mature leukocyte trafficking to and from the bone marrow. A functional consequence of high permeability of blood vessels is that exposure to blood plasma increases bone marrow HSPC ROS levels, augmenting their migration and differentiation, while compromising their long-term repopulation and survival. These findings may have relevance for clinical haematopoietic stem cell transplantation and mobilization protocols.
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Visual Communication in Web Design - Analyzing Visual Communication in Web Design
NASA Astrophysics Data System (ADS)
Thorlacius, Lisbeth
Web sites are rapidly becoming the preferred media choice for information search, company presentation, shopping, entertainment, education, and social contacts. And along with the various forms of communication that the Web offers the aesthetic aspects have begun to play an increasingly important role. However, studies in the design and the relevance of focusing on the aesthetic aspects in planning and using Web sites have only to a smaller degree been subject of theoretical reflection. For example, Miller (2000), Thorlacius (2001, 2002, 2005), Engholm (2002, 2003), and Beaird (2007) have been contributing to set a beginning agenda that address the aesthetic aspects. On the other hand, there is a considerable amount of literature addressing the theoretical and methodological aspects focusing on the technical and functional aspects. In this context it is the aim of this article to introduce a model for analysis of visual communication on websites.
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A model for the solution structure of the rod arrestin tetramer.
Hanson, Susan M; Dawson, Eric S; Francis, Derek J; Van Eps, Ned; Klug, Candice S; Hubbell, Wayne L; Meiler, Jens; Gurevich, Vsevolod V
2008-06-01
Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.
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NASA Astrophysics Data System (ADS)
Schmitter, E. D.
2013-04-01
Remote sensing of the ionosphere bottom using long wave radio signal propagation is a still going strong and inexpensive method for continuous monitoring purposes. We present a propagation model describing the time development of solar flare effects. Based on monitored amplitude and phase data from VLF/LF transmitters gained at a mid-latitude site during the currently increasing solar cycle no. 24 a parameterized electron density profile is calculated as a function of time and fed into propagation calculations using the LWPC (Long Wave Propagation Capability). The model allows to include lower ionosphere recombination and attachment coefficients, as well as to identify the relevant forcing X-ray wavelength band, and is intended to be a small step forward to a better understanding of the solar-lower ionosphere interaction mechanisms within a consistent framework.
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NASA Technical Reports Server (NTRS)
Clegg-Watkins, R. N.; Jolliff, B. L.; Lawrence, S. J.
2016-01-01
Boulders represent a landing hazard that must be addressed in the planning of future landings on the Moon. A boulder under a landing leg can contribute to deck tilt and boulders can damage spacecraft during landing. Using orbital data to characterize boulder populations at locations where landers have safely touched down (Apollo, Luna, Surveyor, and Chang'e-3 sites) is important for determining landing hazard criteria for future missions. Additionally, assessing the distribution of boulders can address broader science issues, e.g., how far craters distribute boulders and how this distribution varies as a function of crater size and age. The availability of new Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) images [1] enables the use of boulder size- and range frequency distributions for a variety of purposes [2-6]. Boulders degrade over time and primarily occur around young or fresh craters that are large enough to excavate bedrock. Here we use NAC images to analyze boulder distributions around Cone crater (340 m diameter) at the Apollo 14 site. Cone crater (CC) was selected because it is the largest crater where astronaut surface photography is available for a radial traverse to the rim. Cone crater is young (approximately 29 Ma [7]) relative to the time required to break down boulders [3,8], giving us a data point for boulder range-frequency distributions (BRFDs) as a function of crater age.
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Impact of mutations on the allosteric conformational equilibrium
Weinkam, Patrick; Chen, Yao Chi; Pons, Jaume; Sali, Andrej
2012-01-01
Allostery in a protein involves effector binding at an allosteric site that changes the structure and/or dynamics at a distant, functional site. In addition to the chemical equilibrium of ligand binding, allostery involves a conformational equilibrium between one protein substate that binds the effector and a second substate that less strongly binds the effector. We run molecular dynamics simulations using simple, smooth energy landscapes to sample specific ligand-induced conformational transitions, as defined by the effector-bound and unbound protein structures. These simulations can be performed using our web server: http://salilab.org/allosmod/. We then develop a set of features to analyze the simulations and capture the relevant thermodynamic properties of the allosteric conformational equilibrium. These features are based on molecular mechanics energy functions, stereochemical effects, and structural/dynamic coupling between sites. Using a machine-learning algorithm on a dataset of 10 proteins and 179 mutations, we predict both the magnitude and sign of the allosteric conformational equilibrium shift by the mutation; the impact of a large identifiable fraction of the mutations can be predicted with an average unsigned error of 1 kBT. With similar accuracy, we predict the mutation effects for an 11th protein that was omitted from the initial training and testing of the machine-learning algorithm. We also assess which calculated thermodynamic properties contribute most to the accuracy of the prediction. PMID:23228330
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Gary, Thomas, E-mail: thomas.gary@medunigraz.at; Prüller, Florian, E-mail: florian.prueller@klinikum-graz.at; Raggam, Reinhard, E-mail: reinhard.raggam@klinikum-graz.at
PurposeAlthough platelet reactivity is routinely inhibited with aspirin after percutaneous angioplasty (PTA) in peripheral arteries, the restenosis rate in the superficial femoral artery (SFA) is high. Interaction of activated platelets and the endothelium in the region of intervention could be one reason for this as collagen in the subendothelium activates platelets.Materials and MethodsA prospective study evaluating on-site platelet reactivity during PTA and its influence on the development of restenosis with a total of 30 patients scheduled for PTA of the SFA. Arterial blood was taken from the PTA site after SFA; platelet function was evaluated with light transmission aggregometry. Aftermore » 3, 6, 12, and 24 months, duplex sonography was performed and the restenosis rate evaluated.ResultsEight out of 30 patients developed a hemodynamically relevant restenosis (>50 % lumen narrowing) in the PTA region during the 24-month follow-up period. High residual collagen-induced platelet reactivity defined as AUC >30 was a significant predictor for the development of restenosis [adjusted odds ratio 11.8 (9.4, 14.2); P = .04].ConclusionsHigh residual collagen-induced platelet reactivity at the interventional site predicts development of restenosis after PTA of the SFA. Platelet function testing may be useful for identifying patients at risk.« less
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Multiscale characterization of the mineral phase at skeletal sites of breast cancer metastasis.
He, Frank; Chiou, Aaron E; Loh, Hyun Chae; Lynch, Maureen; Seo, Bo Ri; Song, Young Hye; Lee, Min Joon; Hoerth, Rebecca; Bortel, Emely L; Willie, Bettina M; Duda, Georg N; Estroff, Lara A; Masic, Admir; Wagermaier, Wolfgang; Fratzl, Peter; Fischbach, Claudia
2017-10-03
Skeletal metastases, the leading cause of death in advanced breast cancer patients, depend on tumor cell interactions with the mineralized bone extracellular matrix. Bone mineral is largely composed of hydroxyapatite (HA) nanocrystals with physicochemical properties that vary significantly by anatomical location, age, and pathology. However, it remains unclear whether bone regions typically targeted by metastatic breast cancer feature distinct HA materials properties. Here we combined high-resolution X-ray scattering analysis with large-area Raman imaging, backscattered electron microscopy, histopathology, and microcomputed tomography to characterize HA in mouse models of advanced breast cancer in relevant skeletal locations. The proximal tibial metaphysis served as a common metastatic site in our studies; we identified that in disease-free bones this skeletal region contained smaller and less-oriented HA nanocrystals relative to ones that constitute the diaphysis. We further observed that osteolytic bone metastasis led to a decrease in HA nanocrystal size and perfection in remnant metaphyseal trabecular bone. Interestingly, in a model of localized breast cancer, metaphyseal HA nanocrystals were also smaller and less perfect than in corresponding bone in disease-free controls. Collectively, these results suggest that skeletal sites prone to tumor cell dissemination contain less-mature HA (i.e., smaller, less-perfect, and less-oriented crystals) and that primary tumors can further increase HA immaturity even before secondary tumor formation, mimicking alterations present during tibial metastasis. Engineered tumor models recapitulating these spatiotemporal dynamics will permit assessing the functional relevance of the detected changes to the progression and treatment of breast cancer bone metastasis.
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Multiscale characterization of the mineral phase at skeletal sites of breast cancer metastasis
Chiou, Aaron E.; Loh, Hyun Chae; Lynch, Maureen; Seo, Bo Ri; Song, Young Hye; Hoerth, Rebecca; Bortel, Emely L.; Willie, Bettina M.; Duda, Georg N.; Masic, Admir; Wagermaier, Wolfgang; Fratzl, Peter; Fischbach, Claudia
2017-01-01
Skeletal metastases, the leading cause of death in advanced breast cancer patients, depend on tumor cell interactions with the mineralized bone extracellular matrix. Bone mineral is largely composed of hydroxyapatite (HA) nanocrystals with physicochemical properties that vary significantly by anatomical location, age, and pathology. However, it remains unclear whether bone regions typically targeted by metastatic breast cancer feature distinct HA materials properties. Here we combined high-resolution X-ray scattering analysis with large-area Raman imaging, backscattered electron microscopy, histopathology, and microcomputed tomography to characterize HA in mouse models of advanced breast cancer in relevant skeletal locations. The proximal tibial metaphysis served as a common metastatic site in our studies; we identified that in disease-free bones this skeletal region contained smaller and less-oriented HA nanocrystals relative to ones that constitute the diaphysis. We further observed that osteolytic bone metastasis led to a decrease in HA nanocrystal size and perfection in remnant metaphyseal trabecular bone. Interestingly, in a model of localized breast cancer, metaphyseal HA nanocrystals were also smaller and less perfect than in corresponding bone in disease-free controls. Collectively, these results suggest that skeletal sites prone to tumor cell dissemination contain less-mature HA (i.e., smaller, less-perfect, and less-oriented crystals) and that primary tumors can further increase HA immaturity even before secondary tumor formation, mimicking alterations present during tibial metastasis. Engineered tumor models recapitulating these spatiotemporal dynamics will permit assessing the functional relevance of the detected changes to the progression and treatment of breast cancer bone metastasis. PMID:28923958
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Structures of a Na+-coupled, substrate-bound MATE multidrug transporter
Lu, Min; Symersky, Jindrich; Radchenko, Martha; Koide, Akiko; Guo, Yi; Nie, Rongxin; Koide, Shohei
2013-01-01
Multidrug transporters belonging to the multidrug and toxic compound extrusion (MATE) family expel dissimilar lipophilic and cationic drugs across cell membranes by dissipating a preexisting Na+ or H+ gradient. Despite its clinical relevance, the transport mechanism of MATE proteins remains poorly understood, largely owing to a lack of structural information on the substrate-bound transporter. Here we report crystal structures of a Na+-coupled MATE transporter NorM from Neisseria gonorrheae in complexes with three distinct translocation substrates (ethidium, rhodamine 6G, and tetraphenylphosphonium), as well as Cs+ (a Na+ congener), all captured in extracellular-facing and drug-bound states. The structures revealed a multidrug-binding cavity festooned with four negatively charged amino acids and surprisingly limited hydrophobic moieties, in stark contrast to the general belief that aromatic amino acids play a prominent role in multidrug recognition. Furthermore, we discovered an uncommon cation–π interaction in the Na+-binding site located outside the drug-binding cavity and validated the biological relevance of both the substrate- and cation-binding sites by conducting drug resistance and transport assays. Additionally, we uncovered potential rearrangement of at least two transmembrane helices upon Na+-induced drug export. Based on our structural and functional analyses, we suggest that Na+ triggers multidrug extrusion by inducing protein conformational changes rather than by directly competing for the substrate-binding amino acids. This scenario is distinct from the canonical antiport mechanism, in which both substrate and counterion compete for a shared binding site in the transporter. Collectively, our findings provide an important step toward a detailed and mechanistic understanding of multidrug transport. PMID:23341609
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Gao, Yu-Fei; Li, Bi-Qing; Cai, Yu-Dong; Feng, Kai-Yan; Li, Zhan-Dong; Jiang, Yang
2013-01-27
Identification of catalytic residues plays a key role in understanding how enzymes work. Although numerous computational methods have been developed to predict catalytic residues and active sites, the prediction accuracy remains relatively low with high false positives. In this work, we developed a novel predictor based on the Random Forest algorithm (RF) aided by the maximum relevance minimum redundancy (mRMR) method and incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility to predict active sites of enzymes and achieved an overall accuracy of 0.885687 and MCC of 0.689226 on an independent test dataset. Feature analysis showed that every category of the features except disorder contributed to the identification of active sites. It was also shown via the site-specific feature analysis that the features derived from the active site itself contributed most to the active site determination. Our prediction method may become a useful tool for identifying the active sites and the key features identified by the paper may provide valuable insights into the mechanism of catalysis.
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Analysis of governmental Web sites on food safety issues: a global perspective.
Namkung, Young; Almanza, Barbara A
2006-10-01
Despite a growing concern over food safety issues, as well as a growing dependence on the Internet as a source of information, little research has been done to examine the presence and relevance of food safety-related information on Web sites. The study reported here conducted Web site analysis in order to examine the current operational status of governmental Web sites on food safety issues. The study also evaluated Web site usability, especially information dimensionalities such as utility, currency, and relevance of content, from the perspective of the English-speaking consumer. Results showed that out of 192 World Health Organization members, 111 countries operated governmental Web sites that provide information about food safety issues. Among 171 searchable Web sites from the 111 countries, 123 Web sites (71.9 percent) were accessible, and 81 of those 123 (65.9 percent) were available in English. The majority of Web sites offered search engine tools and related links for more information, but their availability and utility was limited. In terms of content, 69.9 percent of Web sites offered information on foodborne-disease outbreaks, compared with 31.5 percent that had travel- and health-related information.
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Henríquez, C; Riquelme, T T; Vera, D; Julio-Kalajzić, F; Ehrenfeld, P; Melvin, J E; Figueroa, C D; Sarmiento, J; Flores, C A
2016-01-01
Neutrophils are the first cells to arrive at sites of injury. Nevertheless, many inflammatory diseases are characterized by an uncontrolled infiltration and action of these cells. Cell migration depends on volume changes that are governed by ion channel activity, but potassium channels in neutrophil have not been clearly identified. We aim to test whether KCa3.1 participates in neutrophil migration and other relevant functions of the cell. Cytometer and confocal measurements to determine changes in cell volume were used. Cells isolated from human, mouse and horse were tested for KCa3.1-dependent chemotaxis. Chemokinetics, calcium handling and release of reactive oxygen species were measured to determine the role of KCa3.1 in those processes. A mouse model was used to test for neutrophil recruitment after acute lung injury in vivo. We show for the first time that KCa3.1 is expressed in mammalian neutrophils. When the channel is inhibited by a pharmacological blocker or by genetic silencing, it profoundly affects cell volume regulation, and chemotactic and chemokinetic properties of the cells. We also demonstrated that pharmacological inhibition of KCa3.1 did not affect calcium entry or reactive oxygen species production in neutrophils. Using a mouse model of acute lung injury, we observed that Kca3.1(-/-) mice are significantly less effective at recruiting neutrophils into the site of inflammation. These results demonstrate that KCa3.1 channels are key actors in the migration capacity of neutrophils, and its inhibition did not affect other relevant cellular functions. © 2015 Scandinavian Physiological Society. Published by John Wiley & Sons Ltd.
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Global Impact of Oncogenic Src on a Phosphotyrosine Proteome
Luo, Weifeng; Slebos, Robbert J.; Hill, Salisha; Li, Ming; Brábek, Jan; Amanchy, Ramars; Chaerkady, Raghothama; Pandey, Akhilesh; Ham, Amy-Joan L.; Hanks, Steven K.
2008-01-01
Elevated activity of Src, the first characterized protein-tyrosine kinase, is associated with progression of many human cancers, and Src has attracted interest as a therapeutic target. Src is known to act in various receptor signaling systems to impact cell behavior, yet it remains likely that the spectrum of Src protein substrates relevant to cancer is incompletely understood. To better understand the cellular impact of deregulated Src kinase activity, we extensively applied a mass spectrometry shotgun phosphotyrosine (pTyr) proteomics strategy to obtain global pTyr profiles of Src-transformed mouse fibroblasts as well as their nontransformed counterparts. A total of 867 peptides representing 563 distinct pTyr sites on 374 different proteins were identified from the Src-transformed cells, while 514 peptides representing 275 pTyr sites on 167 proteins were identified from nontransformed cells. Distinct characteristics of the two profiles were revealed by spectral counting, indicative of pTyr site relative abundance, and by complementary quantitative analysis using stable isotope labeling with amino acids in cell culture (SILAC). While both pTyr profiles are replete with sites on signaling and adhesion/cytoskeletal regulatory proteins, the Src-transformed profile is more diverse with enrichment in sites on metabolic enzymes and RNA and protein synthesis and processing machinery. Forty-three pTyr sites (32 proteins) are predicted as major biologically relevant Src targets on the basis of frequent identification in both cell populations. This select group, of particular interest as diagnostic biomarkers, includes well-established Src sites on signaling/adhesion/cytoskeletal proteins, but also uncharacterized sites of potential relevance to the transformed cell phenotype. PMID:18563927
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38 CFR 39.32 - Plan preparation.
Code of Federal Regulations, 2012 CFR
2012-07-01
... been no changes. Relevant information may then be shown on the site plan. If required, the site survey.... Boundaries of an unusual nature (curvilinear, off-set, or having other change or direction between corners... the design, including climate, soil conditions, site boundaries, topography, views, hydrology...
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38 CFR 39.32 - Plan preparation.
Code of Federal Regulations, 2014 CFR
2014-07-01
... been no changes. Relevant information may then be shown on the site plan. If required, the site survey.... Boundaries of an unusual nature (curvilinear, off-set, or having other change or direction between corners... the design, including climate, soil conditions, site boundaries, topography, views, hydrology...
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38 CFR 39.32 - Plan preparation.
Code of Federal Regulations, 2013 CFR
2013-07-01
... been no changes. Relevant information may then be shown on the site plan. If required, the site survey.... Boundaries of an unusual nature (curvilinear, off-set, or having other change or direction between corners... the design, including climate, soil conditions, site boundaries, topography, views, hydrology...
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Genome editing with CompoZr custom zinc finger nucleases (ZFNs).
Hansen, Keith; Coussens, Matthew J; Sago, Jack; Subramanian, Shilpi; Gjoka, Monika; Briner, Dave
2012-06-14
Genome editing is a powerful technique that can be used to elucidate gene function and the genetic basis of disease. Traditional gene editing methods such as chemical-based mutagenesis or random integration of DNA sequences confer indiscriminate genetic changes in an overall inefficient manner and require incorporation of undesirable synthetic sequences or use of aberrant culture conditions, potentially confusing biological study. By contrast, transient ZFN expression in a cell can facilitate precise, heritable gene editing in a highly efficient manner without the need for administration of chemicals or integration of synthetic transgenes. Zinc finger nucleases (ZFNs) are enzymes which bind and cut distinct sequences of double-stranded DNA (dsDNA). A functional CompoZr ZFN unit consists of two individual monomeric proteins that bind a DNA "half-site" of approximately 15-18 nucleotides (see Figure 1). When two ZFN monomers "home" to their adjacent target sites the DNA-cleavage domains dimerize and create a double-strand break (DSB) in the DNA. Introduction of ZFN-mediated DSBs in the genome lays a foundation for highly efficient genome editing. Imperfect repair of DSBs in a cell via the non-homologous end-joining (NHEJ) DNA repair pathway can result in small insertions and deletions (indels). Creation of indels within the gene coding sequence of a cell can result in frameshift and subsequent functional knockout of a gene locus at high efficiency. While this protocol describes the use of ZFNs to create a gene knockout, integration of transgenes may also be conducted via homology-directed repair at the ZFN cut site. The CompoZr Custom ZFN Service represents a systematic, comprehensive, and well-characterized approach to targeted gene editing for the scientific community with ZFN technology. Sigma scientists work closely with investigators to 1) perform due diligence analysis including analysis of relevant gene structure, biology, and model system pursuant to the project goals, 2) apply this knowledge to develop a sound targeting strategy, 3) then design, build, and functionally validate ZFNs for activity in a relevant cell line. The investigator receives positive control genomic DNA and primers, and ready-to-use ZFN reagents supplied in both plasmid DNA and in-vitro transcribed mRNA format. These reagents may then be delivered for transient expression in the investigator's cell line or cell type of choice. Samples are then tested for gene editing at the locus of interest by standard molecular biology techniques including PCR amplification, enzymatic digest, and electrophoresis. After positive signal for gene editing is detected in the initial population, cells are single-cell cloned and genotyped for identification of mutant clones/alleles.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Olsen, Tim; Preus, Robert
Site assessment for small wind energy systems is one of the key factors in the successful installation, operation, and performance of a small wind turbine. A proper site assessment is a difficult process that includes wind resource assessment and the evaluation of site characteristics. These guidelines address many of the relevant parts of a site assessment with an emphasis on wind resource assessment, using methods other than on-site data collection and creating a small wind site assessment report.
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Regional risk assessment for contaminated sites part 2: ranking of potentially contaminated sites.
Pizzol, Lisa; Critto, Andrea; Agostini, Paola; Marcomini, Antonio
2011-11-01
Environmental risks are traditionally assessed and presented in non spatial ways although the heterogeneity of the contaminants spatial distributions, the spatial positions and relations between receptors and stressors, as well as the spatial distribution of the variables involved in the risk assessment, strongly influence exposure estimations and hence risks. Taking into account spatial variability is increasingly being recognized as a further and essential step in sound exposure and risk assessment. To address this issue an innovative methodology which integrates spatial analysis and a relative risk approach was developed. The purpose of this methodology is to prioritize sites at regional scale where a preliminary site investigation may be required. The methodology aimed at supporting the inventory of contaminated sites was implemented within the spatial decision support sYstem for Regional rIsk Assessment of DEgraded land, SYRIADE, and was applied to the case-study of the Upper Silesia region (Poland). The developed methodology and tool are both flexible and easy to adapt to different regional contexts, allowing the user to introduce the regional relevant parameters identified on the basis of user expertise and regional data availability. Moreover, the used GIS functionalities, integrated with mathematical approaches, allow to take into consideration, all at once, the multiplicity of sources and impacted receptors within the region of concern, to assess the risks posed by all contaminated sites in the region and, finally, to provide a risk-based ranking of the potentially contaminated sites. Copyright © 2011. Published by Elsevier Ltd.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Pollesch, N.; Dale, V. H.
In order to aid in transition towards operations that promote sustainability goals, researchers and stakeholders use sustainability assessments. Although assessments take various forms, many utilize diverse sets of indicators that can number anywhere from two to over 2000. Indices, composite indicators, or aggregate values are used to simplify high dimensional and complex data sets and to clarify assessment results. Although the choice of aggregation function is a key component in the development of the assessment, there are few examples to be found in literature to guide appropriate aggregation function selection. This paper develops a connection between the mathematical study ofmore » aggregation functions and sustainability assessment in order to aid in providing criteria for aggregation function selection. Relevant mathematical properties of aggregation functions are presented and interpreted. Lastly, we provide cases of these properties and their relation to previous sustainability assessment research. Examples show that mathematical aggregation properties can be used to address the topics of compensatory behavior and weak versus strong sustainability, aggregation of data under varying units of measurements, multiple site multiple indicator aggregation, and the determination of error bounds in aggregate output for normalized and non-normalized indicator measures.« less
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Rice, Gillian I.; Reijns, Martin A.M.; Coffin, Stephanie R.; Forte, Gabriella M.A.; Anderson, Beverley H.; Szynkiewicz, Marcin; Gornall, Hannah; Gent, David; Leitch, Andrea; Botella, Maria P.; Fazzi, Elisa; Gener, Blanca; Lagae, Lieven; Olivieri, Ivana; Orcesi, Simona; Swoboda, Kathryn J.; Perrino, Fred W.; Jackson, Andrew P.; Crow, Yanick J.
2013-01-01
Aicardi-Goutières syndrome (AGS) is an inflammatory disorder resulting from mutations in TREX1, RNASEH2A/2B/2C, SAMHD1 or ADAR1. Here we provide molecular, biochemical and cellular evidence for the pathogenicity of two synonymous variants in RNASEH2A. Firstly, the c.69G>A (p.Val23Val) mutation causes the formation of a splice donor site within exon 1, resulting in an out of frame deletion at the end of exon 1, leading to reduced RNase H2 protein levels. The second mutation, c.75C>T (p.Arg25Arg), also introduces a splice donor site within exon 1, and the internal deletion of 18 amino acids. The truncated protein still forms a heterotrimeric RNase H2 complex, but lacks catalytic activity. However, as a likely result of leaky splicing, a small amount of full-length active protein is apparently produced in an individual homozygous for this mutation. Recognition of the disease causing status of these variants allows for diagnostic testing in relevant families. PMID:23592335
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Papouin, Thomas; Dunphy, Jaclyn; Tolman, Michaela; Dineley, Kelly T.; Haydon, Philip G.
2017-01-01
Summary The activation of the N-methyl D-aspartate receptor (NMDAR) is controlled by a glutamate-binding site and a distinct, independently regulated, co-agonist-binding site. In most brain regions, the NMDAR co-agonist is the astrocyte-derived gliotransmitter D-serine. We found that D-serine levels oscillate in mouse hippocampus as a function of wakefulness, in vitro and in vivo. This causes a full saturation of the NMDAR co-agonist site in the dark (active)-phase that dissipates to sub-saturating levels during the light (sleep)-phase, and influences learning performance throughout the day. We demonstrate that hippocampal astrocytes sense the wakefulness-dependent activity of septal cholinergic fibers through the α7-nicotinic acetylcholine receptor (α7nAChR), whose activation drives D-serine release. We conclude that astrocytes tune the gating of synaptic NMDARs to the vigilance state and demonstrate that this is directly relevant to schizophrenia, a disorder characterized by NMDAR and cholinergic hypofunctions. Indeed, bypassing cholinergic activity with a clinically-tested α7nAChR agonist successfully enhances NMDARs activation. PMID:28479102
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Structure and dynamics of protein waters revealed by radiolysis and mass spectrometry
Gupta, Sayan; D’Mello, Rhijuta; Chance, Mark R.
2012-01-01
Water is critical for the structure, stability, and functions of macromolecules. Diffraction and NMR studies have revealed structure and dynamics of bound waters at atomic resolution. However, localizing the sites and measuring the dynamics of bound waters, particularly on timescales relevant to catalysis and macromolecular assembly, is quite challenging. Here we demonstrate two techniques: first, temperature-dependent radiolytic hydroxyl radical labeling with a mass spectrometry (MS)-based readout to identify sites of bulk and bound water interactions with surface and internal residue side chains, and second, H218O radiolytic exchange coupled MS to measure the millisecond dynamics of bound water interactions with various internal residue side chains. Through an application of the methods to cytochrome c and ubiquitin, we identify sites of water binding and measure the millisecond dynamics of bound waters in protein crevices. As these MS-based techniques are very sensitive and not protein size limited, they promise to provide unique insights into protein–water interactions and water dynamics for both small and large proteins and their complexes. PMID:22927377
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The γ Class of Carbonic Anhydrases
Ferry, James G.
2009-01-01
Homologs of the γ class of carbonic anhydrases, one of five independently evolved classes, are found in the genomic sequences of diverse species from all three domains of life. The archetype (Cam) from the Archaea domain is a homotrimer of which the crystal structure reveals monomers with a distinctive left-handed parallel β-helix fold. Histidines from adjacent monomers ligate the three active site metals surrounded by residues in a hydrogen bond network essential for activity. Cam is most active with iron, the physiologically relevant metal. Although the active site residues bear little resemblance to the other classes, kinetic analyses indicate a two-step mechanism analogous to all carbonic anhydrases investigated. Phylogenetic analyses of Cam homologs derived from the databases show that Cam is representative of a minor subclass with the great majority belonging to a subclass (CamH) with significant differences in active site residues and apparent mechanism from Cam. A physiological function for any of the Cam and CamH homologs is unknown, although roles in transport of carbon dioxide and bicarbonate across membranes has been proposed. PMID:19747990
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Wang, Shengjun; Mao, Yang; Narimatsu, Yoshiki; Ye, Zilu; Tian, Weihua; Goth, Christoffer K; Lira-Navarrete, Erandi; Pedersen, Nis B; Benito-Vicente, Asier; Martin, Cesar; Uribe, Kepa B; Hurtado-Guerrero, Ramon; Christoffersen, Christina; Seidah, Nabil G; Nielsen, Rikke; Christensen, Erik I; Hansen, Lars; Bennett, Eric P; Vakhrushev, Sergey Y; Schjoldager, Katrine T; Clausen, Henrik
2018-05-11
The low-density lipoprotein receptor (LDLR) and related receptors are important for the transport of diverse biomolecules across cell membranes and barriers. Their functions are especially relevant for cholesterol homeostasis and diseases, including neurodegenerative and kidney disorders. Members of the LDLR-related protein family share LDLR class A (LA) repeats providing binding properties for lipoproteins and other biomolecules. We previously demonstrated that short linker regions between these LA repeats contain conserved O -glycan sites. Moreover, we found that O -glycan modifications at these sites are selectively controlled by the GalNAc-transferase isoform, GalNAc-T11. However, the effects of GalNAc-T11-mediated O -glycosylation on LDLR and related receptor localization and function are unknown. Here, we characterized O -glycosylation of LDLR-related proteins and identified conserved O -glycosylation sites in the LA linker regions of VLDLR, LRP1, and LRP2 (Megalin) from both cell lines and rat organs. Using a panel of gene-edited isogenic cell line models, we demonstrate that GalNAc-T11-mediated LDLR and VLDLR O -glycosylation is not required for transport and cell-surface expression and stability of these receptors but markedly enhances LDL and VLDL binding and uptake. Direct ELISA-based binding assays with truncated LDLR constructs revealed that O -glycosylation increased affinity for LDL by ∼5-fold. The molecular basis for this observation is currently unknown, but these findings open up new avenues for exploring the roles of LDLR-related proteins in disease. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
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Dehghani, Hossein; Ghobakhloo, Sepideh; Neishabury, Maryam
2016-08-01
In our previous studies on the Iranian β-thalassemia (β-thal) patients, we identified an association between the severity of the β-thal phenotype and the polymorphic palindromic site at the 5' hypersensitive site 4-locus control region (5'HS4-LCR) of the β-globin gene cluster. Furthermore, a linkage disequilibrium was observed between this region and XmnI-HBG2 in the patient population. Based on this data, it was suggested that the well-recognized phenotype-ameliorating role assigned to positive XmnI could be associated with its linked elements in the LCR. To investigate the functional significance of polymorphisms at the 5'HS4-LCR, we studied its influence on binding of transcription factors. Web-based predictions of transcription factor binding revealed a binding site for runt-related transcription factor 1 (RUNX1), when the allele at the center of the palindrome (TGGGG(A/G)CCCCA) was A but not when it was G. Furthermore, electromobility shift assay (EMSA) presented evidence in support of allele-specific binding of RUNX1 to 5'HS4. Considering that RUNX1 is a well-known regulator of hematopoiesis, these preliminary data suggest the importance of further studies to confirm this interaction and consequently investigate its functional and phenotypical relevance. These studies could help us to understand the molecular mechanism behind the phenotype modifying role of the 5'HS4-LCR polymorphic palindromic region (rs16912979), which has been observed in previous studies.
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2,3-DPG-Hb complex: a hypothesis for an asymmetric binding.
Pomponi, M; Bertonati, C; Fuglei, E; Wiig, O; Derocher, A E
2000-05-15
This study was undertaken to test the symmetry of 2,3-diphosphoglycerate (2,3-DPG) binding site in hemoglobin (Hb). From Arnone's study [A. Arnone, Nature (London) 237 (1972) 146] the 2,3-DPG binding site is located at the top of the cavity, that runs through the center of the deoxy-Hb molecule. However, it is possible that this symmetry reported by Arnone, for crystals of 2,3-DPG-Hb complex, might not be conserved in solution. In this paper, we report the 31P nuclear magnetic resonances of the 2,3-DPG interaction with Hb. The 2,3-DPG chemical shifts of the P2 and P3 resonance are both pH- and hemoglobin-dependent [protein from man, polar bear (Ursus maritimus), Arctic fox (Alopex lagopus) and bovine]. 2,3-DPG binds tightly to deoxyhemoglobin and weakly, nevertheless significantly, to oxyhemoglobin. In particular, our results suggest similar spatial position of the binding site of 2,3-DPG in both forms of Hb in solutions. However, the most unexpected result was the apparent loss of symmetry in the binding site, which might correlate with the ability of the hemoglobin to modulate its functional behavior. The different interactions of the phosphate groups indicate small differences in the quaternary structure of the different deoxy forms of hemoglobin. Given the above structural perturbation an asymmetric binding in the complex could justify, at least in part, different physiological properties of Hb. Regardless, functionally relevant effects of 2,3-DPG seem to be measured and best elucidated through solution studies.
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Defaus, Sira; Avilés, Manuel; Andreu, David; Gutiérrez-Gallego, Ricardo
2018-04-04
Seminal plasma proteins are relevant for sperm functionality and some appear responsible for establishing sperm interactions with the various environments along the female genital tract towards the oocyte. In recent years, research has focused on characterizing the role of these proteins in the context of reproductive biology, fertility diagnostics and treatment of related problems. Herein, we focus on the main protein of bovine seminal plasma, PDC-109 (BSP-A1/-A2), which by virtue of its lectin properties is involved in fertilization. By means of surface plasmon resonance, the interaction of PDC-109 with a panel of the most relevant glycosidic epitopes of mammals has been qualitatively and quantitatively characterized, and a higher affinity for carbohydrates containing fucose has been observed, in line with previous studies. Additionally, using the orthogonal technique of Carbohydrate REcognition Domain EXcision-Mass Spectrometry (CREDEX-MS), the recognition domain of the interaction complexes between PDC-109 and all fucosylated disaccharides [(Fuc-α1,(3,4,6)-GlcNAc)] has been defined, revealing the specific glycotope and the peptide domain likely to act as the PDC-109 carbohydrate binding site.
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NASA Astrophysics Data System (ADS)
Koch, Jonas; Nowak, Wolfgang
2013-04-01
At many hazardous waste sites and accidental spills, dense non-aqueous phase liquids (DNAPLs) such as TCE, PCE, or TCA have been released into the subsurface. Once a DNAPL is released into the subsurface, it serves as persistent source of dissolved-phase contamination. In chronological order, the DNAPL migrates through the porous medium and penetrates the aquifer, it forms a complex pattern of immobile DNAPL saturation, it dissolves into the groundwater and forms a contaminant plume, and it slowly depletes and bio-degrades in the long-term. In industrial countries the number of such contaminated sites is tremendously high to the point that a ranking from most risky to least risky is advisable. Such a ranking helps to decide whether a site needs to be remediated or may be left to natural attenuation. Both the ranking and the designing of proper remediation or monitoring strategies require a good understanding of the relevant physical processes and their inherent uncertainty. To this end, we conceptualize a probabilistic simulation framework that estimates probability density functions of mass discharge, source depletion time, and critical concentration values at crucial target locations. Furthermore, it supports the inference of contaminant source architectures from arbitrary site data. As an essential novelty, the mutual dependencies of the key parameters and interacting physical processes are taken into account throughout the whole simulation. In an uncertain and heterogeneous subsurface setting, we identify three key parameter fields: the local velocities, the hydraulic permeabilities and the DNAPL phase saturations. Obviously, these parameters depend on each other during DNAPL infiltration, dissolution and depletion. In order to highlight the importance of these mutual dependencies and interactions, we present results of several model set ups where we vary the physical and stochastic dependencies of the input parameters and simulated processes. Under these changes, the probability density functions demonstrate strong statistical shifts in their expected values and in their uncertainty. Considering the uncertainties of all key parameters but neglecting their interactions overestimates the output uncertainty. However, consistently using all available physical knowledge when assigning input parameters and simulating all relevant interactions of the involved processes reduces the output uncertainty significantly back down to useful and plausible ranges. When using our framework in an inverse setting, omitting a parameter dependency within a crucial physical process would lead to physical meaningless identified parameters. Thus, we conclude that the additional complexity we propose is both necessary and adequate. Overall, our framework provides a tool for reliable and plausible prediction, risk assessment, and model based decision support for DNAPL contaminated sites.
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Orr, Larry; Govindjee
2013-07-01
Online access to the Internet and the World Wide Web has become important for public awareness and for educating the world's population, including its political leaders, students, researchers, teachers, and ordinary citizens seeking information. After a brief Introduction, relevant information found on photosynthesis-related Web sites and other online locations is presented under five categories: (a) group sites, (b) sites by subject, (c) individual researcher's sites, (d) sites for educators and students, and (e) other useful sites.
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Relevance of grasp types to assess functionality for personal autonomy.
Gracia-Ibáñez, Verónica; Sancho-Bru, Joaquin L; Vergara, Margarita
Cross-sectional research design. Current assessment of hand function is not focused on evaluating the real abilities required for autonomy. To quantify the relevance of grasp types for autonomy to guide hand recovery and its assessment. Representative tasks of the International Classification of Functioning, Disability and Health activities in which the hands are directly involved were recorded. The videos were analyzed to identify the grasps used with each hand, and their relevance for autonomy was determined by weighting time with the frequency of appearance of each activity in disability and dependency scales. Relevance is provided globally and distinguished by hand (right-left) and bimanual function. Significant differences in relevance are also checked. The most relevant grasps are pad-to-pad pinch (31.9%), lumbrical (15.4%), cylindrical (12%), and special pinch (7.3%) together with the nonprehensile (18.6%) use of the hand. Lumbrical grasp has higher relevance for the left hand (19.9% vs 12%) while cylindrical grasp for the right hand (15.3% vs 7.7%). Relevancies are also different depending on bimanual function. Different relative importance was obtained when considering dependency vs disability scales. Pad-to-pad pinch and nonprehensile grasp are the most relevant grasps for both hands, whereas lumbrical grasp is more relevant for the left hand and cylindrical grasp for the right one. The most significant difference in bimanual function refers to pad-to-pad pinch (more relevant for unimanual actions of the left hand and bimanual actions of the right). The relative importance of each grasp type for autonomy and the differences observed between hand and bimanual action should be used in medical and physical decision-making. N/A. Copyright © 2017 Hanley & Belfus. Published by Elsevier Inc. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1996-03-01
This module, describes the overall role played by ARARs in the Superfund response process; Explains the difference between applicable and relevant and appropriate requirements; Explains how ARARs apply to on- and off-site response actions; Describes how and at what stages of the response process ARARs are identified; Discusses the type and extent of ARARs that may apply to a given respone action; and Discusses specific laws and requirements that may come into play at a Superfund site.
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Quality analysis of patient information about knee arthroscopy on the World Wide Web.
Sambandam, Senthil Nathan; Ramasamy, Vijayaraj; Priyanka, Priyanka; Ilango, Balakrishnan
2007-05-01
This study was designed to ascertain the quality of patient information available on the World Wide Web on the topic of knee arthroscopy. For the purpose of quality analysis, we used a pool of 232 search results obtained from 7 different search engines. We used a modified assessment questionnaire to assess the quality of these Web sites. This questionnaire was developed based on similar studies evaluating Web site quality and includes items on illustrations, accessibility, availability, accountability, and content of the Web site. We also compared results obtained with different search engines and tried to establish the best possible search strategy to attain the most relevant, authentic, and adequate information with minimum time consumption. For this purpose, we first compared 100 search results from the single most commonly used search engine (AltaVista) with the pooled sample containing 20 search results from each of the 7 different search engines. The search engines used were metasearch (Copernic and Mamma), general search (Google, AltaVista, and Yahoo), and health topic-related search engines (MedHunt and Healthfinder). The phrase "knee arthroscopy" was used as the search terminology. Excluding the repetitions, there were 117 Web sites available for quality analysis. These sites were analyzed for accessibility, relevance, authenticity, adequacy, and accountability by use of a specially designed questionnaire. Our analysis showed that most of the sites providing patient information on knee arthroscopy contained outdated information, were inadequate, and were not accountable. Only 16 sites were found to be providing reasonably good patient information and hence can be recommended to patients. Understandably, most of these sites were from nonprofit organizations and educational institutions. Furthermore, our study revealed that using multiple search engines increases patients' chances of obtaining more relevant information rather than using a single search engine. Our study shows the difficulties encountered by patients in obtaining information regarding knee arthroscopy and highlights the duty of knee surgeons in helping patients to identify the relevant and authentic information in the most efficient manner from the World Wide Web. This study highlights the importance of the role of orthopaedic surgeons in helping their patients to identify the best possible information on the World Wide Web.
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Prediction of Hydrologic Characteristics for Ungauged Catchments to Support Hydroecological Modeling
NASA Astrophysics Data System (ADS)
Bond, Nick R.; Kennard, Mark J.
2017-11-01
Hydrologic variability is a fundamental driver of ecological processes and species distribution patterns within river systems, yet the paucity of gauges in many catchments means that streamflow data are often unavailable for ecological survey sites. Filling this data gap is an important challenge in hydroecological research. To address this gap, we first test the ability to spatially extrapolate hydrologic metrics calculated from gauged streamflow data to ungauged sites as a function of stream distance and catchment area. Second, we examine the ability of statistical models to predict flow regime metrics based on climate and catchment physiographic variables. Our assessment focused on Australia's largest catchment, the Murray-Darling Basin (MDB). We found that hydrologic metrics were predictable only between sites within ˜25 km of one another. Beyond this, correlations between sites declined quickly. We found less than 40% of fish survey sites from a recent basin-wide monitoring program (n = 777 sites) to fall within this 25 km range, thereby greatly limiting the ability to utilize gauge data for direct spatial transposition of hydrologic metrics to biological survey sites. In contrast, statistical model-based transposition proved effective in predicting ecologically relevant aspects of the flow regime (including metrics describing central tendency, high- and low-flows intermittency, seasonality, and variability) across the entire gauge network (median R2 ˜ 0.54, range 0.39-0.94). Modeled hydrologic metrics thus offer a useful alternative to empirical data when examining biological survey data from ungauged sites. More widespread use of these statistical tools and modeled metrics could expand our understanding of flow-ecology relationships.
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Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C
2006-01-01
Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.
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NASA Astrophysics Data System (ADS)
Hubbard, Susan S.; Ajo-Franklin, Jonathan B.; Dafflon, Baptiste; Dou, Shan; Kneafsey, Tim J.; Peterson, John E.; Tas, Neslihan; Torn, Margaret S.; Phuong Tran, Anh; Ulrich, Craig; Wainwright, Haruko; Wu, Yuxin; Wullschleger, Stan
2015-04-01
Although accurate prediction of ecosystem feedbacks to climate requires characterization of the properties that influence terrestrial carbon cycling, performing such characterization is challenging due to the disparity of scales involved. This is particularly true in vulnerable Arctic ecosystems, where microbial activities leading to the production of greenhouse gasses are a function of small-scale hydrological, geochemical, and thermal conditions influenced by geomorphology and seasonal dynamics. As part of the DOE Next-Generation Ecosystem Experiment (NGEE-Arctic), we are advancing two approaches to improve the characterization of complex Arctic ecosystems, with an initial application to an ice-wedge polygon dominated tundra site near Barrow, AK, USA. The first advance focuses on developing a new strategy to jointly monitor above- and below- ground properties critical for carbon cycling in the tundra. The strategy includes co-characterization of properties within the three critical ecosystem compartments: land surface (vegetation, water inundation, snow thickness, and geomorphology); active layer (peat thickness, soil moisture, soil texture, hydraulic conductivity, soil temperature, and geochemistry); and permafrost (mineral soil and ice content, nature, and distribution). Using a nested sampling strategy, a wide range of measurements have been collected at the study site over the past three years, including: above-ground imagery (LiDAR, visible, near infrared, NDVI) from various platforms, surface geophysical datasets (electrical, electromagnetic, ground penetrating radar, seismic), and point measurements (such as CO2 and methane fluxes, soil properties, microbial community composition). A subset of the coincident datasets is autonomously collected daily. Laboratory experiments and new inversion approaches are used to improve interpretation of the field geophysical datasets in terms of ecosystem properties. The new strategy has significantly advanced our ability to characterize and monitor ecosystem functioning - within and across permafrost, active layer and land-surface compartments and as a function of geomorphology and seasonal dynamics (thaw, growing season, freeze-up, and winter seasons). The second construct uses statistical approaches with the rich datasets to identify Arctic functional zones. Functional zones are regions in the landscape that have unique assemblages of above- and below-ground properties relevant to ecosystem functioning. Results demonstrate the strong co-variation of above and below ground properties in this Arctic ecosystem, particularly highlighting the critical influence of soil moisture on vegetation dynamics and redox-based active-layer biogeochemistry important for carbon cycling. The results also indicate that polygon types (low centered, high centered) have more power to explain the variations in properties than polygon features (trough, rim, center). This finding allows delineation of functional zones through grouping contiguous, similar types of polygons using remote sensing and surface geophysical datasets. Applied to the tundra NGEE study site, the functional zone approach permitted aggregation of critical properties associated with ~1350 polygons and their individual features, which vary over centimeter-to-meter length scales, into a few functional zones having suites of co-varying properties that were tractably defined over ~hundred meter length scales. The developed above-and-below ground monitoring strategy and functional zone approach are proving to be extremely valuable for gaining new insights about a complex Arctic ecosystem and for characterizing the system properties at high resolution and yet with spatial extents relevant for informing models focused on simulating ecosystem-climate feedbacks.
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Ultrafast All-Optical Switching of Germanium-Based Flexible Metaphotonic Devices.
Lim, Wen Xiang; Manjappa, Manukumara; Srivastava, Yogesh Kumar; Cong, Longqing; Kumar, Abhishek; MacDonald, Kevin F; Singh, Ranjan
2018-03-01
Incorporating semiconductors as active media into metamaterials offers opportunities for a wide range of dynamically switchable/tunable, technologically relevant optical functionalities enabled by strong, resonant light-matter interactions within the semiconductor. Here, a germanium-thin-film-based flexible metaphotonic device for ultrafast optical switching of terahertz radiation is experimentally demonstrated. A resonant transmission modulation depth of 90% is achieved, with an ultrafast full recovery time of 17 ps. An observed sub-picosecond decay constant of 670 fs is attributed to the presence of trap-assisted recombination sites in the thermally evaporated germanium film. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Single molecule optical measurements of orientation and rotations of biological macromolecules.
Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E
2016-11-22
Subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measurement of their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, review the relevant types of probes and labeling techniques, and highlight the advantages and disadvantages of these technologies for addressing specific inquiries.
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Msx homeobox gene family and craniofacial development.
Alappat, Sylvia; Zhang, Zun Yi; Chen, Yi Ping
2003-12-01
Vertebrate Msx genes are unlinked, homeobox-containing genes that bear homology to the Drosophila muscle segment homeobox gene. These genes are expressed at multiple sites of tissue-tissue interactions during vertebrate embryonic development. Inductive interactions mediated by the Msx genes are essential for normal craniofacial, limb and ectodermal organ morphogenesis, and are also essential to survival in mice, as manifested by the phenotypic abnormalities shown in knockout mice and in humans. This review summarizes studies on the expression, regulation, and functional analysis of Msx genes that bear relevance to craniofacial development in humans and mice. Key words: Msx genes, craniofacial, tooth, cleft palate, suture, development, transcription factor, signaling molecule.
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California state information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the state of California. It contains: a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; the full text of relevant statutes and regulations.« less
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Oregon state information handbook formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administater, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Oregon. It contains: a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less
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Iowa state information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, By Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the state of Iowa. It contains: a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; the full test of relevant statutes and regulations.« less
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Oregon state information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Oregon. It contains a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less
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Pennsylvania state information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and State levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of Pennsylvania. It contains a description of themore » state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less
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New Mexico state information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the State of New Mexico. It contains a description ofmore » the state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations.« less
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ATP-binding cassette transporters in reproduction: a new frontier
Bloise, E.; Ortiga-Carvalho, T.M.; Reis, F.M.; Lye, S.J.; Gibb, W.; Matthews, S.G.
2016-01-01
BACKGROUND The transmembrane ATP-binding cassette (ABC) transporters actively efflux an array of clinically relevant compounds across biological barriers, and modulate biodistribution of many physiological and pharmacological factors. To date, over 48 ABC transporters have been identified and shown to be directly and indirectly involved in peri-implantation events and fetal/placental development. They efflux cholesterol, steroid hormones, vitamins, cytokines, chemokines, prostaglandins, diverse xenobiotics and environmental toxins, playing a critical role in regulating drug disposition, immunological responses and lipid trafficking, as well as preventing fetal accumulation of drugs and environmental toxins. METHODS This review examines ABC transporters as important mediators of placental barrier functions and key reproductive processes. Expression, localization and function of all identified ABC transporters were systematically reviewed using PubMed and Google Scholar websites to identify relevant studies examining ABC transporters in reproductive tissues in physiological and pathophysiological states. Only reports written in English were incorporated with no restriction on year of publication. While a major focus has been placed on the human, extensive evidence from animal studies is utilized to describe current understanding of the regulation and function of ABC transporters relevant to human reproduction. RESULTS ABC transporters are modulators of steroidogenesis, fertilization, implantation, nutrient transport and immunological responses, and function as ‘gatekeepers’ at various barrier sites (i.e. blood-testes barrier and placenta) against potentially harmful xenobiotic factors, including drugs and environmental toxins. These roles appear to be species dependent and change as a function of gestation and development. The best-described ABC transporters in reproductive tissues (primarily in the placenta) are the multidrug transporters p-glycoprotein and breast cancer-related protein, the multidrug resistance proteins 1 through 5 and the cholesterol transporters ABCA1 and ABCG1. CONCLUSIONS The ABC transporters have various roles across multiple reproductive tissues. Knowledge of efflux direction, tissue distribution, substrate specificity and regulation of the ABC transporters in the placenta and other reproductive tissues is rapidly expanding. This will allow better understanding of the disposition of specific substrates within reproductive tissues, and facilitate development of novel treatments for reproductive disorders as well as improved approaches to protecting the developing fetus. PMID:26545808
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Su, Dian; Shukla, Anil K.; Chen, Baowei
2013-04-01
S-nitrosylation (SNO) is an important reversible thiol oxidation event that has been increasingly recognized for its role in cell signaling. While many proteins susceptible to S-nitrosylation have been reported, site-specific identification of physiologically relevant SNO modifications remains an analytical challenge due to the low-abundance and labile nature of the modification. Herein we present further improvement and optimization of the recently reported, resin-assisted cysteinyl peptide enrichment protocol for SNO identification and the extension of this application to mouse skeletal muscle to identify specific sites sensitive to S-nitrosylation by quantitative reactivity profiling. The results of our data indicate that the protein- andmore » peptide-level enrichment protocols provide comparable specificity and coverage of SNO-peptide identifications. S-nitrosylation reactivity profiling was performed by quantitatively comparing the site-specific SNO modification levels in samples treated with S-nitrosoglutathione (GSNO), an NO donor, at two different physiologically relevant concentrations (i.e., 10 μM and 100 μM). The reactivity profiling experiments overall identified 489 SNO-modified cysteine sites from 197 proteins with the specificity of 95.2% at the unique-peptide-level based on the percentage of Cys-peptides. Among these sites, 260 sites from 135 proteins were observed with relatively high reactivity to S-nitrosylation; such SNO-sensitive sites are more likely to be physiologically relevant. Many of the SNO-sensitive proteins are preferentially localized in mitochondria, contractile fiber and actin cytoskeleton, suggesting the susceptibility of these subcellular compartments to redox regulation. Moreover, the SNO-sensitive proteins seem to be primarily involved in metabolic pathways, including TCA cycle, glycolysis/gluconeogenesis, glutathione metabolism, and fatty acid metabolism, suggesting the importance of redox regulation in muscle metabolism and insulin action.« less
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Tabares, Leandro C.; Gätjens, Jessica; Hureau, Christelle; Burrell, Matthew R.; Bowater, Laura; Pecoraro, Vincent L.; Bornemann, Stephen; Un, Sun
2009-01-01
A high-field electron paramagnetic resonance (HFEPR) study of oxalate decarboxylase (OxdC) is reported. OxdC breaks down oxalate to carbon dioxide and formate and possesses two distinct manganese(II) binding sites, referred to as site-1 and -2. The Mn(II) zero-field interaction was used to probe the electronic state of the metal ion and to examine chemical/mechanistic roles of each of the Mn(II) centers. High magnetic-fields were exploited not only to resolve the two sites, but also to measure accurately the Mn(II) zero-field parameters of each of the sites. The spectra exhibited surprisingly complex behavior as a function of pH. Six different species were identified based on their zero-field interactions, two corresponding to site-1 and four states to site-2. The assignments were verified using a mutant that only affected site-1. The speciation data determined from the HFEPR spectra for site -2 was consistent with a simple triprotic equilibrium model, while the pH dependence of site-1 could be described by a single pKa. This pH dependence was independent of the presence of the His-tag and of whether the preparations contained 1.2 or 1.6 Mn per subunit. Possible structures of the six species are proposed based on spectroscopic data from model complexes and existing protein crystallographic structures obtained at pH 8 are discussed. Although site-1 has been identified as the active site and no role has been assigned to site-2, the pronounced changes in the electronic structure of the latter and its pH behavior, which also matches the pH-dependent activity of this enzyme, suggests that even if the conversion of oxalate to formate is carried out at site-1, site-2 likely plays a catalytically relevant role. PMID:19505123
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The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers.
Lueders, Tillmann
2017-01-01
The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ 13 C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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Episodic Memory Retrieval Functionally Relies on Very Rapid Reactivation of Sensory Information.
Waldhauser, Gerd T; Braun, Verena; Hanslmayr, Simon
2016-01-06
Episodic memory retrieval is assumed to rely on the rapid reactivation of sensory information that was present during encoding, a process termed "ecphory." We investigated the functional relevance of this scarcely understood process in two experiments in human participants. We presented stimuli to the left or right of fixation at encoding, followed by an episodic memory test with centrally presented retrieval cues. This allowed us to track the reactivation of lateralized sensory memory traces during retrieval. Successful episodic retrieval led to a very early (∼100-200 ms) reactivation of lateralized alpha/beta (10-25 Hz) electroencephalographic (EEG) power decreases in the visual cortex contralateral to the visual field at encoding. Applying rhythmic transcranial magnetic stimulation to interfere with early retrieval processing in the visual cortex led to decreased episodic memory performance specifically for items encoded in the visual field contralateral to the site of stimulation. These results demonstrate, for the first time, that episodic memory functionally relies on very rapid reactivation of sensory information. Remembering personal experiences requires a "mental time travel" to revisit sensory information perceived in the past. This process is typically described as a controlled, relatively slow process. However, by using electroencephalography to measure neural activity with a high time resolution, we show that such episodic retrieval entails a very rapid reactivation of sensory brain areas. Using transcranial magnetic stimulation to alter brain function during retrieval revealed that this early sensory reactivation is causally relevant for conscious remembering. These results give first neural evidence for a functional, preconscious component of episodic remembering. This provides new insight into the nature of human memory and may help in the understanding of psychiatric conditions that involve the automatic intrusion of unwanted memories. Copyright © 2016 the authors 0270-6474/16/360251-10$15.00/0.
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Guo, Zhongyuan; Martucci, Nicole J.; Moreno-Olivas, Fabiola; Tako, Elad; Mahler, Gretchen J.
2017-01-01
Ingestion of titanium dioxide (TiO2) nanoparticles from products such as agricultural chemicals, processed food, and nutritional supplements is nearly unavoidable. The gastrointestinal tract serves as a critical interface between the body and the external environment, and is the site of essential nutrient absorption. The goal of this study was to examine the effects of ingesting the 30 nm TiO2 nanoparticles with an in vitro cell culture model of the small intestinal epithelium, and to determine how acute or chronic exposure to nano-TiO2 influences intestinal barrier function, reactive oxygen species generation, proinflammatory signaling, nutrient absorption (iron, zinc, fatty acids), and brush border membrane enzyme function (intestinal alkaline phosphatase). A Caco-2/HT29-MTX cell culture model was exposed to physiologically relevant doses of TiO2 nanoparticles for acute (four hours) or chronic (five days) time periods. Exposure to TiO2 nanoparticles significantly decreased intestinal barrier function following chronic exposure. Reactive oxygen species (ROS) generation, proinflammatory signaling, and intestinal alkaline phosphatase activity all showed increases in response to nano-TiO2. Iron, zinc, and fatty acid transport were significantly decreased following exposure to TiO2 nanoparticles. This is because nanoparticle exposure induced a decrease in absorptive microvilli in the intestinal epithelial cells. Nutrient transporter protein gene expression was also altered, suggesting that cells are working to regulate the transport mechanisms disturbed by nanoparticle ingestion. Overall, these results show that intestinal epithelial cells are affected at a functional level by physiologically relevant exposure to nanoparticles commonly ingested from food. PMID:28944308
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Schür, R R; Boks, M P; Rutten, B P F; Daskalakis, N P; de Nijs, L; van Zuiden, M; Kavelaars, A; Heijnen, C J; Joëls, M; Kahn, R S; Geuze, E; Vermetten, E; Vinkers, C H
2017-01-01
Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1F region (GR-1F) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1F methylation changes over time in relation to trauma exposure and the development of post-deployment psychopathology. GR-1F methylation (52 loci) was quantified using pyrosequencing in whole blood of 92 military men 1 month before and 6 months after a 4-month deployment period to Afghanistan. GR-1F methylation overall (mean methylation and the number of methylated loci) and functional methylation (methylation at loci associated with GR exon 1F expression) measures were examined. We first investigated the effect of exposure to potentially traumatic events during deployment on these measures. Subsequently, changes in GR-1F methylation were related to changes in mental health problems (total Symptom Checklist-90 score) and posttraumatic stress disorder (PTSD) symptoms (Self-Report Inventory for PTSD). Trauma exposure during deployment was associated with an increase in all methylation measures, but development of mental health problems 6 months after deployment was only significantly associated with an increased functional methylation. Emergence of post-deployment PTSD symptoms was not related to increased functional methylation over time. Pre-deployment methylation levels did not predict post-deployment psychopathology. To our knowledge, this is the first study to prospectively demonstrate trauma-related increases in GR-1F methylation, and it shows that only increases at specific functionally relevant sites predispose for post-deployment psychopathology. PMID:28742078
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An Expanding Range of Functions for the Copper Chaperone/Antioxidant Protein Atox1
Hatori, Yuta
2013-01-01
Abstract Significance: Antioxidant protein 1 (Atox1 in human cells) is a copper chaperone for the copper export pathway with an essential role in cellular copper distribution. In vitro, Atox1 binds and transfers copper to the copper-transporting ATPases, stimulating their catalytic activity. Inactivation of Atox1 in cells inhibits maturation of secreted cuproenzymes as well as copper export from cells. Recent Advances: Accumulating data suggest that cellular functions of Atox1 are not limited to its copper-trafficking role and may include storage of labile copper, modulation of transcription, and antioxidant defense. The conserved metal binding site of Atox1, CxGC, differs from the metal-binding sites of copper-transporting ATPases and has a physiologically relevant redox potential that equilibrates with the GSH:GSSG pair. Critical Issues: Tight relationship appears to exist between intracellular copper levels and glutathione (GSH) homeostasis. The biochemical properties of Atox1 place it at the intersection of cellular networks that regulate copper distribution and cellular redox balance. Mechanisms through which Atox1 facilitates copper export and contributes to oxidative defense are not fully understood. Future Directions: The current picture of cellular redox homeostasis and copper physiology will be enhanced by further mechanistic studies of functional interactions between the GSH:GSSG pair and copper-trafficking machinery. Antioxid. Redox Signal. 19, 945–957. PMID:23249252
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Stuermer, Claudia A. O.; Plattner, Helmut
2013-01-01
The SPFH protein superfamily is assumed to occur universally in eukaryotes, but information from protozoa is scarce. In the Paramecium genome, we found only Stomatins, 20 paralogs grouped in 8 families, STO1 to STO8. According to cDNA analysis, all are expressed, and molecular modeling shows the typical SPFH domain structure for all subgroups. For further analysis we used family-specific sequences for fluorescence and immunogold labeling, gene silencing, and functional tests. With all family members tested, we found a patchy localization at/near the cell surface and on vesicles. The Sto1p and Sto4p families are also associated with the contractile vacuole complex. Sto4p also makes puncta on some food vacuoles and is abundant on vesicles recycling from the release site of spent food vacuoles to the site of nascent food vacuole formation. Silencing of the STO1 family reduces mechanosensitivity (ciliary reversal upon touching an obstacle), thus suggesting relevance for positioning of mechanosensitive channels in the plasmalemma. Silencing of STO4 members increases pulsation frequency of the contractile vacuole complex and reduces phagocytotic activity of Paramecium cells. In summary, Sto1p and Sto4p members seem to be involved in positioning specific superficial and intracellular microdomain-based membrane components whose functions may depend on mechanosensation (extracellular stimuli and internal osmotic pressure). PMID:23376944
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Heusser, Stephanie A.; Howard, Rebecca J.; Borghese, Cecilia M.; Cullins, Madeline A.; Broemstrup, Torben; Lee, Ui S.; Lindahl, Erik; Carlsson, Jens
2013-01-01
GABAA receptors play a crucial role in the actions of general anesthetics. The recently published crystal structure of the general anesthetic propofol bound to Gloeobacter violaceus ligand-gated ion channel (GLIC), a bacterial homolog of GABAA receptors, provided an opportunity to explore structure-based ligand discovery for pentameric ligand-gated ion channels (pLGICs). We used molecular docking of 153,000 commercially available compounds to identify molecules that interact with the propofol binding site in GLIC. In total, 29 compounds were selected for functional testing on recombinant GLIC, and 16 of these compounds modulated GLIC function. Active compounds were also tested on recombinant GABAA receptors, and point mutations around the presumed binding pocket were introduced into GLIC and GABAA receptors to test for binding specificity. The potency of active compounds was only weakly correlated with properties such as lipophilicity or molecular weight. One compound was found to mimic the actions of propofol on GLIC and GABAA, and to be sensitive to mutations that reduce the action of propofol in both receptors. Mutant receptors also provided insight about the position of the binding sites and the relevance of the receptor’s conformation for anesthetic actions. Overall, the findings support the feasibility of the use of virtual screening to discover allosteric modulators of pLGICs, and suggest that GLIC is a valid model system to identify novel GABAA receptor ligands. PMID:23950219
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NASA Astrophysics Data System (ADS)
Guadagno, Liberata; Naddeo, Carlo; Raimondo, Marialuigia; Barra, Giuseppina; Vertuccio, Luigi; Russo, Salvatore; Lafdi, Khalid; Tucci, Vincenzo; Spinelli, Giovanni; Lamberti, Patrizia
2017-03-01
The focus of this study is to design new nano-modified epoxy formulations using carbon nanofillers, such as carbon nanotubes, carbon nanofibers and graphene-based nanoparticles (CpEG), that reduce the moisture content and provide additional functional performance. The chemical structure of epoxy mixture, using a non-stoichiometric amount of hardener, exhibits unique properties in regard to the water sorption for which the equilibrium concentration of water (C eq) is reduced up to a maximum of 30%. This result, which is very relevant for several industrial applications (aeronautical, shipbuilding industries, wind turbine blades, etc), is due to a strong reduction of the polar groups and/or sites responsible to bond water molecules. All nanofillers are responsible of a second phase at lower glass transition temperature (Tg). Compared with other carbon nanofillers, functionalized graphene-based nanoparticles exhibit the best performance in the multifunctionality. The lowest moisture content, the high performance in the mechanical properties, the low electrical percolation threshold (EPT) have been all ascribed to particular arrangements of the functionalized graphene sheets embedded in the polymeric matrix. Exfoliation degree and edge carboxylated groups are responsible of self-assembled architectures which entrap part of the resin fraction hindering the interaction of water molecules with the polar sites of the resin, also favouring the EPT paths and the attractive/covalent interactions with the matrix.
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Mudraia, I S; Kirpatovskiĭ, V I
1993-01-01
The paper describes impedance methods of investigating upper urinary tracts (UUT) which may serve adjuvants in the diagnosis of the urinary tract wall disturbances due to diseases caused by impaired urine evacuation from the kidney and which may prove helpful in the choice of therapeutic policy, evaluation of the postoperative period and outcomes prognosis. UUT impedance tests can be performed during endoscopic manipulations or under open operative interventions. Two-frequency impedancemetry allows rapid detection of non-functioning UUT parts or sclerosal sites of the UUT wall, relevant criteria being the ratio of basic impedances of the site under low and high scanning current. This value is computed by an urological two-frequency impedancemeter IDU-M. To assess the UUT wall functionally, use should be made of 6-channel urological rheograph REUR-6 providing multichannel registration of immediate impedance ureterograms. In this manner one can obtain qualitative and quantitative assessment of the ureteral peristalsis through its all length, the criteria being the amplitude of impedance ureterographic complexes, their shape, duration, frequency, rhythm, sequence and rate of distribution. Loading tests increase the accuracy of UUT impedance measurements, are able to define compensatory reserves of the wall contractility. The introduction of rheological methods in urological practice makes broader the armory of diagnostic techniques in urology, upgrade pathogenetic validity of surgical and therapeutic measures.
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Guadagno, Liberata; Naddeo, Carlo; Raimondo, Marialuigia; Barra, Giuseppina; Vertuccio, Luigi; Russo, Salvatore; Lafdi, Khalid; Tucci, Vincenzo; Spinelli, Giovanni; Lamberti, Patrizia
2017-03-03
The focus of this study is to design new nano-modified epoxy formulations using carbon nanofillers, such as carbon nanotubes, carbon nanofibers and graphene-based nanoparticles (CpEG), that reduce the moisture content and provide additional functional performance. The chemical structure of epoxy mixture, using a non-stoichiometric amount of hardener, exhibits unique properties in regard to the water sorption for which the equilibrium concentration of water (C eq ) is reduced up to a maximum of 30%. This result, which is very relevant for several industrial applications (aeronautical, shipbuilding industries, wind turbine blades, etc), is due to a strong reduction of the polar groups and/or sites responsible to bond water molecules. All nanofillers are responsible of a second phase at lower glass transition temperature (Tg). Compared with other carbon nanofillers, functionalized graphene-based nanoparticles exhibit the best performance in the multifunctionality. The lowest moisture content, the high performance in the mechanical properties, the low electrical percolation threshold (EPT) have been all ascribed to particular arrangements of the functionalized graphene sheets embedded in the polymeric matrix. Exfoliation degree and edge carboxylated groups are responsible of self-assembled architectures which entrap part of the resin fraction hindering the interaction of water molecules with the polar sites of the resin, also favouring the EPT paths and the attractive/covalent interactions with the matrix.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Berg, Larry K.; Gustafson, William I.; Kassianov, Evgueni I.
A new treatment for shallow clouds has been introduced into the Weather Research and Forecasting (WRF) model. The new scheme, called the cumulus potential (CuP) scheme, replaces the ad-hoc trigger function used in the Kain-Fritsch cumulus parameterization with a trigger function related to the distribution of temperature and humidity in the convective boundary layer via probability density functions (PDFs). An additional modification to the default version of WRF is the computation of a cumulus cloud fraction based on the time scales relevant for shallow cumuli. Results from three case studies over the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM)more » site in north central Oklahoma are presented. These days were selected because of the presence of shallow cumuli over the ARM site. The modified version of WRF does a much better job predicting the cloud fraction and the downwelling shortwave irradiance thancontrol simulations utilizing the default Kain-Fritsch scheme. The modified scheme includes a number of additional free parameters, including the number and size of bins used to define the PDF, the minimum frequency of a bin within the PDF before that bin is considered for shallow clouds to form, and the critical cumulative frequency of bins required to trigger deep convection. A series of tests were undertaken to evaluate the sensitivity of the simulations to these parameters. Overall, the scheme was found to be relatively insensitive to each of the parameters.« less
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Dehalogenation and coupling of a polycyclic hydrocarbon on an atomically thin insulator.
Dienel, Thomas; Gómez-Díaz, Jaime; Seitsonen, Ari P; Widmer, Roland; Iannuzzi, Marcella; Radican, Kevin; Sachdev, Hermann; Müllen, Klaus; Hutter, Jürg; Gröning, Oliver
2014-07-22
Catalytic activity is of pivotal relevance in enabling efficient and selective synthesis processes. Recently, covalent coupling reactions catalyzed by solid metal surfaces opened the rapidly evolving field of on-surface chemical synthesis. Tailored molecular precursors in conjunction with the catalytic activity of the metal substrate allow the synthesis of novel, technologically highly relevant materials such as atomically precise graphene nanoribbons. However, the reaction path on the metal substrate remains unclear in most cases, and the intriguing question is how a specific atomic configuration between reactant and catalyst controls the reaction processes. In this study, we cover the metal substrate with a monolayer of hexagonal boron nitride (h-BN), reducing the reactivity of the metal, and gain unique access to atomistic details during the activation of a polyphenylene precursor by sequential dehalogenation and the subsequent coupling to extended oligomers. We use scanning tunneling microscopy and density functional theory to reveal a reaction site anisotropy, induced by the registry mismatch between the precursor and the nanostructured h-BN monolayer.
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Modelling the Impact of Soil Management on Soil Functions
NASA Astrophysics Data System (ADS)
Vogel, H. J.; Weller, U.; Rabot, E.; Stößel, B.; Lang, B.; Wiesmeier, M.; Urbanski, L.; Wollschläger, U.
2017-12-01
Due to an increasing soil loss and an increasing demand for food and energy there is an enormous pressure on soils as the central resource for agricultural production. Besides the importance of soils for biomass production there are other essential soil functions, i.e. filter and buffer for water, carbon sequestration, provision and recycling of nutrients, and habitat for biological activity. All these functions have a direct feed back to biogeochemical cycles and climate. To render agricultural production efficient and sustainable we need to develop model tools that are capable to predict quantitatively the impact of a multitude of management measures on these soil functions. These functions are considered as emergent properties produced by soils as complex systems. The major challenge is to handle the multitude of physical, chemical and biological processes interacting in a non-linear manner. A large number of validated models for specific soil processes are available. However, it is not possible to simulate soil functions by coupling all the relevant processes at the detailed (i.e. molecular) level where they are well understood. A new systems perspective is required to evaluate the ensemble of soil functions and their sensitivity to external forcing. Another challenge is that soils are spatially heterogeneous systems by nature. Soil processes are highly dependent on the local soil properties and, hence, any model to predict soil functions needs to account for the site-specific conditions. For upscaling towards regional scales the spatial distribution of functional soil types need to be taken into account. We propose a new systemic model approach based on a thorough analysis of the interactions between physical, chemical and biological processes considering their site-specific characteristics. It is demonstrated for the example of soil compaction and the recovery of soil structure, water capacity and carbon stocks as a result of plant growth and biological activity. Coupling of the observed nonlinear interactions allows for modeling the stability and resilience of soil systems in terms of their essential functions.
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LenVarDB: database of length-variant protein domains.
Mutt, Eshita; Mathew, Oommen K; Sowdhamini, Ramanathan
2014-01-01
Protein domains are functionally and structurally independent modules, which add to the functional variety of proteins. This array of functional diversity has been enabled by evolutionary changes, such as amino acid substitutions or insertions or deletions, occurring in these protein domains. Length variations (indels) can introduce changes at structural, functional and interaction levels. LenVarDB (freely available at http://caps.ncbs.res.in/lenvardb/) traces these length variations, starting from structure-based sequence alignments in our Protein Alignments organized as Structural Superfamilies (PASS2) database, across 731 structural classification of proteins (SCOP)-based protein domain superfamilies connected to 2 730 625 sequence homologues. Alignment of sequence homologues corresponding to a structural domain is available, starting from a structure-based sequence alignment of the superfamily. Orientation of the length-variant (indel) regions in protein domains can be visualized by mapping them on the structure and on the alignment. Knowledge about location of length variations within protein domains and their visual representation will be useful in predicting changes within structurally or functionally relevant sites, which may ultimately regulate protein function. Non-technical summary: Evolutionary changes bring about natural changes to proteins that may be found in many organisms. Such changes could be reflected as amino acid substitutions or insertions-deletions (indels) in protein sequences. LenVarDB is a database that provides an early overview of observed length variations that were set among 731 protein families and after examining >2 million sequences. Indels are followed up to observe if they are close to the active site such that they can affect the activity of proteins. Inclusion of such information can aid the design of bioengineering experiments.
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Gouran, Hossein; Chakraborty, Sandeep; Rao, Basuthkar J; Asgeirsson, Bjarni; Dandekar, Abhaya
2014-01-01
Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction.
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Rao, Basuthkar J.; Asgeirsson, Bjarni; Dandekar, Abhaya
2014-01-01
Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction. PMID:25717364
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Wong, Michael H L; Bryan, Holly K; Copple, Ian M; Jenkins, Rosalind E; Chiu, Pak Him; Bibby, Jaclyn; Berry, Neil G; Kitteringham, Neil R; Goldring, Christopher E; O'Neill, Paul M; Park, B Kevin
2016-03-24
Semisynthetic triterpenoids such as bardoxolone methyl (methyl-2-cyano 3,12-dioxooleano-1,9-dien-28-oate; CDDO-Me) (4) are potent inducers of antioxidant and anti-inflammatory signaling pathways, including those regulated by the transcription factor Nrf2. However, the reversible nature of the interaction between triterpenoids and thiols has hindered attempts to identify pharmacologically relevant targets and characterize the sites of interaction. Here, we report a shortened synthesis and SAR profiling of 4, enabling the design of analogues that react irreversibly with model thiols, as well as the model protein glutathione S-transferase P1, in vitro. We show that one of these analogues, CDDO-epoxide (13), is comparable to 4 in terms of cytotoxicity and potency toward Nrf2 in rat hepatoma cells and stably modifies specific cysteine residues (namely, Cys-257, -273, -288, -434, -489, and -613) within Keap1, the major repressor of Nrf2, both in vitro and in living cells. Supported by molecular modeling, these data demonstrate the value of 13 for identifying site(s) of interaction with pharmacologically relevant targets and informing the continuing development of triterpenoids as novel drug candidates.
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NASA Astrophysics Data System (ADS)
Rodrigo-Ilarri, J.; Li, T.; Grathwohl, P.; Blum, P.; Bayer, P.
2009-04-01
The design of geothermal systems such as aquifer thermal energy storage systems (ATES) must account for a comprehensive characterisation of all relevant parameters considered for the numerical design model. Hydraulic and thermal conductivities are the most relevant parameters and its distribution determines not only the technical design but also the economic viability of such systems. Hence, the knowledge of the spatial distribution of these parameters is essential for a successful design and operation of such systems. This work shows the first results obtained when applying geostatistical techniques to the characterisation of the Esseling Site in Germany. In this site a long-term thermal tracer test (> 1 year) was performed. On this open system the spatial temperature distribution inside the aquifer was observed over time in order to obtain as much information as possible that yield to a detailed characterisation both of the hydraulic and thermal relevant parameters. This poster shows the preliminary results obtained for the Esseling Site. It has been observed that the common homogeneous approach is not sufficient to explain the observations obtained from the TRT and that parameter heterogeneity must be taken into account.
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Zheng, Wenjun
2017-02-01
In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
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Dal Santo, Vladimiro; Liguori, Francesca; Pirovano, Claudio; Guidotti, Matteo
2010-05-26
Nanostructured single-site heterogeneous catalysts possess the advantages of classical solid catalysts, in terms of easy recovery and recycling, together with a defined tailored chemical and steric environment around the catalytically active metal site. The use of inorganic oxide supports with selected shape and porosity at a nanometric level may have a relevant impact on the regio- and stereochemistry of the catalytic reaction. Analogously, by choosing the optimal preparation techniques to obtain spatially isolated and well-characterised active sites, it is possible to achieve performances that are comparable to (or, in the most favourable cases, better than) those obtained with homogeneous systems. Such catalysts are therefore particularly suitable for the transformation of highly-functionalised fine chemicals and some relevant examples where high chemo-, regio- and stereoselectivity are crucial will be described.
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Martinez, Andres W; Phillips, Scott T; Carrilho, Emanuel; Thomas, Samuel W; Sindi, Hayat; Whitesides, George M
2008-05-15
This article describes a prototype system for quantifying bioassays and for exchanging the results of the assays digitally with physicians located off-site. The system uses paper-based microfluidic devices for running multiple assays simultaneously, camera phones or portable scanners for digitizing the intensity of color associated with each colorimetric assay, and established communications infrastructure for transferring the digital information from the assay site to an off-site laboratory for analysis by a trained medical professional; the diagnosis then can be returned directly to the healthcare provider in the field. The microfluidic devices were fabricated in paper using photolithography and were functionalized with reagents for colorimetric assays. The results of the assays were quantified by comparing the intensities of the color developed in each assay with those of calibration curves. An example of this system quantified clinically relevant concentrations of glucose and protein in artificial urine. The combination of patterned paper, a portable method for obtaining digital images, and a method for exchanging results of the assays with off-site diagnosticians offers new opportunities for inexpensive monitoring of health, especially in situations that require physicians to travel to patients (e.g., in the developing world, in emergency management, and during field operations by the military) to obtain diagnostic information that might be obtained more effectively by less valuable personnel.
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Huang, Yandong; Yue, Zhi; Tsai, Cheng-Chieh; Henderson, Jack A; Shen, Jana
2018-03-15
Despite the relevance of understanding structure-function relationships, robust prediction of proton donors and nucleophiles in enzyme active sites remains challenging. Here we tested three types of state-of-the-art computational methods to calculate the p K a 's of the buried and hydrogen bonded catalytic dyads in five enzymes. We asked the question what determines the p K a order, i.e., what makes a residue proton donor vs a nucleophile. The continuous constant pH molecular dynamics simulations captured the experimental p K a orders and revealed that the negative nucleophile is stabilized by increased hydrogen bonding and solvent exposure as compared to the proton donor. Surprisingly, this simple trend is not apparent from crystal structures and the static structure-based calculations. While the generality of the findings awaits further testing via a larger set of data, they underscore the role of dynamics in bridging enzyme structures and functions.
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BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements.
Bhagwat, Anand S; Roe, Jae-Seok; Mok, Beverly Y L; Hohmann, Anja F; Shi, Junwei; Vakoc, Christopher R
2016-04-19
The bromodomain and extraterminal (BET) protein BRD4 can physically interact with the Mediator complex, but the relevance of this association to the therapeutic effects of BET inhibitors in cancer is unclear. Here, we show that BET inhibition causes a rapid release of Mediator from a subset of cis-regulatory elements in the genome of acute myeloid leukemia (AML) cells. These sites of Mediator eviction were highly correlated with transcriptional suppression of neighboring genes, which are enriched for targets of the transcription factor MYB and for functions related to leukemogenesis. A shRNA screen of Mediator in AML cells identified the MED12, MED13, MED23, and MED24 subunits as performing a similar regulatory function to BRD4 in this context, including a shared role in sustaining a block in myeloid maturation. These findings suggest that the interaction between BRD4 and Mediator has functional importance for gene-specific transcriptional activation and for AML maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
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Callaghan, Brid; Furness, John B; Pustovit, Ruslan V
2018-03-01
Narrative review. The purpose is to review the organisation of the nerve pathways that control defecation and to relate this knowledge to the deficits in colorectal function after SCI. A literature review was conducted to identify salient features of defecation control pathways and the functional consequences of damage to these pathways in SCI. The control pathways for defecation have separate pontine centres under cortical control that influence defecation. The pontine centres connect, separately, with autonomic preganglionic neurons of the spinal defecation centres and somatic motor neurons of Onuf's nucleus in the sacral spinal cord. Organised propulsive motor patterns can be generated by stimulation of the spinal defecation centres. Activation of the somatic neurons contracts the external sphincter. The analysis aids in interpreting the consequences of SCI and predicts therapeutic strategies. Analysis of the bowel control circuits identifies sites at which bowel function may be modulated after SCI. Colokinetic drugs that elicit propulsive contractions of the colorectum may provide valuable augmentation of non-pharmacological bowel management procedures.
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Mounir, Zineb; Korn, Joshua M; Westerling, Thomas; Lin, Fallon; Kirby, Christina A; Schirle, Markus; McAllister, Gregg; Hoffman, Greg; Ramadan, Nadire; Hartung, Anke; Feng, Yan; Kipp, David Randal; Quinn, Christopher; Fodor, Michelle; Baird, Jason; Schoumacher, Marie; Meyer, Ronald; Deeds, James; Buchwalter, Gilles; Stams, Travis; Keen, Nicholas; Sellers, William R; Brown, Myles; Pagliarini, Raymond A
2016-05-16
The TMPRSS2:ERG gene fusion is common in androgen receptor (AR) positive prostate cancers, yet its function remains poorly understood. From a screen for functionally relevant ERG interactors, we identify the arginine methyltransferase PRMT5. ERG recruits PRMT5 to AR-target genes, where PRMT5 methylates AR on arginine 761. This attenuates AR recruitment and transcription of genes expressed in differentiated prostate epithelium. The AR-inhibitory function of PRMT5 is restricted to TMPRSS2:ERG-positive prostate cancer cells. Mutation of this methylation site on AR results in a transcriptionally hyperactive AR, suggesting that the proliferative effects of ERG and PRMT5 are mediated through attenuating AR's ability to induce genes normally involved in lineage differentiation. This provides a rationale for targeting PRMT5 in TMPRSS2:ERG positive prostate cancers. Moreover, methylation of AR at arginine 761 highlights a mechanism for how the ERG oncogene may coax AR towards inducing proliferation versus differentiation.
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Production of Pseudomonas aeruginosa Intercellular Small Signaling Molecules in Human Burn Wounds
Que, Yok-Ai; Hazan, Ronen; Ryan, Colleen M.; Milot, Sylvain; Lépine, François; Lydon, Martha; Rahme, Laurence G.
2011-01-01
Pseudomonas aeruginosa has developed a complex cell-to-cell communication system that relies on low-molecular weight excreted molecules to control the production of its virulence factors. We previously characterized the transcriptional regulator MvfR, that controls a major network of acute virulence functions in P. aeruginosa through the control of its ligands, the 4-hydroxy-2-alkylquinolines (HAQs)—4-hydroxy-2-heptylquinoline (HHQ) and 3,4-dihydroxy-2-heptylquinoline (PQS). Though HHQ and PQS are produced in infected animals, their ratios differ from those in bacterial cultures. Because these molecules are critical for the potency of activation of acute virulence functions, here we investigated whether they are also produced during human P. aeruginosa acute wound infection and whether their ratio is similar to that observed in P. aeruginosa-infected mice. We found that a clinically relevant P. aeruginosa isolate produced detectable levels of HAQs with ratios of HHQ and PQS that were similar to those produced in burned and infected animals, and not resembling ratios in bacterial cultures. These molecules could be isolated from wound tissue as well as from drainage liquid. These results demonstrate for the first time that HAQs can be isolated and quantified from acute human wound infection sites and validate the relevance of previous studies conducted in mammalian models of infection. PMID:23533774
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Newell, Nicholas E
2011-12-15
The extraction of the set of features most relevant to function from classified biological sequence sets is still a challenging problem. A central issue is the determination of expected counts for higher order features so that artifact features may be screened. Cascade detection (CD), a new algorithm for the extraction of localized features from sequence sets, is introduced. CD is a natural extension of the proportional modeling techniques used in contingency table analysis into the domain of feature detection. The algorithm is successfully tested on synthetic data and then applied to feature detection problems from two different domains to demonstrate its broad utility. An analysis of HIV-1 protease specificity reveals patterns of strong first-order features that group hydrophobic residues by side chain geometry and exhibit substantial symmetry about the cleavage site. Higher order results suggest that favorable cooperativity is weak by comparison and broadly distributed, but indicate possible synergies between negative charge and hydrophobicity in the substrate. Structure-function results for the Schellman loop, a helix-capping motif in proteins, contain strong first-order features and also show statistically significant cooperativities that provide new insights into the design of the motif. These include a new 'hydrophobic staple' and multiple amphipathic and electrostatic pair features. CD should prove useful not only for sequence analysis, but also for the detection of multifactor synergies in cross-classified data from clinical studies or other sources. Windows XP/7 application and data files available at: https://sites.google.com/site/cascadedetect/home. nacnewell@comcast.net Supplementary information is available at Bioinformatics online.
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Site-preference and valency for rare-earth sites in (R-Ce)2Fe14B [R =La,Nd] magnets
NASA Astrophysics Data System (ADS)
Alam, Aftab; Khan, Mahmud; McCallum, R. W.; Johnson, D. D.
2013-03-01
Rare-earth (R) permanent magnets of R2Fe14B have technological importance due to their high energy products, and they have two symmetry distinct R-sites (Wyckoff 4f and 4g) that affect chemistry and valence. Designing magnetic behavior and stability via alloying is technologically relevant to reduce critical (expensive) R-content while retaining key properties; cerium, an abundant (cheap) R-element, offers this potential. We calculate magnetic properties and Ce site preference in (R1-xCex)Fe14B [R=La,Nd] using density functional theory (DFT) methods. The Fe moments compare well with neutron scattering data - remain weakly affected by Hubbard U, but improved with spin-orbit coupling. In (La,Ce)2Fe14B, Ce alloys for 0 < x < 1 with a preference for smaller R(4f) sites, as observed, a trend we find unaffected by valence. Whereas in (Nd,Ce)2Fe14B, Ce is predicted to have limited alloying (x < 0.3) with a preference for larger R(4g) sites, resulting in weak partial ordering and segregation. Curie temperatures versus x were predicted for a typical sample processing and verified experimentally. We shall also present some initial results on the critical mixed valency of Ce in related compounds. Work at Ames Laboratory was supported by the U.S. Department of Energy, ARPA-E under the REACT program (0472-1526)
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Stapleton, Brian; Walker, Lawrence R; Logan, Timothy M
2013-03-19
Thermodynamic measurements of Fe(II) binding and activation of repressor function in the iron-dependent repressor from Mycobacterium tuberculosis (IdeR) are reported. IdeR, a member of the diphtheria toxin repressor family of proteins, regulates iron homeostasis and contributes to the virulence response in M. tuberculosis. Although iron is the physiological ligand, this is the first detailed analysis of iron binding and activation in this protein. The results showed that IdeR binds 2 equiv of Fe(II) with dissociation constants that differ by a factor of 25. The high- and low-affinity iron binding sites were assigned to physical binding sites I and II, respectively, using metal binding site mutants. IdeR was also found to contain a high-affinity Zn(II) binding site that was assigned to physical metal binding site II through the use of binding site mutants and metal competition assays. Fe(II) binding was modestly weaker in the presence of Zn(II), but the coupled metal binding-DNA binding affinity was significantly stronger, requiring 30-fold less Fe(II) to activate DNA binding compared to Fe(II) alone. Together, these results suggest that IdeR is a mixed-metal repressor, where Zn(II) acts as a structural metal and Fe(II) acts to trigger the physiologically relevant promoter binding. This new model for IdeR activation provides a better understanding of IdeR and the biology of iron homeostasis in M. tuberculosis.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Truex, Michael J.; Oostrom, Martinus; Last, George V.
At the DOE Hanford Site, contaminants were discharged to the subsurface through engineered waste sites in the Hanford Central Plateau. Additional waste was released through waste storage tank leaks. Much of the contaminant inventory is still present within the unsaturated vadose zone sediments. The nature and extent of future groundwater contaminant plumes and the growth or decline of current groundwater plumes beneath the Hanford Central Plateau are a function of the contaminant flux from the vadose zone to the groundwater. In general, contaminant transport is slow through the vadose zone and it is difficult to directly measure contaminant flux inmore » the vadose zone. Predictive analysis, supported by site characterization and monitoring data, was applied using a structured, systems-based approach to estimate the future contaminant flux to groundwater in support of remediation decisions for the vadose zone and groundwater (Truex and Carroll 2013). The SX Tank Farm was used as a case study because of the existing contaminant inventory in the vadose zone, observations of elevated moisture content in portions of the vadose zone, presence of a limited-extent groundwater plume, and the relatively large amount and wide variety of data available for the site. Although the SX Tank Farm case study is most representative of conditions at tank farm sites, the study has elements that are also relevant to other types of disposal sites in the Hanford Central Plateau.« less
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NASA Technical Reports Server (NTRS)
Cescatti, Alessandro; Marcolla, Barbara; Vannan, Suresh K. Santhana; Pan, Jerry Yun; Roman, Miguel O.; Yang, Xiaoyuan; Ciais, Philippe; Cook, Robert B.; Law, Beverly E.; Matteucci, Girogio;
2012-01-01
Surface albedo is a key parameter in the Earth's energy balance since it affects the amount of solar radiation directly absorbed at the planet surface. Its variability in time and space can be globally retrieved through the use of remote sensing products. To evaluate and improve the quality of satellite retrievals, careful intercomparisons with in situ measurements of surface albedo are crucial. For this purpose we compared MODIS albedo retrievals with surface measurements taken at 53 FLUXNET sites that met strict conditions of land cover homogeneity. A good agreement between mean yearly values of satellite retrievals and in situ measurements was found (R(exp 2)= 0.82). The mismatch is correlated to the spatial heterogeneity of surface albedo, stressing the relevance of land cover homogeneity when comparing point to pixel data. When the seasonal patterns of MODIS albedo is considered for different plant functional types, the match with surface observation is extremely good at all forest sites. On the contrary, in non-forest sites satellite retrievals underestimate in situ measurements across the seasonal cycle. The mismatch observed at grasslands and croplands sites is likely due to the extreme fragmentation of these landscapes, as confirmed by geostatistical attributes derived from high resolution scenes.
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Nodulman, Jessica A.; Starling, Randall; Kong, Alberta S.; Buller, David B.; Wheeler, Cosette M.; Woodall, W. Gill
2015-01-01
BACKGROUND In several countries worldwide, school-based human papillomavirus (HPV) vaccination programs have been successful; however, little research has explored US stakeholders’ acceptance toward school-based HPV vaccination programs. METHODS A total of 13 focus groups and 12 key informant interviews (N = 117; 85% females; 66% racial/ethnic minority) were conducted with 5 groups of stakeholders: parents of adolescent girls, parents of adolescent boys, adolescent girls, middle school nurses, and middle school administrators throughout the 5 public health regions of New Mexico. RESULTS All groups of stakeholders lacked knowledge on HPV and HPV vaccines. Stakeholders were interested in—but apprehensive about—the benefits of HPV vaccination. Despite previous literature showing the benefits of using middle schools as an HPV vaccination site, stakeholders did not deem middle schools as a viable site for vaccination. Nurses reported that using the school as an HPV vaccination site had not occurred to them; parents and adolescents stated they were uncertain about using this type of program. School administrators indicated that they lacked implementation authority. CONCLUSIONS Our study uncovered barriers to using middle schools as a site of HPV vaccination. Resources should be directed toward increased support and education for middle school nurses who function as opinion leaders relevant to the uptake of HPV vaccination. PMID:25846308
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Cation-exchanged zeolites for the selective oxidation of methane to methanol
Kulkarni, Ambarish R.; Zhao, Zhi-Jian; Siahrostami, Samira; ...
2017-10-19
Motivated by the increasing availability of cheap natural gas resources, considerable experimental and computational research efforts have focused on identifying selective catalysts for the direct conversion of methane to methanol. One promising class of catalysts are cation-exchanged zeolites, which have steadily increased in popularity over the past decade. Here, in this article, we first present a broad overview of this field from a conceptual perspective, and highlight the role of theory in developing a molecular-level understanding of the reaction. Next, by performing and analyzing a large database of density functional theory (DFT) calculations for a wide range of transition metalmore » cations, zeolite topologies and active site motifs, we present a unifying picture of the methane activation process in terms of active site stability, C–H bond activation and methanol extraction. Based on the trade-offs of active site stability and reactivity, we propose a framework for identifying new, promising active site motifs in these systems. Further, we show that the high methanol selectivity arises due to the strong binding nature of the C–H activation products. Lastly, using the atomistic and mechanistic insight obtained from these analyses, we summarize the key challenges and future strategies for improving the performance of cation-exchanged zeolites for this industrially relevant conversion.« less
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Cation-exchanged zeolites for the selective oxidation of methane to methanol
DOE Office of Scientific and Technical Information (OSTI.GOV)
Kulkarni, Ambarish R.; Zhao, Zhi-Jian; Siahrostami, Samira
Motivated by the increasing availability of cheap natural gas resources, considerable experimental and computational research efforts have focused on identifying selective catalysts for the direct conversion of methane to methanol. One promising class of catalysts are cation-exchanged zeolites, which have steadily increased in popularity over the past decade. Here, in this article, we first present a broad overview of this field from a conceptual perspective, and highlight the role of theory in developing a molecular-level understanding of the reaction. Next, by performing and analyzing a large database of density functional theory (DFT) calculations for a wide range of transition metalmore » cations, zeolite topologies and active site motifs, we present a unifying picture of the methane activation process in terms of active site stability, C–H bond activation and methanol extraction. Based on the trade-offs of active site stability and reactivity, we propose a framework for identifying new, promising active site motifs in these systems. Further, we show that the high methanol selectivity arises due to the strong binding nature of the C–H activation products. Lastly, using the atomistic and mechanistic insight obtained from these analyses, we summarize the key challenges and future strategies for improving the performance of cation-exchanged zeolites for this industrially relevant conversion.« less
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Westgeest, Annette; Morales, Merche; Cabib, Christopher; Valls-Sole, Josep
2014-12-01
Conscious perception of sensory signals depends in part on stimulus salience, relevance and topography. Letting aside differences at skin receptor level and afferent fibres, it is the CNS that makes a contextual selection of relevant sensory inputs. We hypothesized that subjective awareness (AW) of the time at which a sensory stimulus is perceived, a cortical function, may be differently modified by cortical stimulation, according to site and type of the stimulus. In 24 healthy volunteers, we examined the effects of transcranial direct current stimulation (tDCS) on the assessment of AW to heat pain or weak electrical stimuli applied to either the hand palm or dorsum. We also recorded the vertex-evoked potentials to the same stimuli. The assessment was done before, during and after cathodal or anodal tDCS over the parietal cortex contralateral to the hand receiving the stimuli. At baseline, AW to thermal stimuli was significantly longer for palm than for dorsum (P < 0.01), while no differences between stimulation sites were observed for the electrical stimuli. Both cathodal and anodal tDCS caused a significant shortening of AW to thermal stimuli in the palm but not in the dorsum, and no effects on AW to electrical stimuli. Longer AW in the palm than in the dorsum may be attributable to differences in skin thickness. However, the selectivity of the effects of tDCS on AW to thermal stimulation of the glabrous skin reflects the specificity of CNS processing for site and type of sensory inputs. © 2014 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.
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ERIC Educational Resources Information Center
Web Feet K-8, 2001
2001-01-01
This annotated subject guide to Web sites and additional resources focuses on biomes. Specifies age levels for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; includes professional resources; and presents a relevant class activity. (LRW)
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16 CFR 1031.18 - Method of review and comment.
Code of Federal Regulations, 2010 CFR
2010-01-01
... Commission staff is involved shall have a unique Web link on the Commission Web site with relevant... forwarded to appropriate staff for consideration and/or response. (c) On the voluntary standards Web site...
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16 CFR 1031.18 - Method of review and comment.
Code of Federal Regulations, 2012 CFR
2012-01-01
... Commission staff is involved shall have a unique Web link on the Commission Web site with relevant... forwarded to appropriate staff for consideration and/or response. (c) On the voluntary standards Web site...
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16 CFR 1031.18 - Method of review and comment.
Code of Federal Regulations, 2011 CFR
2011-01-01
... Commission staff is involved shall have a unique Web link on the Commission Web site with relevant... forwarded to appropriate staff for consideration and/or response. (c) On the voluntary standards Web site...
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Endocannabinoids and the Immune System in Health and Disease.
Cabral, Guy A; Ferreira, Gabriela A; Jamerson, Melissa J
2015-01-01
Endocannabinoids are bioactive lipids that have the potential to signal through cannabinoid receptors to modulate the functional activities of a variety of immune cells. Their activation of these seven-transmembranal, G protein-coupled receptors sets in motion a series of signal transductional events that converge at the transcriptional level to regulate cell migration and the production of cytokines and chemokines. There is a large body of data that supports a functional relevance for 2-arachidonoylglycerol (2-AG) as acting through the cannabinoid receptor type 2 (CB2R) to inhibit migratory activities for a diverse array of immune cell types. However, unequivocal data that supports a functional linkage of anandamide (AEA) to a cannabinoid receptor in immune modulation remains to be obtained. Endocannabinoids, as typical bioactive lipids, have a short half-life and appear to act in an autocrine and paracrine fashion. Their immediate effective action on immune function may be at localized sites in the periphery and within the central nervous system. It is speculated that endocannabinoids play an important role in maintaining the overall "fine-tuning" of the immune homeostatic balance within the host.
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Kapetanopoulos, Katharina; Braukmann, Sandra; Gebauer, Wolfgang; Tenzer, Stefan; Markl, Jürgen
2012-01-01
Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod acetylcholine-binding proteins (AChBP) which represent soluble structural and functional homologues of the ligand-binding domain of nAChR. All these proteins are ring-like pentamers. Here we report that AChBP exists in the hemolymph of the planorbid snail Biomphalaria glabrata (vector of the schistosomiasis parasite) as a regular pentagonal dodecahedron, 22 nm in diameter (12 pentamers, 60 active sites). We sequenced and recombinantly expressed two ∼25 kDa polypeptides (BgAChBP1 and BgAChBP2) with a specific active site, N-glycan site and disulfide bridge variation. We also provide the exon/intron structures. Recombinant BgAChBP1 formed pentamers and dodecahedra, recombinant BgAChBP2 formed pentamers and probably disulfide-bridged di-pentamers, but not dodecahedra. Three-dimensional electron cryo-microscopy (3D-EM) yielded a 3D reconstruction of the dodecahedron with a resolution of 6 Å. Homology models of the pentamers docked to the 6 Å structure revealed opportunities for chemical bonding at the inter-pentamer interfaces. Definition of the ligand-binding pocket and the gating C-loop in the 6 Å structure suggests that 3D-EM might lead to the identification of functional states in the BgAChBP dodecahedron. PMID:22916297
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Role of dimensionality in preferential attachment growth in the Bianconi-Barabási model
NASA Astrophysics Data System (ADS)
Nunes, Thiago C.; Brito, Samurai; da Silva, Luciano R.; Tsallis, Constantino
2017-09-01
Scale-free networks are quite popular nowadays since many systems are well represented by such structures. In order to study these systems, several models were proposed. However, most of them do not take into account the node-to-node Euclidean distance, i.e. the geographical distance. In real networks, the distance between sites can be very relevant, e.g. those cases where it is intended to minimize costs. Within this scenario we studied the role of dimensionality d in the Bianconi-Barabási model with a preferential attachment growth involving Euclidean distances. The preferential attachment in this model follows the rule \\Pii \\propto ηi k_i/rijα_A (1 ≤slant i < j; αA ≥slant 0) , where ηi characterizes the fitness of the ith site and is randomly chosen within the (0, 1] interval. We verified that the degree distribution P(k) for dimensions d=1, 2, 3, 4 are well fitted by P(k) \\propto e_q-k/κ , where e_q-k/κ is the q-exponential function naturally emerging within nonextensive statistical mechanics. We determine the index q and κ as functions of the quantities αA and d, and numerically verify that both present a universal behavior with respect to the scaled variable α_A/d . The same behavior also has been displayed by the dynamical β exponent which characterizes the steadily growing number of links of a given site.
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Toschki, Andreas; Jänsch, Stephan; Roß-Nickoll, Martina; Römbke, Jörg; Züghart, Wiebke
2015-01-01
In the Directive 2001/18/EC on the deliberate release of genetically modified organisms (GMO) into the environment, a monitoring of potential risks is prescribed after their deliberate release or placing on the market. Experience and data of already existing monitoring networks should be included. The present paper summarizes the major findings of a project funded by the Federal Agency for Nature Conservation (Nutzungsmöglichkeiten der Boden-Dauerbeobachtung der Länder für das Monitoring der Umweltwirkungen gentechnisch veränderter Pflanzen. BfN Skripten, Bonn-Bad Godesberg 369, 2014). The full report in german language can be accessed on http://www.bfn.de and is available as Additional file 1. The aim of the project was to check if it is possible to use the German permanent soil monitoring program (PSM) for the monitoring of GMO. Soil organism communities are highly diverse and relevant with respect to the sustainability of soil functions. They are exposed to GMO material directly by feeding or indirectly through food chain interactions. Other impacts are possible due to their close association to soil particles. The PSM program can be considered as representative with regard to different soil types and ecoregions in Germany, but not for all habitat types relevant for soil organisms. Nevertheless, it is suitable as a basic grid for monitoring the potential effects of GMO on soil invertebrates. PSM sites should be used to derive reference values, i.e. range of abundance and presence of different relevant species of soil organisms. Based on these references, it is possible to derive threshold values to define the limit of acceptable change or impact. Therefore, a minimum set of sites and minimum set of standardized methods are needed, i.e. characterization of each site, sampling of selected soil organism groups, adequate adaptation of methods for the purpose of monitoring of potential effects of GMO. Finally, and probably most demanding, it is needed to develop a harmonized evaluation concept.
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30 CFR 585.626 - What must I include in my COP?
Code of Federal Regulations, 2014 CFR
2014-07-01
...) Hydrates; or (v) Ice scour of seabed sediments. (2) Geological survey relevant to the design and siting of... COP? (a) You must submit the results of the following surveys for the proposed site(s) of your...) Shallow hazards The results of the shallow hazards survey with supporting data Information sufficient to...
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30 CFR 585.626 - What must I include in my COP?
Code of Federal Regulations, 2012 CFR
2012-07-01
...) Hydrates; or (v) Ice scour of seabed sediments. (2) Geological survey relevant to the design and siting of... COP? (a) You must submit the results of the following surveys for the proposed site(s) of your...) Shallow hazards The results of the shallow hazards survey with supporting data Information sufficient to...
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30 CFR 585.626 - What must I include in my COP?
Code of Federal Regulations, 2013 CFR
2013-07-01
...) Hydrates; or (v) Ice scour of seabed sediments. (2) Geological survey relevant to the design and siting of... COP? (a) You must submit the results of the following surveys for the proposed site(s) of your...) Shallow hazards The results of the shallow hazards survey with supporting data Information sufficient to...
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Library Facility Siting and Location Handbook. The Greenwood Library Management Collection.
ERIC Educational Resources Information Center
Koontz, Christine M.
This handbook is a guide to the complex process of library facility siting and location. It includes relevant research and professionals' siting experiences, as well as actual case studies of closures, openings, mergers, and relocations of library facilities. While the bulk of the volume provides practical information, the work also presents an…
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Chironomidae traits and life history strategies as indicators of anthropogenic disturbance.
Serra, Sónia R Q; Graça, Manuel A S; Dolédec, Sylvain; Feio, Maria João
2017-07-01
In freshwater ecosystems, Chironomidae are currently considered indicators of poor water quality because the family is often abundant in degraded sites. However, it incorporates taxa with a large ecological and physiological diversity and different sensitivity to impairment. Yet, the usual identification of Chironomidae at coarse taxonomic levels (family or subfamily) masks genus and species sensitivities. In this study, we investigate the potential of taxonomic and functional (traits) composition of Chironomidae to detect anthropogenic disturbance. In this context, we tested some a priori hypotheses regarding the ability of Chironomidae taxonomic and trait compositions to discriminate Mediterranean streams affected by multiple stressors from least-disturbed streams. Both taxonomic and Eltonian trait composition discriminated sites according to their disturbance level. Disturbance resulted in the predicted increase of Chironomidae with higher number of stages with hibernation/diapause and of taxa with resistance forms and unpredicted increase of the proportion of taxa with longer life cycles and few generations per year. Life history strategies (LHS), corresponding to multivoltine Chironomidae that do not invest in hemoglobin and lack strong spring synchronization, were well adapted to all our Mediterranean sites with highly changeable environmental conditions. Medium-size animals favored in disturbed sites where the Mediterranean hydrological regime is altered, but the reduced number of larger-size/carnivore Chironomids suggests a limitation to secondary production. Results indicate that Chironomidae genus and respective traits could be a useful tool in the structural and functional assessment of Mediterranean streams. The ubiquitous nature of Chironomidae should be also especially relevant in the assessment of water bodies naturally poor in other groups such as the Ephemeroptera, Plecoptera, and Trichoptera, such as the lowland rivers with sandy substrates, lakes, or reservoirs.
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Mendt, Matthias; Barth, Benjamin; Hartmann, Martin; Pöppl, Andreas
2017-12-14
The low-temperature binding of nitric oxide (NO) in the metal-organic framework MIL-100(Al) has been investigated by pulsed electron nuclear double resonance and hyperfine sublevel correlation spectroscopy. Three NO adsorption species have been identified. Among them, one species has been verified experimentally to bind directly to an 27 Al atom and all its relevant 14 N and 27 Al hyperfine interaction parameters have been determined spectroscopically. Those parameters fit well to the calculated ones of a theoretical cluster model, which was derived by density functional theory (DFT) in the present work and describes the low temperature binding of NO to the regular coordinatively unsaturated Al 3+ site of the MIL-100(Al) structure. As a result, the Lewis acidity of that site has been characterized using the NO molecule as an electron paramagnetic resonance active probe. The DFT derived wave function analysis revealed a bent end-on coordination of the NO molecule adsorbed at that site which is almost purely ionic and has a weak binding energy. The calculated flat potential energy surface of this species indicates the ability of the NO molecule to freely rotate at intermediate temperatures while it is still binding to the Al 3+ site. For the other two NO adsorption species, no structural models could be derived, but one of them is indicated to be adsorbed at the organic part of the metal-organic framework. Hyperfine interactions with protons, weakly coupled to the observed NO adsorption species, have also been measured by pulsed electron paramagnetic resonance and found to be consistent with their attribution to protons of the MIL-100(Al) benzenetricarboxylate ligand molecules.
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Kim, Ingu; Saito, Takeshi; Fujii, Norihiko; Kanamoto, Takashi; Fujii, Noriko
2016-12-01
The eye lens is a transparent organ that functions to focus light and images on the retina. The transparency and high refraction of the lens are maintained by the function of α-, β-, and γ-crystallins. These long-lived proteins are subject to various post-translational modifications, such as oxidation, deamidation, truncation and isomerization, which occur gradually during the aging process. Such modifications, which are generated by UV light and oxidative stress, decrease crystallin solubility and lens transparency, and ultimately lead to the development of age-related cataracts. Here, we irradiated young rat lenses with γ-rays (5-500 Gy) and extracted the water-soluble (WS) and water-insoluble (WI) protein fractions. The WS and WI lens proteins were digested with trypsin, and the resulting peptides were analyzed by one-shot LC-MS/MS to determine the specific sites of oxidation of methionine and tryptophan, deamidation sites of asparagine and glutamine, and isomerization of aspartyl in rat α- and β-crystallins in the WS and WI fractions. Oxidation and deamidation occurred in several crystallins after irradiation at more than, respectively, 50 and 5 Gy; however, isomerization did not occur in any crystallin even after exposure to 500 Gy of irradiation. The number of oxidation and deamidation sites was much higher in the WI than in the WS fraction. Furthermore, the oxidation and deamidation sites in rat crystallins resemble those reported in crystallins from human age-related cataracts. Thus, this study on post-translational modifications of crystallins induced by ionizing irradiation may provide useful information relevant to the formation of human age-related cataracts.
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Riato, Luisa; Leira, Manel; Della Bella, Valentina; Oberholster, Paul J
2018-01-15
Acid mine drainage (AMD) from coal mining in the Mpumalanga Highveld region of South Africa has caused severe chemical and biological degradation of aquatic habitats, specifically depressional wetlands, as mines use these wetlands for storage of AMD. Diatom-based multimetric indices (MMIs) to assess wetland condition have mostly been developed to assess agricultural and urban land use impacts. No diatom MMI of wetland condition has been developed to assess AMD impacts related to mining activities. Previous approaches to diatom-based MMI development in wetlands have not accounted for natural variability. Natural variability among depressional wetlands may influence the accuracy of MMIs. Epiphytic diatom MMIs sensitive to AMD were developed for a range of depressional wetland types to account for natural variation in biological metrics. For this, we classified wetland types based on diatom typologies. A range of 4-15 final metrics were selected from a pool of ~140 candidate metrics to develop the MMIs based on their: (1) broad range, (2) high separation power and (3) low correlation among metrics. Final metrics were selected from three categories: similarity to reference sites, functional groups, and taxonomic composition, which represent different aspects of diatom assemblage structure and function. MMI performances were evaluated according to their precision in distinguishing reference sites, responsiveness to discriminate reference and disturbed sites, sensitivity to human disturbances and relevancy to AMD-related stressors. Each MMI showed excellent discriminatory power, whether or not it accounted for natural variation. However, accounting for variation by grouping sites based on diatom typologies improved overall performance of MMIs. Our study highlights the usefulness of diatom-based metrics and provides a model for the biological assessment of depressional wetland condition in South Africa and elsewhere. Copyright © 2017 Elsevier B.V. All rights reserved.
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Vibrational and vibronic coherences in the dynamics of the FMO complex
NASA Astrophysics Data System (ADS)
Liu, Xiaomeng; Kühn, Oliver
2016-12-01
The coupled exciton-vibrational dynamics of a seven site Frenkel exciton model of the Fenna-Matthews-Olson (FMO) complex is investigated using a Quantum Master Equation approach. Thereby, one vibrational mode per monomer is treated explicitly as being part of the relevant system. Emphasis is put on the comparison of this model with that of a purely excitonic relevant system. Further, the effects of two different approximations to the exciton-vibrational basis are investigated, namely the one- and two-particle description. Analysis of the vibronic and vibrational density matrix in the site basis points to the importance of on- and inter-site coherences for the exciton transfer. Here, one- and two-particle approximations give rise to qualitatively different results.
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47 CFR 1.1311 - Environmental information to be included in the environmental assessment (EA).
Code of Federal Regulations, 2011 CFR
2011-10-01
... environmental and other considerations which led to the selection of the particular site and, if relevant, the..., natural migration paths for birds and other wildlife, and sites of historic, architectural, or...
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ERIC Educational Resources Information Center
Web Feet K-8, 2001
2001-01-01
This annotated subject guide to Web sites and additional resources focuses on mythology. Specific age levels are given for resources that include Web sites, CD-ROMs and software, videos, books, audios, and magazines; offers professional resources; and presents a relevant class activity. (LRW)
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ERIC Educational Resources Information Center
Web Feet K-8, 2001
2001-01-01
This annotated subject guide to Web sites and additional resources focuses on space and astronomy. Specifies age levels for resources that include Web sites, CD-ROMS and software, videos, books, audios, and magazines; offers professional resources; and presents a relevant class activity. (LRW)
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Cording, Jimmi; Günther, Ramona; Vigolo, Emilia; Tscheik, Christian; Winkler, Lars; Schlattner, Isabella; Lorenz, Dorothea; Haseloff, Reiner F; Schmidt-Ott, Kai M; Wolburg, Hartwig; Blasig, Ingolf E
2015-11-01
Tight junctions (TJs) seal paracellular clefts in epithelia/endothelia and form tissue barriers for proper organ function. TJ-associated marvel proteins (TAMPs; tricellulin, occludin, marvelD3) are thought to be relevant to regulation. Under normal conditions, tricellulin tightens tricellular junctions against macromolecules. Traces of tricellulin occur in bicellular junctions. As pathological disturbances have not been analyzed, the structure and function of human tricellulin, including potentially redox-sensitive Cys sites, were investigated under reducing/oxidizing conditions at 3- and 2-cell contacts. Ischemia, hypoxia, and reductants redistributed tricellulin from 3- to 2-cell contacts. The extracellular loop 2 (ECL2; conserved Cys321, Cys335) trans-oligomerized between three opposing cells. Substitutions of these residues caused bicellular localization. Cys362 in transmembrane domain 4 contributed to bicellular heterophilic cis-interactions along the cell membrane with claudin-1 and marvelD3, while Cys395 in the cytosolic C-terminal tail promoted homophilic tricellullar cis-interactions. The Cys sites included in homo-/heterophilic bi-/tricellular cis-/trans-interactions contributed to cell barrier tightness for small/large molecules. Tricellulin forms TJs via trans- and cis-association in 3-cell contacts, as demonstrated electron and quantified fluorescence microscopically; it tightens 3- and 2-cell contacts. Tricellulin's ECL2 specifically seals 3-cell contacts redox dependently; a structural model is proposed. TAMP ECL2 and claudins' ECL1 share functionally and structurally similar features involved in homo-/heterophilic tightening of cell-cell contacts. Tricellulin is a specific redox sensor and sealing element at 3-cell contacts and may compensate as a redox mediator for occludin loss at 2-cell contacts in vivo and in vitro. Molecular interaction mechanisms were proposed that contribute to tricellulin's function. In conclusion, tricellulin is a junctional redox regulator for ischemia-related alterations.
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The accessibility, readability, and quality of online resources for gender affirming surgery.
Vargas, Christina R; Ricci, Joseph A; Lee, Michelle; Tobias, Adam M; Medalie, Daniel A; Lee, Bernard T
2017-09-01
The transgender population is disproportionally affected by health disparities related to access to care. In many communities, transgender specialists are geographically distant and locally available medical professionals may be unfamiliar with unique needs of transgender patients. As a result, use of Internet resources for information about gender affirming surgery is particularly important. This study simulates a patient search for online educational material about gender affirming surgery and evaluates the accessibility, readability, and quality of the information. An Internet search for the term "transgender surgery" was performed, and the first 10 relevant hits were identified. Readability was assessed using 10 established tests: Coleman-Liau, Flesch-Kincaid, FORCAST, Fry, Gunning Fog, New Dale-Chall, New Fog Count, Raygor Estimate, Simple Measure of Gobbledygook, and Flesch Reading Ease. Quality was assessed using Journal of the American Medical Association criteria and the DISCERN instrument. Review of 69 results was required to identify 10 sites with relevant patient information. There were 97 articles collected; overall mean reading level was 14.7. Individual Web site reading levels ranged from 12.0 to 17.5. All articles and Web sites exceeded the recommended sixth grade level. Quality ranged from 0 to 4 (Journal of the American Medical Association) and 35 to 79 (DISCERN) across Web sites. Web sites with relevant patient information about gender affirming surgery were difficult to identify from search results. The content of these sites universally exceeded the recommended reading level. A wide range of Web site quality was noted, and this may further complicate successful navigation. Barriers in access to appropriately written patient information on the Internet may contribute to disparities in referral, involvement, satisfaction, and outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.
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Monitoring Volatile Organic Compounds (VOCs) in real-time on oil and natural gas production sites
NASA Astrophysics Data System (ADS)
Lupardus, R.; Franklin, S. B.
2017-12-01
Oil and Natural Gas (O&NG) development, production, infrastructure, and associated processing activities can be a substantial source of air pollution, yet relevant data and real-time quantification methods are lacking. In the current study, O&NG fugitive emissions of Volatile Organic Compounds (VOCs) were quantified in real-time and used to determine the spatial and temporal windows of exposure for proximate flora and fauna. Eleven O&NG sites on the Pawnee National Grassland in Northeastern Colorado were randomly selected and grouped according to production along with 13 control sites from three geographical locations. At each site, samples were collected 25 m from the wellhead in NE, SE, and W directions. In each direction, two samples were collected with a Gasmet DX4040 gas analyzer every hour from 8:00 am to 2:00 pm (6 hours total), July to October, 2016 (N=864). VOC concentrations generally increased during the 6 hr. day with the exception of N2O and were predominately the result of O&NG production and not vehicle exhaust. Thirteen of 24 VOCs had significantly different levels between production groups, frequently above reference standards and at biologically relevant levels for flora and fauna. The most biologically relevant VOCs, found at concentrations exceeding time weighted average permissible exposure limits (TWA PELs), were benzene and acrolein. Generalized Estimating Equations (GEEs) measured the relative quality of statistical models predicting benzene concentrations on sites. The data not only confirms that O&NG emissions are impacting the region, but also that this influence is present at all sites, including controls. Increased real-time VOC monitoring on O&NG sites is required to identify and contain fugitive emissions and to protect human and environmental health.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
None, None
This report on evaporite mineralization was completed as an Ancillary Work Plan for the Applied Studies and Technology program under the U.S. Department of Energy (DOE) Office of Legacy Management (LM). This study reviews all LM sites under Title I and Title II of the Uranium Mill Tailings Radiation Control Act (UMTRCA) and one Decontamination and Decommissioning site to provide (1) a summary of which sites have evaporite deposits, (2) any available quantitative geochemical and mineralogical analyses, and (3) references to relevant reports. In this study, “evaporite” refers to any secondary mineral precipitate that occurs due to a loss ofmore » water through evaporative processes. This includes efflorescent salt crusts, where this term refers to a migration of dissolved constituents to the surface with a resulting salt crust, where “salt” can refer to any secondary precipitate, regardless of constituents. The potential for the formation of evaporites at LM sites has been identified, and may have relevance to plume persistence issues. Evaporite deposits have the potential to concentrate and store contaminants at LM sites that could later be re-released. These deposits can also provide a temporary storage mechanism for carbonate, chloride, and sulfate salts along with uranium and other contaminants of concern (COCs). Identification of sites with evaporites will be used in a new technical task plan (TTP), Persistent Secondary Contaminant Sources (PeSCS), for any proposed additional sampling and analyses. This additional study is currently under development and will focus on determining if the dissolution of evaporites has the potential to hinder natural flushing strategies and impact plume persistence. This report provides an initial literature review on evaporites followed by details for each site with identified evaporites. The final summary includes a table listing of all relevant LM sites regardless of evaporite identification.« less
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Preparation of sumoylated substrates for biochemical analysis.
Knipscheer, Puck; Klug, Helene; Sixma, Titia K; Pichler, Andrea
2009-01-01
Covalent modification of proteins with SUMO (small ubiquitin related modifier) affects many cellular processes like transcription, nuclear transport, DNA repair and cell cycle progression. Although hundreds of SUMO targets have been identified, for several of them the function remains obscure. In the majority of cases sumoylation is investigated via "loss of modification" analysis by mutating the relevant target lysine. However, in other cases this approach is not successful since mapping of the modification site is problematic or mutation does not cause an obvious phenotype. These latter cases ask for different approaches to investigate the target modification. One possibility is to choose the opposite approach, a "gain in modification" analysis by producing both SUMO modified and unmodified protein in vitro and comparing them in functional assays. Here, we describe the purification of the ubiquitin conjugating enzyme E2-25K, its in vitro sumoylation with recombinant enzymes and the subsequent separation and purification of the modified and the unmodified forms.
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Identification of genetic elements in metabolism by high-throughput mouse phenotyping.
Rozman, Jan; Rathkolb, Birgit; Oestereicher, Manuela A; Schütt, Christine; Ravindranath, Aakash Chavan; Leuchtenberger, Stefanie; Sharma, Sapna; Kistler, Martin; Willershäuser, Monja; Brommage, Robert; Meehan, Terrence F; Mason, Jeremy; Haselimashhadi, Hamed; Hough, Tertius; Mallon, Ann-Marie; Wells, Sara; Santos, Luis; Lelliott, Christopher J; White, Jacqueline K; Sorg, Tania; Champy, Marie-France; Bower, Lynette R; Reynolds, Corey L; Flenniken, Ann M; Murray, Stephen A; Nutter, Lauryl M J; Svenson, Karen L; West, David; Tocchini-Valentini, Glauco P; Beaudet, Arthur L; Bosch, Fatima; Braun, Robert B; Dobbie, Michael S; Gao, Xiang; Herault, Yann; Moshiri, Ala; Moore, Bret A; Kent Lloyd, K C; McKerlie, Colin; Masuya, Hiroshi; Tanaka, Nobuhiko; Flicek, Paul; Parkinson, Helen E; Sedlacek, Radislav; Seong, Je Kyung; Wang, Chi-Kuang Leo; Moore, Mark; Brown, Steve D; Tschöp, Matthias H; Wurst, Wolfgang; Klingenspor, Martin; Wolf, Eckhard; Beckers, Johannes; Machicao, Fausto; Peter, Andreas; Staiger, Harald; Häring, Hans-Ulrich; Grallert, Harald; Campillos, Monica; Maier, Holger; Fuchs, Helmut; Gailus-Durner, Valerie; Werner, Thomas; Hrabe de Angelis, Martin
2018-01-18
Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated. We compared human orthologues of these uncharacterized genes in five GWAS consortia and indeed 23 candidate genes are associated with metabolic disease. We further identify common regulatory elements in promoters of candidate genes. As each regulatory element is composed of several transcription factor binding sites, our data reveal an extensive metabolic phenotype-associated network of co-regulated genes. Our systematic mouse phenotype analysis thus paves the way for full functional annotation of the genome.
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Accredited hand surgery fellowship Web sites: analysis of content and accessibility.
Trehan, Samir K; Morrell, Nathan T; Akelman, Edward
2015-04-01
To assess the accessibility and content of accredited hand surgery fellowship Web sites. A list of all accredited hand surgery fellowships was obtained from the online database of the American Society for Surgery of the Hand (ASSH). Fellowship program information on the ASSH Web site was recorded. All fellowship program Web sites were located via Google search. Fellowship program Web sites were analyzed for accessibility and content in 3 domains: program overview, application information/recruitment, and education. At the time of this study, there were 81 accredited hand surgery fellowships with 169 available positions. Thirty of 81 programs (37%) had a functional link on the ASSH online hand surgery fellowship directory; however, Google search identified 78 Web sites. Three programs did not have a Web site. Analysis of content revealed that most Web sites contained contact information, whereas information regarding the anticipated clinical, research, and educational experiences during fellowship was less often present. Furthermore, information regarding past and present fellows, salary, application process/requirements, call responsibilities, and case volume was frequently lacking. Overall, 52 of 81 programs (64%) had the minimal online information required for residents to independently complete the fellowship application process. Hand fellowship program Web sites could be accessed either via the ASSH online directory or Google search, except for 3 programs that did not have Web sites. Although most fellowship program Web sites contained contact information, other content such as application information/recruitment and education, was less frequently present. This study provides comparative data regarding the clinical and educational experiences outlined on hand fellowship program Web sites that are of relevance to residents, fellows, and academic hand surgeons. This study also draws attention to various ways in which the hand surgery fellowship application process can be made more user-friendly and efficient. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.
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Wang, Dong-Yuan Debbie; Richard, F Dan; Ray, Brittany
2016-01-01
The stimulus-response correspondence (SRC) effect refers to advantages in performance when stimulus and response correspond in dimensions or features, even if the common features are irrelevant to the task. Previous research indicated that the SRC effect depends on the temporal course of stimulus information processing. The current study investigated how the temporal overlap between relevant and irrelevant stimulus processing influences the SRC effect. In this experiment, the irrelevant stimulus (a previously associated tone) preceded the relevant stimulus (a coloured rectangle). The irrelevant and relevant stimuli onset asynchrony was varied to manipulate the temporal overlap between the irrelevant and relevant stimuli processing. Results indicated that the SRC effect size varied as a quadratic function of the temporal overlap between the relevant stimulus and irrelevant stimulus. This finding extends previous experimental observations that the SRC effect size varies in an increasing or decreasing function with reaction time. The current study demonstrated a quadratic function between effect size and the temporal overlap.
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Applications of aggregation theory to sustainability assessment
Pollesch, N.; Dale, V. H.
2015-04-01
In order to aid in transition towards operations that promote sustainability goals, researchers and stakeholders use sustainability assessments. Although assessments take various forms, many utilize diverse sets of indicators that can number anywhere from two to over 2000. Indices, composite indicators, or aggregate values are used to simplify high dimensional and complex data sets and to clarify assessment results. Although the choice of aggregation function is a key component in the development of the assessment, there are few examples to be found in literature to guide appropriate aggregation function selection. This paper develops a connection between the mathematical study ofmore » aggregation functions and sustainability assessment in order to aid in providing criteria for aggregation function selection. Relevant mathematical properties of aggregation functions are presented and interpreted. Lastly, we provide cases of these properties and their relation to previous sustainability assessment research. Examples show that mathematical aggregation properties can be used to address the topics of compensatory behavior and weak versus strong sustainability, aggregation of data under varying units of measurements, multiple site multiple indicator aggregation, and the determination of error bounds in aggregate output for normalized and non-normalized indicator measures.« less
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Bloudoff, Kristjan; Schmeing, T Martin
2017-11-01
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes, each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes. This review discusses some of the important insights into the structure, catalytic mechanism, specificity, and gatekeeping functions of C domains revealed since their discovery. In addition, C domains are the archetypal members of the C domain superfamily, which includes several other members that also function as NRPS domains. The other family members can replace the C domain in NRP synthesis, can work in concert with a C domain, or can fulfill diverse and novel functions. These domains include the epimerization (E) domain, the heterocyclization (Cy) domain, the ester-bond forming C domain, the fungal NRPS terminal C domain (C T ), the β-lactam ring forming C domain, and the X domain. We also discuss structural and function insight into C, E, Cy, C T and X domains, to present a holistic overview of historical and current knowledge of the C domain superfamily. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.
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Exploring protein structure and dynamics through a project-oriented biochemistry laboratory module.
Lipchock, James M; Ginther, Patrick S; Douglas, Bonnie B; Bird, Kelly E; Patrick Loria, J
2017-09-01
Here, we present a 10-week project-oriented laboratory module designed to provide a course-based undergraduate research experience in biochemistry that emphasizes the importance of biomolecular structure and dynamics in enzyme function. This module explores the impact of mutagenesis on an important active site loop for a biomedically-relevant human enzyme, protein tyrosine phosphatase 1B (PTP1B). Over the course of the semester students guide their own mutant of PTP1B from conception to characterization in a cost-effective manner and gain exposure to fundamental techniques in biochemistry, including site-directed DNA mutagenesis, bacterial recombinant protein expression, affinity column purification, protein quantitation, SDS-PAGE, and enzyme kinetics. This project-based approach allows an instructor to simulate a research setting and prepare students for productive research beyond the classroom. Potential modifications to expand or contract this module are also provided. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):403-410, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.
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The transcriptional landscape of age in human peripheral blood
Peters, Marjolein J.; Joehanes, Roby; Pilling, Luke C.; Schurmann, Claudia; Conneely, Karen N.; Powell, Joseph; Reinmaa, Eva; Sutphin, George L.; Zhernakova, Alexandra; Schramm, Katharina; Wilson, Yana A.; Kobes, Sayuko; Tukiainen, Taru; Nalls, Michael A.; Hernandez, Dena G.; Cookson, Mark R.; Gibbs, Raphael J.; Hardy, John; Ramasamy, Adaikalavan; Zonderman, Alan B.; Dillman, Allissa; Traynor, Bryan; Smith, Colin; Longo, Dan L.; Trabzuni, Daniah; Troncoso, Juan; van der Brug, Marcel; Weale, Michael E.; O'Brien, Richard; Johnson, Robert; Walker, Robert; Zielke, Ronald H.; Arepalli, Sampath; Ryten, Mina; Singleton, Andrew B.; Ramos, Yolande F.; Göring, Harald H. H.; Fornage, Myriam; Liu, Yongmei; Gharib, Sina A.; Stranger, Barbara E.; De Jager, Philip L.; Aviv, Abraham; Levy, Daniel; Murabito, Joanne M.; Munson, Peter J.; Huan, Tianxiao; Hofman, Albert; Uitterlinden, André G.; Rivadeneira, Fernando; van Rooij, Jeroen; Stolk, Lisette; Broer, Linda; Verbiest, Michael M. P. J.; Jhamai, Mila; Arp, Pascal; Metspalu, Andres; Tserel, Liina; Milani, Lili; Samani, Nilesh J.; Peterson, Pärt; Kasela, Silva; Codd, Veryan; Peters, Annette; Ward-Caviness, Cavin K.; Herder, Christian; Waldenberger, Melanie; Roden, Michael; Singmann, Paula; Zeilinger, Sonja; Illig, Thomas; Homuth, Georg; Grabe, Hans-Jörgen; Völzke, Henry; Steil, Leif; Kocher, Thomas; Murray, Anna; Melzer, David; Yaghootkar, Hanieh; Bandinelli, Stefania; Moses, Eric K.; Kent, Jack W.; Curran, Joanne E.; Johnson, Matthew P.; Williams-Blangero, Sarah; Westra, Harm-Jan; McRae, Allan F.; Smith, Jennifer A.; Kardia, Sharon L. R.; Hovatta, Iiris; Perola, Markus; Ripatti, Samuli; Salomaa, Veikko; Henders, Anjali K.; Martin, Nicholas G.; Smith, Alicia K.; Mehta, Divya; Binder, Elisabeth B.; Nylocks, K Maria; Kennedy, Elizabeth M.; Klengel, Torsten; Ding, Jingzhong; Suchy-Dicey, Astrid M.; Enquobahrie, Daniel A.; Brody, Jennifer; Rotter, Jerome I.; Chen, Yii-Der I.; Houwing-Duistermaat, Jeanine; Kloppenburg, Margreet; Slagboom, P. Eline; Helmer, Quinta; den Hollander, Wouter; Bean, Shannon; Raj, Towfique; Bakhshi, Noman; Wang, Qiao Ping; Oyston, Lisa J.; Psaty, Bruce M.; Tracy, Russell P.; Montgomery, Grant W.; Turner, Stephen T.; Blangero, John; Meulenbelt, Ingrid; Ressler, Kerry J.; Yang, Jian; Franke, Lude; Kettunen, Johannes; Visscher, Peter M.; Neely, G. Gregory; Korstanje, Ron; Hanson, Robert L.; Prokisch, Holger; Ferrucci, Luigi; Esko, Tonu; Teumer, Alexander; van Meurs, Joyce B. J.; Johnson, Andrew D.
2015-01-01
Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts. PMID:26490707
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Thermal characteristics of the lunar surface layer.
NASA Technical Reports Server (NTRS)
Cremers, C. J.; Birkebak, R. C.; White, J. E.
1972-01-01
The thermophysical properties of the fines from the Apollo 12 landing site have been determined as a function of their relevant parameters. These properties include the thermal conductivity, thermal diffusivity, directional reflectance and emittance. The density used was the same as that observed from the returned core-tube samples and so should be close to the true density of the surface layer at the Apollo 12 site. The measured properties are used to calculate the diurnal temperature variation of the moon's surface as well as for several depths below the surface. The maximum surface of 389 K is obtained at lunar noon while the minimum temperature of 86.1 K is obtained at sunrise. It is shown that the most significant effects on temperature, as compared with previous calculations, are caused by using the directional reflectance which controls the amount of solar energy absorption during the day in place of a constant hemispherical reflectance. The results are compared with previous analyses and remote measurements.
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Hydrogen migration modeling in a symmetric tilt boundary of the Iron-Chromium system
NASA Astrophysics Data System (ADS)
Ramunni, V. P.
2018-03-01
Previous experimental studies of H permeation in 9%Cr-Fe alloys have found a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure annealed Fe. In an effort to shed some light on the microscopic origin of these findings, we perform an extensive study of Fe, Cr, and H migration in a high-angle symmetric tilt grain boundary in bcc Fe, both via vacancy and interstitial mechanism. This is undertaken in the framework of transition state theory with the relevant energies obtained from classical interatomic potentials, and partially from Density Functional Theory calculations, in order to check the consistency of structures. Trapping sites for H and possible migration paths are explored. We find that the presence of Cr and its migration via vacancy and interstitials creates the conditions in produce stable preferential trapping sites for H in the grain boundary, that delay the H migration, thereby explaining the experimental results.
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Effective use of nanocarriers as drug delivery systems for the treatment of selected tumors
Ullah, Izhar; Qureshi, Omer Salman; Mustapha, Omer; Shafique, Shumaila; Zeb, Alam
2017-01-01
Nanotechnology has recently gained increased attention for its capability to effectively diagnose and treat various tumors. Nanocarriers have been used to circumvent the problems associated with conventional antitumor drug delivery systems, including their nonspecificity, severe side effects, burst release and damaging the normal cells. Nanocarriers improve the bioavailability and therapeutic efficiency of antitumor drugs, while providing preferential accumulation at the target site. A number of nanocarriers have been developed; however, only a few of them are clinically approved for the delivery of antitumor drugs for their intended actions at the targeted sites. The present review is divided into three main parts: first part presents introduction of various nanocarriers and their relevance in the delivery of anticancer drugs, second part encompasses targeting mechanisms and surface functionalization on nanocarriers and third part covers the description of selected tumors, including breast, lungs, colorectal and pancreatic tumors, and applications of relative nanocarriers in these tumors. This review increases the understanding of tumor treatment with the promising use of nanotechnology. PMID:29042776
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Pöhler, Robert; Krahn, Jan H; van den Boom, Johannes; Dobrynin, Grzegorz; Kaschani, Farnusch; Eggenweiler, Hans-Michael; Zenke, Frank T; Kaiser, Markus; Meyer, Hemmo
2018-02-05
AAA ATPases have pivotal functions in diverse cellular processes essential for survival and proliferation. Revealing strategies for chemical inhibition of this class of enzymes is therefore of great interest for the development of novel chemotherapies or chemical tools. Here, we characterize the compound MSC1094308 as a reversible, allosteric inhibitor of the type II AAA ATPase human ubiquitin-directed unfoldase (VCP)/p97 and the type I AAA ATPase VPS4B. Subsequent proteomic, genetic and biochemical studies indicate that MSC1094308 binds to a previously characterized drugable hotspot of p97, thereby inhibiting the D2 ATPase activity. Our results furthermore indicate that a similar allosteric site exists in VPS4B, suggesting conserved allosteric circuits and drugable sites in both type I and II AAA ATPases. Our results may thus guide future chemical tool and drug discovery efforts for the biomedically relevant AAA ATPases. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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Rice, Gillian I; Reijns, Martin A M; Coffin, Stephanie R; Forte, Gabriella M A; Anderson, Beverley H; Szynkiewicz, Marcin; Gornall, Hannah; Gent, David; Leitch, Andrea; Botella, Maria P; Fazzi, Elisa; Gener, Blanca; Lagae, Lieven; Olivieri, Ivana; Orcesi, Simona; Swoboda, Kathryn J; Perrino, Fred W; Jackson, Andrew P; Crow, Yanick J
2013-08-01
Aicardi-Goutières syndrome is an inflammatory disorder resulting from mutations in TREX1, RNASEH2A/2B/2C, SAMHD1, or ADAR1. Here, we provide molecular, biochemical, and cellular evidence for the pathogenicity of two synonymous variants in RNASEH2A. Firstly, the c.69G>A (p.Val23Val) mutation causes the formation of a splice donor site within exon 1, resulting in an out of frame deletion at the end of exon 1, leading to reduced RNase H2 protein levels. The second mutation, c.75C>T (p.Arg25Arg), also introduces a splice donor site within exon 1, and the internal deletion of 18 amino acids. The truncated protein still forms a heterotrimeric RNase H2 complex, but lacks catalytic activity. However, as a likely result of leaky splicing, a small amount of full-length active protein is apparently produced in an individual homozygous for this mutation. Recognition of the disease causing status of these variants allows for diagnostic testing in relevant families. © 2013 WILEY PERIODICALS, INC.
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Chymase Cleavage of Stem Cell Factor Yields a Bioactive, Soluble Product
NASA Astrophysics Data System (ADS)
Longley, B. Jack; Tyrrell, Lynda; Ma, Yongsheng; Williams, David A.; Halaban, Ruth; Langley, Keith; Lu, Hsieng S.; Schechter, Norman M.
1997-08-01
Stem cell factor (SCF) is produced by stromal cells as a membrane-bound molecule, which may be proteolytically cleaved at a site close to the membrane to produce a soluble bioactive form. The proteases producing this cleavage are unknown. In this study, we demonstrate that human mast cell chymase, a chymotrypsin-like protease, cleaves SCF at a novel site. Cleavage is at the peptide bond between Phe-158 and Met-159, which are encoded by exon 6 of the SCF gene. This cleavage results in a soluble bioactive product that is 7 amino acids shorter at the C terminus than previously identified soluble SCF. This research shows the identification of a physiologically relevant enzyme that specifically cleaves SCF. Because mast cells express the KIT protein, the receptor for SCF, and respond to SCF by proliferation and degranulation, this observation identifies a possible feedback loop in which chymase released from mast cell secretory granules may solubilize SCF bound to the membrane of surrounding stromal cells. The liberated soluble SCF may in turn stimulate mast cell proliferation and differentiated functions; this loop could contribute to abnormal accumulations of mast cells in the skin and hyperpigmentation at sites of chronic cutaneous inflammation.
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Indication of pesticide effects and recolonization in streams.
Knillmann, Saskia; Orlinskiy, Polina; Kaske, Oliver; Foit, Kaarina; Liess, Matthias
2018-07-15
The agricultural use of pesticides leads to environmentally relevant pesticide concentrations that cause adverse effects on stream ecosystems. These effects on invertebrate community composition can be identified by the bio-indicator SPEAR pesticides . However, refuge areas have been found to partly confound the indicator. On the basis of three monitoring campaigns of 41 sites in Central Germany, we identified 11 refuge taxa. The refuge taxa, mainly characterized by dispersal-based resilience, were observed only nearby uncontaminated stream sections and independent of the level of pesticide pressure. Through incorporation of this information into the revised SPEAR pesticides indicator, the community structure specifically identified the toxic pressure and no longer depended on the presence of refuge areas. With regard to ecosystem functions, leaf litter degradation was predicted by the revised SPEAR pesticides and the median water temperature at a site (R 2 = 0.38, P = 0.003). Furthermore, we designed the bio-indicator SPEAR refuge to quantify the magnitude of general recolonization at a given stream site. We conclude that the taxonomic composition of aquatic invertebrate communities enables a specific indication of anthropogenic stressors and resilience of ecosystems. Copyright © 2018 Elsevier B.V. All rights reserved.
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30 CFR 250.906 - What must I do to obtain approval for the proposed site of my platform?
Code of Federal Regulations, 2011 CFR
2011-07-01
... geological survey relevant to the design and siting of your platform. Your geological survey must assess: (1..., the possibility and effects of seafloor subsidence. (c) Subsurface surveys. Depending upon the design... obtain approval for the proposed site of my platform? (a) Shallow hazards surveys. You must perform a...
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Students as Web Site Authors: Effects on Motivation and Achievement
ERIC Educational Resources Information Center
Jones, Brett D.
2003-01-01
This study examined the effects of a Web site design project on students' motivation and achievement. Tenth-grade biology students worked together in teams on an ecology project that required them to locate relevant information on the Internet, decide which information should be included on their Web site, organize the information into Web pages,…
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1001 Best Internet Sites for Educators. 2nd Edition.
ERIC Educational Resources Information Center
Treadwell, Mark
This second edition of a resource designed to help teachers find relevant information on the Internet for both themselves and their students, provides concise reviews of more than 1,000 Web sites sorted by subject area. Each site is evaluated with one to five stars for content, presentation and grade level. Easy-to-follow explanations are provided…
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Protein Tyrosine Nitration: Biochemical Mechanisms and Structural Basis of its Functional Effects
Radi, Rafael
2012-01-01
CONSPECTUS The nitration of protein tyrosine residues to 3-nitrotyrosine represents an oxidative postranslational modification that unveils the disruption of nitric oxide (•NO) signaling and metabolism towards pro-oxidant processes. Indeed, excess levels of reactive oxygen species in the presence of •NO or •NO-derived metabolites lead to the formation of nitrating species such as peroxynitrite. Thus, protein 3-nitrotyrosine has been established as a biomarker of cell, tissue and systemic “nitroxidative stress”. Moreover, tyrosine nitration modifies key properties of the amino acid (i.e. phenol group pKa, redox potential, hydrophobicity and volume). Thus, the incorporation of a nitro group (−NO2) to protein tyrosines can lead to profound structural and functional changes, some of which contribute to altered cell and tissue homeostasis. In this Account, I describe our current efforts to define 1) biologically-relevant mechanisms of protein tyrosine nitration and 2) how this modification can cause changes in protein structure and function at the molecular level. First, the relevance of protein tyrosine nitration via free radical-mediated reactions (in both peroxynitrite-dependent or independent pathways) involving the intermediacy of tyrosyl radical (Tyr•) will be underscored. This feature of the nitration process becomes critical as Tyr• can take variable fates, including the formation of 3-nitrotyrosine. Fast kinetic techniques, electron paramagnetic resonance (EPR) studies, bioanalytical methods and kinetic simulations have altogether assisted to characterize and fingerprint the reactions of tyrosine with peroxynitrite and one-electron oxidants and its further evolution to 3-nitrotyrosine. Recent findings show that nitration of tyrosines in proteins associated to biomembranes is linked to the lipid peroxidation process via a connecting reaction that involves the one-electron oxidation of tyrosine by lipid peroxyl radicals (LOO•). Second, immunochemical and proteomic-based studies indicate that protein tyrosine nitration is a selective process in vitro and in vivo, preferentially directed to a subset of proteins, and within those proteins, typically one or two tyrosine residues are site-specifically modified. The nature and site(s) of formation of the proximal oxidizing/nitrating species, the physico-chemical characteristics of the local microenvironment and also structural features of the protein account for part of this selectivity. Then, how this relatively subtle chemical modification in one tyrosine residue can sometimes cause dramatic changes in protein activity has remained elusive. Herein, I will analyze recent structural biology data of two pure and homogenously nitrated mitochondrial proteins (i.e. cytochrome c and MnSOD) to illustrate regio-selectivity and structural effects of tyrosine nitration, and subsequent impact in protein loss- or even gain-of-function. PMID:23157446
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Task relevance induces momentary changes in the functional visual field during reading.
Kaakinen, Johanna K; Hyönä, Jukka
2014-02-01
In the research reported here, we examined whether task demands can induce momentary tunnel vision during reading. More specifically, we examined whether the size of the functional visual field depends on task relevance. Forty participants read an expository text with a specific task in mind while their eye movements were recorded. A display-change paradigm with random-letter strings as preview masks was used to study the size of the functional visual field within sentences that contained task-relevant and task-irrelevant information. The results showed that orthographic parafoveal-on-foveal effects and preview benefits were observed for words within task-irrelevant but not task-relevant sentences. The results indicate that the size of the functional visual field is flexible and depends on the momentary processing demands of a reading task. The higher cognitive processing requirements experienced when reading task-relevant text rather than task-irrelevant text induce momentary tunnel vision, which narrows the functional visual field.
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Single molecule optical measurements of orientation and rotations of biological macromolecules
Shroder, Deborah Y; Lippert, Lisa G; Goldman, Yale E
2016-01-01
The subdomains of macromolecules often undergo large orientation changes during their catalytic cycles that are essential for their activity. Tracking these rearrangements in real time opens a powerful window into the link between protein structure and functional output. Site-specific labeling of individual molecules with polarized optical probes and measuring their spatial orientation can give insight into the crucial conformational changes, dynamics, and fluctuations of macromolecules. Here we describe the range of single molecule optical technologies that can extract orientation information from these probes, we review the relevant types of probes and labeling techniques, and we highlight the advantages and disadvantages of these technologies for addressing specific inquiries. PMID:28192292
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CANE FIBERBOARD DEGRADATION WITHIN THE 9975 SHIPPING PACKAGE DURING LONG-TERM STORAGE APPLICATION
DOE Office of Scientific and Technical Information (OSTI.GOV)
Daugherty, W.; Dunn, K.; Hackney, B.
The 9975 shipping package is used as part of the configuration for long-term storage of special nuclear materials in the K Area Complex at the Savannah River Site. The cane fiberboard overpack in the 9975 package provides thermal insulation, impact absorption and criticality control functions relevant to this application. The Savannah River National Laboratory has conducted physical, mechanical and thermal tests on aged fiberboard samples to identify degradation rates and support the development of aging models and service life predictions in a storage environment. This paper reviews the data generated to date, and preliminary models describing degradation rates of canemore » fiberboard in elevated temperature – elevated humidity environments.« less
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Responses of woody species to spatial and temporal ground water changes in coastal sand dune systems
NASA Astrophysics Data System (ADS)
Máguas, C.; Rascher, K. G.; Martins-Loução, A.; Carvalho, P.; Pinho, P.; Ramos, M.; Correia, O.; Werner, C.
2011-12-01
In spite of the relative importance of groundwater in costal dune systems, studies concerning the responses of vegetation to ground water (GW) availability variations, particularly in Mediterranean regions, are scarce. Thus, the main purpose of this study is to compare the responses of co-occurring species possessing different functional traits, to changes in GW levels (i.e. the lowering of GW levels) in a sand dune ecosystem. For that, five sites were established within a 1 km2 area in a meso-mediterranean sand dune ecosystem dominated by a Pinus pinaster forest. Due to natural topographic variability and anthropogenic GW exploitation, substantial variability in depth to GW between sites was found. Under these conditions it was possible to identify the degree of usage and dependence on GW of different plant species (two deep-rooted trees, a drought adapted shrub, a phreatophyte and a non-native woody invader) and how GW dependence varied seasonally and between the heterogeneous sites. Results indicated that the plant species had differential responses to changes in GW depth according to specific functional traits (i.e. rooting depth, leaf morphology, and water use strategy). Species comparison revealed that variability in pre-dawn water potential (Ψpre) and bulk leaf δ13C was related to site differences in GW use in the deep-rooted (Pinus pinaster, Myrica faya) and phreatophyte (Salix repens) species. However, such variation was more evident during spring than during summer drought. The exotic invader, Acacia longifolia, which does not possess a very deep root system, presented the largest seasonal variability in Ψpre and bulk leaf δ13C. In contrast, the response of Corema album, an endemic understory drought-adapted shrub, seemed to be independent of water availability across seasons and sites. Thus, the susceptibility to lowering of GW due to anthropogenic exploitation, in plant species from sand dunes, is variable, being particularly relevant for deep rooted species and phreatophytes, which seem to depend heavily on access to GW.
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d-Aspartate oxidase influences glutamatergic system homeostasis in mammalian brain.
Cristino, Luigia; Luongo, Livio; Squillace, Marta; Paolone, Giovanna; Mango, Dalila; Piccinin, Sonia; Zianni, Elisa; Imperatore, Roberta; Iannotta, Monica; Longo, Francesco; Errico, Francesco; Vescovi, Angelo Luigi; Morari, Michele; Maione, Sabatino; Gardoni, Fabrizio; Nisticò, Robert; Usiello, Alessandro
2015-05-01
We have investigated the relevance of d-aspartate oxidase, the only enzyme known to selectively degrade d-aspartate (d-Asp), in modulating glutamatergic system homeostasis. Interestingly, the lack of the Ddo gene, by raising d-Asp content, induces a substantial increase in extracellular glutamate (Glu) levels in Ddo-mutant brains. Consistent with an exaggerated and persistent N-methyl-d-aspartate receptor (NMDAR) stimulation, we documented in Ddo knockouts severe age-dependent structural and functional alterations mirrored by expression of active caspases 3 and 7 along with appearance of dystrophic microglia and reactive astrocytes. In addition, prolonged elevation of d-Asp triggered in mutants alterations of NMDAR-dependent synaptic plasticity associated to reduction of hippocampal GluN1 and GluN2B subunits selectively located at synaptic sites and to increase in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-to-N-methyl-d-aspartate ratio. These effects, all of which converged on a progressive hyporesponsiveness at NMDAR sites, functionally resulted in a greater vulnerability to phencyclidine-induced prepulse inhibition deficits in mutants. In conclusion, our results indicate that d-aspartate oxidase, by strictly regulating d-Asp levels, impacts on the homeostasis of glutamatergic system, thus preventing accelerated neurodegenerative processes. Copyright © 2015 Elsevier Inc. All rights reserved.
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Replication Cycle and Molecular Biology of the West Nile Virus
Brinton, Margo A.
2013-01-01
West Nile virus (WNV) is a member of the genus Flavivirus in the family Flaviviridae. Flaviviruses replicate in the cytoplasm of infected cells and modify the host cell environment. Although much has been learned about virion structure and virion-endosomal membrane fusion, the cell receptor(s) used have not been definitively identified and little is known about the early stages of the virus replication cycle. Members of the genus Flavivirus differ from members of the two other genera of the family by the lack of a genomic internal ribosomal entry sequence and the creation of invaginations in the ER membrane rather than double-membrane vesicles that are used as the sites of exponential genome synthesis. The WNV genome 3' and 5' sequences that form the long distance RNA-RNA interaction required for minus strand initiation have been identified and contact sites on the 5' RNA stem loop for NS5 have been mapped. Structures obtained for many of the viral proteins have provided information relevant to their functions. Viral nonstructural protein interactions are complex and some may occur only in infected cells. Although interactions between many cellular proteins and virus components have been identified, the functions of most of these interactions have not been delineated. PMID:24378320
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Hodonsky, Chani J.; Kleinbrink, Erica L.; Charney, Kira N.; Prasad, Megana; Bessling, Seneca L.; Jones, Erin A.; Srinivasan, Rajini; Svaren, John; McCallion, Andrew S.; Antonellis, Anthony
2011-01-01
The transcription factor SOX10 has essential roles in neural crest-derived cell populations, including myelinating Schwann cells—specialized glial cells responsible for ensheathing axons in the peripheral nervous system. Importantly, SOX10 directly regulates the expression of genes essential for proper myelin function. To date, only a handful of SOX10 target loci have been characterized in Schwann cells. Addressing this lack of knowledge will provide a better understanding of Schwann cell biology and candidate loci for relevant diseases such as demyelinating peripheral neuropathies. We have identified a highly-conserved SOX10 binding site within an alternative promoter at the SH3-domain kinase binding protein 1 (Sh3kbp1) locus. The genomic segment identified at Sh3kbp1 binds to SOX10 and displays strong promoter activity in Schwann cells in vitro and in vivo. Mutation of the SOX10 binding site ablates promoter activity, and ectopic expression of SOX10 in SOX10-negative cells promotes the expression of endogenous Sh3kbp1. Combined, these data reveal Sh3kbp1 as a novel target of SOX10 and raise important questions regarding the function of SH3KBP1 isoforms in Schwann cells. PMID:22037207
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Sonntag, Eric; Milbradt, Jens; Svrlanska, Adriana; Strojan, Hanife; Häge, Sigrun; Kraut, Alexandra; Hesse, Anne-Marie; Amin, Bushra; Sonnewald, Uwe; Couté, Yohann; Marschall, Manfred
2017-10-01
Nuclear egress of herpesvirus capsids is mediated by a multi-component nuclear egress complex (NEC) assembled by a heterodimer of two essential viral core egress proteins. In the case of human cytomegalovirus (HCMV), this core NEC is defined by the interaction between the membrane-anchored pUL50 and its nuclear cofactor, pUL53. NEC protein phosphorylation is considered to be an important regulatory step, so this study focused on the respective role of viral and cellular protein kinases. Multiply phosphorylated pUL50 varieties were detected by Western blot and Phos-tag analyses as resulting from both viral and cellular kinase activities. In vitro kinase analyses demonstrated that pUL50 is a substrate of both PKCα and CDK1, while pUL53 can also be moderately phosphorylated by CDK1. The use of kinase inhibitors further illustrated the importance of distinct kinases for core NEC phosphorylation. Importantly, mass spectrometry-based proteomic analyses identified five major and nine minor sites of pUL50 phosphorylation. The functional relevance of core NEC phosphorylation was confirmed by various experimental settings, including kinase knock-down/knock-out and confocal imaging, in which it was found that (i) HCMV core NEC proteins are not phosphorylated solely by viral pUL97, but also by cellular kinases; (ii) both PKC and CDK1 phosphorylation are detectable for pUL50; (iii) no impact of PKC phosphorylation on NEC functionality has been identified so far; (iv) nonetheless, CDK1-specific phosphorylation appears to be required for functional core NEC interaction. In summary, our findings provide the first evidence that the HCMV core NEC is phosphorylated by cellular kinases, and that the complex pattern of NEC phosphorylation has functional relevance.
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Photosynthesis and the web: 2001.
Orr, L
2001-01-01
First, a brief history of the Internet and the World Wide Web is presented. This is followed by relevant information on photosynthesis-related web sites grouped into several categories: (1) large group sites, (2) comprehensive overview sites, (3) specific subject sites, (4) individual researcher sites, (5) kindergarten through high school (K-12) educational sites, (6) books and journals, and, 7) other useful sites. A section on searching the Web is also included. Finally, we have included an appendix with all of the web sites discussed herein as well as other web sites that space did not allow. Readers are requested to send comments, corrections and additions to gov@uiuc.edu.
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10 CFR 503.22 - Site limitations.
Code of Federal Regulations, 2013 CFR
2013-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... of these regulations. Note: Examples of the types of site limitations to which a petitioner may... of a specific physical limitation; (ii) Unavailability of transportation facilities for alternate...
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10 CFR 503.22 - Site limitations.
Code of Federal Regulations, 2014 CFR
2014-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... of these regulations. Note: Examples of the types of site limitations to which a petitioner may... of a specific physical limitation; (ii) Unavailability of transportation facilities for alternate...
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Final ecosystem goods and services enhance societal relevance of contaminated-site remediation
Background/Question/Methods Exposure to environmental stressors can adversely affect both human health and ecological receptors and impacts on the latter influence the community's overall vulnerability. Risk assessment guidance promotes conceptual site models to integrate multip...
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Effect of particle surface area on ice active site densities retrieved from droplet freezing spectra
NASA Astrophysics Data System (ADS)
Beydoun, Hassan; Polen, Michael; Sullivan, Ryan C.
2016-10-01
Heterogeneous ice nucleation remains one of the outstanding problems in cloud physics and atmospheric science. Experimental challenges in properly simulating particle-induced freezing processes under atmospherically relevant conditions have largely contributed to the absence of a well-established parameterization of immersion freezing properties. Here, we formulate an ice active, surface-site-based stochastic model of heterogeneous freezing with the unique feature of invoking a continuum assumption on the ice nucleating activity (contact angle) of an aerosol particle's surface that requires no assumptions about the size or number of active sites. The result is a particle-specific property g that defines a distribution of local ice nucleation rates. Upon integration, this yields a full freezing probability function for an ice nucleating particle. Current cold plate droplet freezing measurements provide a valuable and inexpensive resource for studying the freezing properties of many atmospheric aerosol systems. We apply our g framework to explain the observed dependence of the freezing temperature of droplets in a cold plate on the concentration of the particle species investigated. Normalizing to the total particle mass or surface area present to derive the commonly used ice nuclei active surface (INAS) density (ns) often cannot account for the effects of particle concentration, yet concentration is typically varied to span a wider measurable freezing temperature range. A method based on determining what is denoted an ice nucleating species' specific critical surface area is presented and explains the concentration dependence as a result of increasing the variability in ice nucleating active sites between droplets. By applying this method to experimental droplet freezing data from four different systems, we demonstrate its ability to interpret immersion freezing temperature spectra of droplets containing variable particle concentrations. It is shown that general active site density functions, such as the popular ns parameterization, cannot be reliably extrapolated below this critical surface area threshold to describe freezing curves for lower particle surface area concentrations. Freezing curves obtained below this threshold translate to higher ns values, while the ns values are essentially the same from curves obtained above the critical area threshold; ns should remain the same for a system as concentration is varied. However, we can successfully predict the lower concentration freezing curves, which are more atmospherically relevant, through a process of random sampling from g distributions obtained from high particle concentration data. Our analysis is applied to cold plate freezing measurements of droplets containing variable concentrations of particles from NX illite minerals, MCC cellulose, and commercial Snomax bacterial particles. Parameterizations that can predict the temporal evolution of the frozen fraction of cloud droplets in larger atmospheric models are also derived from this new framework.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Maheras, Steven J.; Best, Ralph E.; Ross, Steven B.
A preliminary evaluation of removing spent nuclear fuel (SNF) from 13 shutdown nuclear power reactor sites was conducted. At these shutdown sites the nuclear power reactors have been permanently shut down and the sites have been decommissioned or are undergoing decommissioning. The shutdown sites were Maine Yankee, Yankee Rowe, Connecticut Yankee, Humboldt Bay, Big Rock Point, Rancho Seco, Trojan, La Crosse, Zion, Crystal River, Kewaunee, San Onofre, and Vermont Yankee. The evaluation was divided into four components: (1) characterization of the SNF and greater-than-Class C low-level radioactive waste (GTCC waste) inventory, (2) a description of the on-site infrastructure and conditionsmore » relevant to transportation of SNF and GTCC waste, (3) an evaluation of the near-site transportation infrastructure and experience relevant to shipping transportation casks containing SNF and GTCC waste, including identification of gaps in information, and (4) an evaluation of the actions necessary to prepare for and remove SNF and GTCC waste. Every site was found to have at least one off-site transportation mode option for removing its SNF and GTCC waste; some have multiple options. Experience removing large components during reactor decommissioning provided an important source of information used to identify the transportation mode options for the sites. Especially important in conducting the evaluation were site visits, through which information was obtained that would not have been available otherwise. Extensive photographs taken during the site visits proved to be particularly useful in documenting the current conditions at or near the sites. It is expected that additional site visits will be conducted to add to the information presented in the evaluation.« less
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Gagliardo, A.; Odetti, F.; Ioalè, P.
2001-01-01
Whether pigeons use visual landmarks for orientation from familiar locations has been a subject of debate. By recording the directional choices of both anosmic and control pigeons while exiting from a circular arena we were able to assess the relevance of olfactory and visual cues for orientation from familiar sites. When the birds could see the surroundings, both anosmic and control pigeons were homeward oriented. When the view of the landscape was prevented by screens that surrounded the arena, the control pigeons exited from the arena approximately in the home direction, while the anosmic pigeons' distribution was not different from random. Our data suggest that olfactory and visual cues play a critical, but interchangeable, role for orientation at familiar sites. PMID:11571054
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The Relevance of Rodent-Specific Tumors in Cancer Risk Assessment
Laboratory animal species have organs that do not specifically occur in humans and somtimes tumors arise in these organs. The lack of direct site concordance frequently results in significant debate on the human relevance of tumors that arise from rodent specific organs. The re...
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NASA Astrophysics Data System (ADS)
Fleming, Z. L.; von Schneidemesser, E.; Doherty, R. M.; Malley, C.; Cooper, O. R.; Pinto, J. P.; Colette, A.; Xu, X.; Simpson, D.; Schultz, M.; Hamad, S.; Moola, R.; Solberg, S.; Feng, Z.
2017-12-01
Ozone is an air pollutant formed in the atmosphere from precursor species (NOx, VOCs, CH4, CO) that is detrimental to human health and ecosystems. The global Tropospheric Ozone Assessment Report (TOAR) initiative has assembled a global database of surface ozone observations and generated ozone exposure metrics at thousands of measurement sites around the world. This talk will present results from the assessment focused on those indicators most relevant to human health. Specifically, the trends in ozone, comparing different time periods and patterns across regions and among metrics will be addressed. In addition, the fraction of population exposed to high ozone levels and how this has changed between 2000 and 2014 will also be discussed. The core time period analyzed for trends was 2000-2014, selected to include a greater number of sites in East Asia. Negative trends were most commonly observed at many US and some European sites, whereas many sites in East Asia showed positive trends, while sites in Japan showed more of a mix of positive and negative trends. More than half of the sites showed a common direction and significance in the trends for all five human-health relevant metrics. The peak ozone metrics indicate a reduction in exposure to peak levels of ozone related to photochemical episodes in Europe and the US. A considerable number of European countries and states within the US have shown a decrease in population-weighted ozone over time. The 2000-2014 results will be augmented and compared to the trend analysis for additional time periods that cover a greater number of years, but by necessity are based on fewer sites. Trends are found to be statistically significant at a larger fraction of sites with longer time series, compared to the shorter (2000-2014) time series.
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Kleefstra, Sophia Martine; Zandbelt, Linda C; Borghans, Ine; de Haes, Hanneke J C J M; Kool, Rudolf B
2016-07-20
Over the last decades, the patient perspective on health care quality has been unconditionally integrated into quality management. For several years now, patient rating sites have been rapidly gaining attention. These offer a new approach toward hearing the patient's perspective on the quality of health care. The aim of our study was to explore whether and how patient reviews of hospitals, as reported on rating sites, have the potential to contribute to health care inspector's daily supervision of hospital care. Given the unexplored nature of the topic, an interview study among hospital inspectors was designed in the Netherlands. We performed 2 rounds of interviews with 10 senior inspectors, addressing their use and their judgment on the relevance of review data from a rating site. All 10 Dutch senior hospital inspectors participated in this research. The inspectors initially showed some reluctance to use the major patient rating site in their daily supervision. This was mainly because of objections such as worries about how representative they are, subjectivity, and doubts about the relevance of patient reviews for supervision. However, confrontation with, and assessment of, negative reviews by the inspectors resulted in 23% of the reviews being deemed relevant for risk identification. Most inspectors were cautiously positive about the contribution of the reviews to their risk identification. Patient rating sites may be of value to the risk-based supervision of hospital care carried out by the Health Care Inspectorate. Health care inspectors do have several objections against the use of patient rating sites for daily supervision. However, when they are presented with texts of negative reviews from a hospital under their supervision, it appears that most inspectors consider it as an additional source of information to detect poor quality of care. Still, it should always be accompanied and verified by other quality and safety indicators. More research on the value and usability of patient rating sites in daily hospital supervision and other health settings is needed.
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Stiffler, Michael A; Subramanian, Subu K; Salinas, Victor H; Ranganathan, Rama
2016-07-03
Site-directed mutagenesis has long been used as a method to interrogate protein structure, function and evolution. Recent advances in massively-parallel sequencing technology have opened up the possibility of assessing the functional or fitness effects of large numbers of mutations simultaneously. Here, we present a protocol for experimentally determining the effects of all possible single amino acid mutations in a protein of interest utilizing high-throughput sequencing technology, using the 263 amino acid antibiotic resistance enzyme TEM-1 β-lactamase as an example. In this approach, a whole-protein saturation mutagenesis library is constructed by site-directed mutagenic PCR, randomizing each position individually to all possible amino acids. The library is then transformed into bacteria, and selected for the ability to confer resistance to β-lactam antibiotics. The fitness effect of each mutation is then determined by deep sequencing of the library before and after selection. Importantly, this protocol introduces methods which maximize sequencing read depth and permit the simultaneous selection of the entire mutation library, by mixing adjacent positions into groups of length accommodated by high-throughput sequencing read length and utilizing orthogonal primers to barcode each group. Representative results using this protocol are provided by assessing the fitness effects of all single amino acid mutations in TEM-1 at a clinically relevant dosage of ampicillin. The method should be easily extendable to other proteins for which a high-throughput selection assay is in place.
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Johnson, Colin; Fitzsimmons, Deborah; Gilbert, Jacqueline; Arrarras, Juan-Ignacio; Hammerlid, Eva; Bredart, Anne; Ozmen, Mahir; Dilektasli, Evren; Coolbrandt, Anne; Kenis, Cindy; Young, Teresa; Chow, Edward; Venkitaraman, Ramachandran; Howse, Frances; George, Steve; O'Connor, Steve; Yadegarfar, Ghasem
2010-08-01
There is a lack of instruments that focus on the specific health-related quality of life (HRQOL) issues that affect older people with cancer. The aim of this study was to develop a HRQOL questionnaire module to supplement the European Organisation for Research and Treatment of Cancer (EORTC) core questionnaire, the EORTC QLQ-C30 for older (>70years) patients with cancer. Phases 1-3 were conducted in seven countries following modified EORTC Quality of Life Group guidelines for module development. Phase 1: potentially relevant issues were identified by a systematic literature review, a questionnaire survey of 17 multi-disciplinary health professionals and two rounds of qualitative interviews. The first round included 9 patients aged >70. The second round was a comparative series of interviews with 49 patients >70years with a range of cancer diagnoses and 40 patients aged 50-69years matched for gender and disease site. In Phase 2 the issues were formulated into a long provisional item list. This was administered in Phase 3 together with the QLQ-C30 to two further groups of cancer patients aged >70 (n=97) or 50-69years (n=85) to determine the importance, relevance and acceptability of each item. Redundant and duplicate items were removed; issues specific to the older group were selected for the final questionnaire. In Phase 1, 75 issues were identified. These were reduced in Phase 2 to create a 45 item provisional list. Phase 3 testing of the provisional list led to the selection of 15 items with good range of response, high scores of importance and relevance in the older patients. This resulted in the EORTC QLQ-ELD15, containing five conceptually coherent scales (functional independence, relationships with family and friends, worries about the future, autonomy and burden of illness). The EORTC QLQ-ELD15 in combination with the EORTC QLQ-C30 is ready for large-scale validation studies, and will assess HRQOL issues of most relevance and concern for older people with cancer across a wide range of cancer sites and treatment stages. Copyright 2010 Elsevier Ltd. All rights reserved.
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ERIC Educational Resources Information Center
Noel-Levitz, Inc, 2009
2009-01-01
Have you updated your Web site today? Is it possible that answering "yes" to this simple question is the key to the success of your marketing and recruiting efforts? In the current recruitment arena, the ability to update and maintain this one high-value asset (your Web site) might be the key to the potency of your institutional…
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Rampelotto, Pabulo Henrique; de Siqueira Ferreira, Adão; Barboza, Anthony Diego Muller; Roesch, Luiz Fernando Wurdig
2013-10-01
The Brazilian Savanna, also known as "Cerrado", is the richest and most diverse savanna in the world and has been ranked as one of the main hotspots of biodiversity. The Cerrado is a representative biome in Central Brazil and the second largest biome in species diversity of South America. Nevertheless, large areas of native vegetation have been converted to agricultural land including grain production, livestock, and forestry. In this view, understanding how land use affects microbial communities is fundamental for the sustainable management of agricultural ecosystems. The aim of this work was to analyze and compare the soil bacterial communities from the Brazilian Cerrado associated with different land use systems using high throughput pyrosequencing of 16S rRNA genes. Relevant differences were observed in the abundance and structure of bacterial communities in soils under different land use systems. On the other hand, the diversity of bacterial communities was not relevantly changed among the sites studied. Land use systems had also an important impact on specific bacterial groups in soil, which might change the soil function and the ecological processes. Acidobacteria, Proteobacteria, and Actinobacteria were the most abundant groups in the Brazilian Cerrado. These findings suggest that more important than analyzing the general diversity is to analyze the composition of the communities. Since soil type was the same among the sites, we might assume that land use was the main factor defining the abundance and structure of bacterial communities.
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Eickenscheidt, Max; Zeck, Günther
2014-06-01
The initiation of an action potential by extracellular stimulation occurs after local depolarization of the neuronal membrane above threshold. Although the technique shows remarkable clinical success, the site of action and the relevant stimulation parameters are not completely understood. Here we identify the site of action potential initiation in rabbit retinal ganglion cells (RGCs) interfaced to an array of extracellular capacitive stimulation electrodes. We determine which feature of the extracellular potential governs action potential initiation by simultaneous stimulation and recording RGCs interfaced in epiretinal configuration. Stimulation electrodes were combined to areas of different size and were presented at different positions with respect to the RGC. Based on stimulation by electrodes beneath the RGC soma and simultaneous sub-millisecond latency measurement we infer axonal initiation at the site of maximal curvature of the extracellular potential. Stimulation by electrodes at different positions along the axon reveals a nearly constant threshold current density except for a narrow region close to the cell soma. These findings are explained by the concept of the activating function modified to consider a region of lower excitability close to the cell soma. We present a framework how to estimate the site of action potential initiation and the stimulus required to cross threshold in neurons tightly interfaced to capacitive stimulation electrodes. Our results underscore the necessity of rigorous electrical characterization of the stimulation electrodes and of the interfaced neural tissue.
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Wan, Emily S.; Qiu, Weiliang; Morrow, Jarrett; Beaty, Terri H.; Hetmanski, Jacqueline; Make, Barry J.; Lomas, David A.; Silverman, Edwin K.; DeMeo, Dawn L.
2015-01-01
Klinefelter syndrome (KS) (47 XXY) is a common sex-chromosome aneuploidy with an estimated prevalence of 1 in every 660 male births. Investigations into the associations between DNA methylation and the highly variable clinical manifestations of KS have largely focused on the supernumerary X chromosome; systematic investigations of the epigenome have been limited. We obtained genome-wide DNA methylation data from peripheral blood using the Illumina HumanMethylation450K platform in 5 KS (47 XXY), 102 male (46 XY), and 113 female (46 XX) control subjects participating in the chronic obstructive pulmonary disease (COPD) Gene Study. Empirical Bayes-mediated models were used to test for differential methylation by KS status. CpG sites with a false-discovery rate <0.05 from the first-generation HumanMethylation27K platform were further examined in an independent replication cohort of 2 KS subjects, 590 male, and 495 female controls drawn from the International COPD Genetics Network (ICGN). Differential methylation at sites throughout the genome were identified, including 86 CpG sites that were differentially methylated in KS subjects relative to both male and female controls. CpG sites annotated to the HEN1 methyltransferase homolog 1 (HENMT1), calcyclin-binding protein (CACYBP), and GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) genes were among the “KS-specific” loci that were replicated in ICGN. We therefore conclude that site-specific differential methylation exists throughout the genome in KS. The functional impact and clinical relevance of these differentially methylated loci should be explored in future studies. PMID:25988574
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Galka, Marek M.; Rajagopalan, Nandhakishore; Buhrow, Leann M.; Nelson, Ken M.; Switala, Jacek; Cutler, Adrian J.; Palmer, David R. J.; Loewen, Peter C.; Abrams, Suzanne R.; Loewen, Michele C.
2015-01-01
Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a Kd of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (Ki of 2.1 mM), but more potent inhibition of Rubisco activation (Ki of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation. PMID:26197050
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Galka, Marek M; Rajagopalan, Nandhakishore; Buhrow, Leann M; Nelson, Ken M; Switala, Jacek; Cutler, Adrian J; Palmer, David R J; Loewen, Peter C; Abrams, Suzanne R; Loewen, Michele C
2015-01-01
Abscisic acid ((+)-ABA) is a phytohormone involved in the modulation of developmental processes and stress responses in plants. A chemical proteomics approach using an ABA mimetic probe was combined with in vitro assays, isothermal titration calorimetry (ITC), x-ray crystallography and in silico modelling to identify putative (+)-ABA binding-proteins in crude extracts of Arabidopsis thaliana. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) was identified as a putative ABA-binding protein. Radiolabelled-binding assays yielded a Kd of 47 nM for (+)-ABA binding to spinach Rubisco, which was validated by ITC, and found to be similar to reported and experimentally derived values for the native ribulose-1,5-bisphosphate (RuBP) substrate. Functionally, (+)-ABA caused only weak inhibition of Rubisco catalytic activity (Ki of 2.1 mM), but more potent inhibition of Rubisco activation (Ki of ~ 130 μM). Comparative structural analysis of Rubisco in the presence of (+)-ABA with RuBP in the active site revealed only a putative low occupancy (+)-ABA binding site on the surface of the large subunit at a location distal from the active site. However, subtle distortions in electron density in the binding pocket and in silico docking support the possibility of a higher affinity (+)-ABA binding site in the RuBP binding pocket. Overall we conclude that (+)-ABA interacts with Rubisco. While the low occupancy (+)-ABA binding site and weak non-competitive inhibition of catalysis may not be relevant, the high affinity site may allow ABA to act as a negative effector of Rubisco activation.
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Lavine; Snyder
1996-11-01
In two experiments, we examined the hypothesis that subjective perceptions of message quality mediate the functional matching effect in persuasion. In Experiment 1, participants whose attitudes and behaviors serve primarily a value-expressive function (i.e., low self-monitors) or a social-adjustive function (i.e., high self-monitors) were exposed to persuasive messages that contained value-expressive, social-adjustive, or both types of arguments in favor of voting. Functionally-relevant messages (i.e., the social-adjustive message for high self-monitors and the value-expressive message for low self-monitors) produced enhanced perceptions of message quality and persuasiveness, more positive attitudes, and more message-related behavior than functionally nonrelevant messages. Functionally mixed messages were generally more effective than messages containing only functionally nonrelevant arguments, but less effective than messages containing only functionally relevant arguments. Path analyses indicated that the influence of functional relevance on attitudes and behavior was significantly mediated by subjective perceptions of the quality of the message. In Experiment 2, we exposed participants to a functionally relevant or nonrelevant voting appeal five days before a presidential election. Results replicated those of Experiment 1; functionally relevant messages produced more favorable attitudes, and this effect was mediated by enhanced perceptions of message quality. Finally, postmessage attitudes exerted a significant influence on whether participants voted in the election, and this effect was mediated by voting intentions. Discussion focuses on the subjective nature of message evaluation and on the cognitive processes underlying the functional matching effect in persuasion.
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NASA Astrophysics Data System (ADS)
McCann, C.; Repasky, K. S.; Morin, M.; Lawrence, R. L.; Powell, S. L.
2016-12-01
Compact, cost-effective, flight-based hyperspectral imaging systems can provide scientifically relevant data over large areas for a variety of applications such as ecosystem studies, precision agriculture, and land management. To fully realize this capability, unsupervised classification techniques based on radiometrically-calibrated data that cluster based on biophysical similarity rather than simply spectral similarity are needed. An automated technique to produce high-resolution, large-area, radiometrically-calibrated hyperspectral data sets based on the Landsat surface reflectance data product as a calibration target was developed and applied to three subsequent years of data covering approximately 1850 hectares. The radiometrically-calibrated data allows inter-comparison of the temporal series. Advantages of the radiometric calibration technique include the need for minimal site access, no ancillary instrumentation, and automated processing. Fitting the reflectance spectra of each pixel using a set of biophysically relevant basis functions reduces the data from 80 spectral bands to 9 parameters providing noise reduction and data compression. Examination of histograms of these parameters allows for determination of natural splitting into biophysical similar clusters. This method creates clusters that are similar in terms of biophysical parameters, not simply spectral proximity. Furthermore, this method can be applied to other data sets, such as urban scenes, by developing other physically meaningful basis functions. The ability to use hyperspectral imaging for a variety of important applications requires the development of data processing techniques that can be automated. The radiometric-calibration combined with the histogram based unsupervised classification technique presented here provide one potential avenue for managing big-data associated with hyperspectral imaging.
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ERIC Educational Resources Information Center
Street, Chris; Stang, Kristin
2008-01-01
Asking students to explore teacher-selected Web sites is an effective way to provide students with appropriate links to credible online resources. This article provides several links to relevant sites that cover the Holocaust and Nazi Germany in general. It also provides several sites that focus on one particularly controversial and significant…
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Federal Register 2010, 2011, 2012, 2013, 2014
2013-02-06
....; Blanchester Plant, Including On-Site Leased Workers From Adecco and Sims Bros., Inc.; Blanchester, OH; Amended... workers from Sims Bros., Inc. were working on-site at the subject firm during the relevant period and that the services supplied by Sims Bros., Inc. were related to the production of gear boxes (and parts...
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Federal government information handbook: formerly utilized sites remedial action program
DOE Office of Scientific and Technical Information (OSTI.GOV)
Not Available
This volume is one of a series produced under contract with the DOE, by Politech Corporation to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Formerly Utilized Sites Remedial Action Program. This Information Handbook series contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the Federal Government. It contains a summary of the organizationmore » and responsibilities of agencies within the executive branch of the Federal government which may be relevant to FUSRAP activities; a brief summary of relevant Federal statutes and regulations; a description of the structure of the US Congress, identification of the officers, relevant committees and committee chairmen; a description of the Federal legislative process; a summary of legislation enacted and considered in the recently-adjourned 96th Congress; a description of the Federal budgetary process; a summary of the Carter Administration's comprehensive radioactive waste management program; and excerpts from the text of relevant federal statutes and regulations.« less
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New Jersey state information handbook: Formerly Utilized Sites Remedial Action Program
DOE Office of Scientific and Technical Information (OSTI.GOV)
None
Under the implied authority of the Atomic Energy Act of 1954, as amended, radiological surveys and research work has been conducted to determine radiological conditions at former MED/AEC sites. As of this time, 31 sites in 13 states have been identified that require or may require remedial action. This volume is one of a series produced under contract with DOE, Office of Nuclear Waste Management, by POLITECH CORPORATION to develop a legislative and regulatory data base to assist the FUSRAP management in addressing the institutional and socioeconomic issues involved in carrying out the Remedial Action Program. This Information Handbook seriesmore » contains information about all relevant government agencies at the Federal and state levels, the pertinent programs they administer, each affected state legislature, and current Federal and state legislative and regulatory initiatives. This volume is a compilation of information about the state of New Jersey. It contains: a description of the state executive branch structure; a summary of relevant state statutes and regulations; a description of the structure of the state legislature, identification of the officers and committee chairmen, and a summary of recent relevant legislative action; and the full text of relevant statutes and regulations. The loose-leaf format used in these volumes will allow the material to be updated periodically as the Remedial Action Program progresses.« less
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Adaptation of A-to-I RNA editing in Drosophila
Zhang, Hong
2017-01-01
Adenosine-to-inosine (A-to-I) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach. However, it is challenging to provide evidences to support this hypothesis at the whole editome level. In this study, we systematically characterized 2,114 A-to-I RNA editing sites in female and male brains of D. melanogaster, and nearly half of these sites had events evolutionarily conserved across Drosophila species. We detected strong signatures of positive selection on the nonsynonymous editing sites in Drosophila brains, and the beneficial editing sites were significantly enriched in genes related to chemical and electrical neurotransmission. The signal of adaptation was even more pronounced for the editing sites located in X chromosome or for those commonly observed across Drosophila species. We identified a set of gene candidates (termed “PSEB” genes) that had nonsynonymous editing events favored by natural selection. We presented evidence that editing preferentially increased mutation sequence space of evolutionarily conserved genes, which supported the adaptive evolution hypothesis of editing. We found prevalent nonsynonymous editing sites that were favored by natural selection in female and male adults from five strains of D. melanogaster. We showed that temperature played a more important role than gender effect in shaping the editing levels, although the effect of temperature is relatively weaker compared to that of species effect. We also explored the relevant factors that shape the selective patterns of the global editomes. Altogether we demonstrated that abundant nonsynonymous editing sites in Drosophila brains were adaptive and maintained by natural selection during evolution. Our results shed new light on the evolutionary principles and functional consequences of RNA editing. PMID:28282384
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Evaluation of deep vadose zone contaminant flux into groundwater: Approach and case study
NASA Astrophysics Data System (ADS)
Oostrom, M.; Truex, M. J.; Last, G. V.; Strickland, C. E.; Tartakovsky, G. D.
2016-06-01
For sites with a contaminant source located in the vadose zone, the nature and extent of groundwater contaminant plumes are a function of the contaminant flux from the vadose zone to groundwater. Especially for thick vadose zones, transport may be relatively slow making it difficult to directly measure contaminant flux. An integrated assessment approach, supported by site characterization and monitoring data, is presented to explain current vadose zone contaminant distributions and to estimate future contaminant flux to groundwater in support of remediation decisions. The U.S. Department of Energy Hanford Site (WA, USA) SX Tank Farm was used as a case study because of a large existing contaminant inventory in its deep vadose zone, the presence of a limited-extent groundwater plume, and the relatively large amount of available data for the site. A predictive quantitative analysis was applied to refine a baseline conceptual model through the completion of a series of targeted simulations. The analysis revealed that site recharge is the most important flux-controlling process for future contaminant flux. Tank leak characteristics and subsurface heterogeneities appear to have a limited effect on long-term contaminant flux into groundwater. The occurrence of the current technetium-99 groundwater plume was explained by taking into account a considerable historical water-line leak adjacent to one of the tanks. The analysis further indicates that the vast majority of technetium-99 is expected to migrate into the groundwater during the next century. The approach provides a template for use in evaluating contaminant flux to groundwater using existing site data and has elements that are relevant to other disposal sites with a thick vadose zone.
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Holocaust Exposure Induced Intergenerational Effects on FKBP5 Methylation.
Yehuda, Rachel; Daskalakis, Nikolaos P; Bierer, Linda M; Bader, Heather N; Klengel, Torsten; Holsboer, Florian; Binder, Elisabeth B
2016-09-01
The involvement of epigenetic mechanisms in intergenerational transmission of stress effects has been demonstrated in animals but not in humans. Cytosine methylation within the gene encoding for FK506 binding protein 5 (FKBP5) was measured in Holocaust survivors (n = 32), their adult offspring (n = 22), and demographically comparable parent (n = 8) and offspring (n = 9) control subjects, respectively. Cytosine-phosphate-guanine sites for analysis were chosen based on their spatial proximity to the intron 7 glucocorticoid response elements. Holocaust exposure had an effect on FKBP5 methylation that was observed in exposed parents as well in their offspring. These effects were observed at bin 3/site 6. Interestingly, in Holocaust survivors, methylation at this site was higher in comparison with control subjects, whereas in Holocaust offspring, methylation was lower. Methylation levels for exposed parents and their offspring were significantly correlated. In contrast to the findings at bin 3/site 6, offspring methylation at bin 2/sites 3 to 5 was associated with childhood physical and sexual abuse in interaction with an FKBP5 risk allele previously associated with vulnerability to psychological consequences of childhood adversity. The findings suggest the possibility of site specificity to environmental influences, as sites in bins 3 and 2 were differentially associated with parental trauma and the offspring's own childhood trauma, respectively. FKBP5 methylation averaged across the three bins examined was associated with wake-up cortisol levels, indicating functional relevance of the methylation measures. This is the first demonstration of an association of preconception parental trauma with epigenetic alterations that is evident in both exposed parent and offspring, providing potential insight into how severe psychophysiological trauma can have intergenerational effects. Published by Elsevier Inc.
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Evaluation of deep vadose zone contaminant flux into groundwater: Approach and case study.
Oostrom, M; Truex, M J; Last, G V; Strickland, C E; Tartakovsky, G D
2016-06-01
For sites with a contaminant source located in the vadose zone, the nature and extent of groundwater contaminant plumes are a function of the contaminant flux from the vadose zone to groundwater. Especially for thick vadose zones, transport may be relatively slow making it difficult to directly measure contaminant flux. An integrated assessment approach, supported by site characterization and monitoring data, is presented to explain current vadose zone contaminant distributions and to estimate future contaminant flux to groundwater in support of remediation decisions. The U.S. Department of Energy Hanford Site (WA, USA) SX Tank Farm was used as a case study because of a large existing contaminant inventory in its deep vadose zone, the presence of a limited-extent groundwater plume, and the relatively large amount of available data for the site. A predictive quantitative analysis was applied to refine a baseline conceptual model through the completion of a series of targeted simulations. The analysis revealed that site recharge is the most important flux-controlling process for future contaminant flux. Tank leak characteristics and subsurface heterogeneities appear to have a limited effect on long-term contaminant flux into groundwater. The occurrence of the current technetium-99 groundwater plume was explained by taking into account a considerable historical water-line leak adjacent to one of the tanks. The analysis further indicates that the vast majority of technetium-99 is expected to migrate into the groundwater during the next century. The approach provides a template for use in evaluating contaminant flux to groundwater using existing site data and has elements that are relevant to other disposal sites with a thick vadose zone. Copyright © 2016 Elsevier B.V. All rights reserved.
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Evaluation of Deep Vadose Zone Contaminant Flux into Groundwater: Approach and Case Study
DOE Office of Scientific and Technical Information (OSTI.GOV)
Oostrom, Martinus; Truex, Michael J.; Last, George V.
For sites with a contaminant source located in the vadose zone, the nature and extent of groundwater contaminant plumes are a function of the contaminant flux from the vadose zone to groundwater. Especially for thick vadose zones, transport may be relatively slow making it difficult to directly measure contaminant flux. An integrated assessment approach, supported by site characterization and monitoring data, is presented to explain current vadose zone contaminant distributions and to estimate future contaminant flux to groundwater in support of remediation decisions. The U.S. Department of Energy Hanford Site (WA, USA) SX Tank Farm was used as a casemore » study because of a large existing contaminant inventory in its deep vadose zone, the presence of a limited-extent groundwater plume, and the relatively large amount of available data for the site. A predictive quantitative analysis was applied to refine a baseline conceptual model through the completion of a series of targeted simulations. The analysis revealed that site recharge is the most important flux-controlling process for future contaminant flux. Tank leak characteristics and subsurface heterogeneities appear to have a limited effect on long-term contaminant flux into groundwater. The occurrence of the current technetium-99 groundwater plume was explained by taking into account a considerable historical water-line leak adjacent to one of the tanks. The analysis further indicates that the vast majority of technetium-99 is expected to migrate into the groundwater during the next century. The approach provides a template for use in evaluating contaminant flux to groundwater using existing site data and has elements that are relevant to other disposal sites with a thick vadose zone.« less
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Zheng, Lu-Lu; Niu, Shen; Hao, Pei; Feng, KaiYan; Cai, Yu-Dong; Li, Yixue
2011-01-01
Pyrrolidone carboxylic acid (PCA) is formed during a common post-translational modification (PTM) of extracellular and multi-pass membrane proteins. In this study, we developed a new predictor to predict the modification sites of PCA based on maximum relevance minimum redundancy (mRMR) and incremental feature selection (IFS). We incorporated 727 features that belonged to 7 kinds of protein properties to predict the modification sites, including sequence conservation, residual disorder, amino acid factor, secondary structure and solvent accessibility, gain/loss of amino acid during evolution, propensity of amino acid to be conserved at protein-protein interface and protein surface, and deviation of side chain carbon atom number. Among these 727 features, 244 features were selected by mRMR and IFS as the optimized features for the prediction, with which the prediction model achieved a maximum of MCC of 0.7812. Feature analysis showed that all feature types contributed to the modification process. Further site-specific feature analysis showed that the features derived from PCA's surrounding sites contributed more to the determination of PCA sites than other sites. The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations. PMID:22174779
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Weber, David; Heisig, Julia; Kneitz, Susanne; Wolf, Elmar; Eilers, Martin; Gessler, Manfred
2015-02-01
Hey bHLH transcription factors are critical effectors of Notch signaling. During mammalian heart development they are expressed in atrial and ventricular cardiomyocytes and in the developing endocardium. Hey knockout mice suffer from lethal cardiac defects, such as ventricular septum defects, valve defects and cardiomyopathy. Despite this functional relevance, little is known about the regulation of downstream targets in relevant cell types. The objective of this study was to elucidate the regulatory mechanisms by which Hey proteins affect gene expression in a cell type specific manner. We used an in vitro cardiomyocyte differentiation system with inducible Hey1 or Hey2 expression to study target gene regulation in cardiomyocytes (CM) generated from murine embryonic stem cells (ESC). The effects of Hey1 and Hey2 are largely redundant, but cell type specific. The number of regulated genes is comparable between ESC and CM, but the total number of binding sites is much higher, especially in ESC, targeting mainly genes involved in transcriptional regulation and developmental processes. Repression by Hey proteins generally correlates with the extent of Hey-binding to target promoters, Hdac recruitment and lower histone acetylation. Functionally, treatment with the Hdac inhibitor TSA abolished Hey target gene regulation. However, in CM the repressive effect of Hey-binding is lost for a subset of genes. These also lack Hey-dependent histone deacetylation in CM and are enriched for binding sites of cardiac specific activators like Srf, Nkx2-5, and Gata4. Ectopic Nkx2-5 overexpression in ESC blocks Hey-mediated repression of these genes. Thus, Hey proteins mechanistically repress target genes via Hdac recruitment and histone deacetylation. In CM Hey-repression is counteracted by cardiac activators, which recruit histone acetylases and prevent Hey mediated deacetylation and subsequent repression for a subset of genes. Copyright © 2014 Elsevier Ltd. All rights reserved.
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Jacobsen, Jacob P R; Plenge, Per; Sachs, Benjamin D; Pehrson, Alan L; Cajina, Manuel; Du, Yunzhi; Roberts, Wendy; Rudder, Meghan L; Dalvi, Prachiti; Robinson, Taylor J; O'Neill, Sharon P; Khoo, King S; Morillo, Connie Sanchez; Zhang, Xiaodong; Caron, Marc G
2014-12-01
Escitalopram appears to be a superior antidepressant to racemic citalopram. It has been hypothesized that binding of R-citalopram to the serotonin transporter (SERT) antagonizes escitalopram binding to and inhibition of the SERT, there by curtailing the elevation of extracellular 5-hydroxytryptamine (5-HTExt), and hence anti-depressant efficacy. Further, it has been suggested that a putative allosteric binding site is important for binding of escitalopram to the primary, orthosteric, site, and for R-citalopram's inhibition here of. Primary: Investigate at the human (h)SERT, at clinical relevant doses, whether R-citalopram antagonizes escitalopram-induced 5-HTExt elevation. Secondary: Investigate whether abolishing the putative allosteric site affects escitalopram-induced 5-HTExt elevation and/or modulates the effect of R-citalopram. Recombinant generation of hSERT transgenic mice; in vivo microdialysis; SERT binding; pharmacokinetics; 5-HT sensitive behaviors (tail suspension, marble burying). We generated mice expressing either the wild-type human SERT (hSERT(WT)) or hSERT carrying amino acid substitutions (A505V, L506F, I507L, S574T and I575T) collectively abolishing the putative allosteric site (hSERT(ALI/VFL+SI/TT)). One mg/kg escitalopram yielded clinical relevant plasma levels and brain levels consistent with therapeutic SERT occupancy. The hSERT mice showed normal basal 5-HTExt levels. Escitalopram-induced 5-HTExt elevation was not decreased by R-citalopram co-treatment and was unaffected by loss of the allosteric site. The behavioral effects of the clinically relevant escitalopram dose were small and tended to be enhanced by R-citalopram co-administration. We find no evidence that R-citalopram directly antagonizes escitalopram or that the putative allosteric site is important for hSERT inhibition by escitalopram.
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The Integron: Adaptation On Demand.
Escudero, José Antonio; Loot, Céline; Nivina, Aleksandra; Mazel, Didier
2015-04-01
The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".
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Barberà, M; Martínez-Torres, D
2017-10-01
Insect hormones control essential aspects of physiology, behaviour and development in insects. The majority of insect hormones are peptide hormones that perform a highly diverse catalogue of functions. Prothoracicotropic hormone (PTTH) is a brain neuropeptide hormone whose main function is to stimulate the secretion of ecdysone (the moulting hormone) by the prothoracic glands in insect larvae thus playing a key role in the control of moulting and metamorphosis. Moreover, both PTTH release or blockade have been reported to act as a switch to terminate or initiate larval and pupal diapauses. In insects, diapause is a prevalent response often regulated by the photoperiod. It has been shown that PTTH participates as an output of the circadian clock and a role in photoperiodic processes is suggested in some insect species. Aphids (Hemiptera: Aphididae) reproduce by cyclical parthenogenesis with a sexual phase, induced by short photoperiods, that leads to the production of diapausing eggs. With the availability of the pea aphid (Acyrthosiphon pisum) genome, efforts to identify and characterize genes relevant to essential aspects of aphid biology have multiplied. In spite of its relevance, several genomic and transcriptomic studies on aphid neuropeptides failed to detect aphid PTTH amongst them. Here we report on the first identification of the aphid PTTH coding gene and the neuroanatomical localization of its expression in the aphid brain. © 2017 The Royal Entomological Society.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Kriger, A.
1978-01-31
This report is a part of the interim report documentation for the Global Spent Fuel Logistics System (GSFLS) study. The technical and financial considerations underlying a global spent fuel logistics systems have been studied and are reported. The Pacific Basin is used as a model throughout this report; however the stated methodology and, in many cases, considerations and conclusions are applicable to other global regions. Spent fuel discharge profiles for Pacific Basin Countries were used to determine the technical systems requirements for alternative concepts. Functional analyses and flows were generated to define both system design requirements and logistics parameters. Amore » technology review was made to ascertain the state-of-the-art of relevant GSFLS technical systems. Modular GSFLS facility designs were developed using the information generated from the functional analysis and technology review. The modular facility designs were used as a basis for siting and cost estimates for various GSFLS alternatives. Various GSFLS concepts were analyzed from a financial and economic perspective in order to provide total concepts costs and ascertain financial and economic sensitivities to key GSFLS variations. Results of the study include quantification of GSFLS facility and hardware requirements; drawings of relevant GSFLS facility designs; system cost estimates; financial reports - including user service charges; and comparative analyses of various GSFLS alternatives.« less
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Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.
2012-01-01
Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA) (PLoS One 6(1): e15827), for partitioning the conformational landscape into a hierarchy of functionally relevant sub-states. The unique capabilities of QAA are enabled by exploiting anharmonicity in the form of fourth-order statistics for characterizing atomic fluctuations. In this paper, we extend QAA for analyzing long time-scale simulations online. In particular, we present HOST4MD - a higher-order statistical toolbox for molecular dynamics simulations, which (1) identifies key dynamical events as simulations are in progress, (2) explores potential sub-states and (3) identifies conformational transitions that enable the protein to access those sub-states. We demonstrate HOST4MD on micro-second time-scale simulations of the enzyme adenylate kinase in its apo state. HOST4MD identifies several conformational events in these simulations, revealing how the intrinsic coupling between the three sub-domains (LID, CORE and NMP) changes during the simulations. Further, it also identifies an inherent asymmetry in the opening/closing of the two binding sites. We anticipate HOST4MD will provide a powerful and extensible framework for detecting biophysically relevant conformational coordinates from long time-scale simulations. PMID:22733562
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Altermann, Eric; Lu, Jingli; McCulloch, Alan
2017-01-01
Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use. PMID:28386247
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Altermann, Eric; Lu, Jingli; McCulloch, Alan
2017-01-01
Expert curated annotation remains one of the critical steps in achieving a reliable biological relevant annotation. Here we announce the release of GAMOLA2, a user friendly and comprehensive software package to process, annotate and curate draft and complete bacterial, archaeal, and viral genomes. GAMOLA2 represents a wrapping tool to combine gene model determination, functional Blast, COG, Pfam, and TIGRfam analyses with structural predictions including detection of tRNAs, rRNA genes, non-coding RNAs, signal protein cleavage sites, transmembrane helices, CRISPR repeats and vector sequence contaminations. GAMOLA2 has already been validated in a wide range of bacterial and archaeal genomes, and its modular concept allows easy addition of further functionality in future releases. A modified and adapted version of the Artemis Genome Viewer (Sanger Institute) has been developed to leverage the additional features and underlying information provided by the GAMOLA2 analysis, and is part of the software distribution. In addition to genome annotations, GAMOLA2 features, among others, supplemental modules that assist in the creation of custom Blast databases, annotation transfers between genome versions, and the preparation of Genbank files for submission via the NCBI Sequin tool. GAMOLA2 is intended to be run under a Linux environment, whereas the subsequent visualization and manual curation in Artemis is mobile and platform independent. The development of GAMOLA2 is ongoing and community driven. New functionality can easily be added upon user requests, ensuring that GAMOLA2 provides information relevant to microbiologists. The software is available free of charge for academic use.
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McDowell, S. Elizabeth; Jun, Jesse M.; Walter, Nils G.
2010-01-01
Enzymes generally are thought to derive their functional activity from conformational motions. The limited chemical variation in RNA suggests that such structural dynamics may play a particularly important role in RNA function. Minimal hammerhead ribozymes are known to cleave efficiently only in ∼10-fold higher than physiologic concentrations of Mg2+ ions. Extended versions containing native loop–loop interactions, however, show greatly enhanced catalytic activity at physiologically relevant Mg2+ concentrations, for reasons that are still ill-understood. Here, we use Mg2+ titrations, activity assays, ensemble, and single molecule fluorescence resonance energy transfer (FRET) approaches, combined with molecular dynamics (MD) simulations, to ask what influence the spatially distant tertiary loop–loop interactions of an extended hammerhead ribozyme have on its structural dynamics. By comparing hammerhead variants with wild-type, partially disrupted, and fully disrupted loop–loop interaction sequences we find that the tertiary interactions lead to a dynamic motional sampling that increasingly populates catalytically active conformations. At the global level the wild-type tertiary interactions lead to more frequent, if transient, encounters of the loop-carrying stems, whereas at the local level they lead to an enrichment in favorable in-line attack angles at the cleavage site. These results invoke a linkage between RNA structural dynamics and function and suggest that loop–loop interactions in extended hammerhead ribozymes—and Mg2+ ions that bind to minimal ribozymes—may generally allow more frequent access to a catalytically relevant conformation(s), rather than simply locking the ribozyme into a single active state. PMID:20921269
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Contaminant-associated health effects in fishes from the Ottawa and Ashtabula Rivers, Ohio
Iwanowicz, Luke R.; Blazer, Vicki S.; Walsh, Heather L.; Shaw, Cassidy H.; DeVault, David S.; Banda, Jo A.
2018-01-01
The health of resident fishes serves as a biologically relevant barometer of aquatic ecosystem integrity. Here, the health of the Ottawa River and Ashtabula River (both within the Lake Erie Basin) were assessed using morphological and immunological biomarkers in brown bullheads (Ameiurus nebulosus) and largemouth bass (Micropterus salmoides). Biomarker metrics were compared to fish collected from a reference site (Conneaut Creek). Data utilized for analyses were collected between 2003 and 2011. Fish collected from all three river systems had markedly different contaminant profiles. Total PCBs were the dominant contaminant class by mass. In bullhead, PCBs were highest in fish from the Ashtabula River and there were no differences in fish collected pre- or post-remediation of Ashtabula Harbor (median = 4.6 and 5.5 mg/kg respectively). Excluding PCBs, the Ottawa River was dominated by organochlorine pesticides. Liver tumor prevalence exceeded the 5% trigger level at both the Ashtabula (7.7%) and Ottawa Rivers (10.2%), but was not statistically different than that at the reference site. There was no statistically significant association between microscopic lesions, gross pathology and contaminant body burdens. Collectively, contaminant body burdens were generally negatively correlated with functional immune responses including bactericidal, cytotoxic-cell and respiratory burst activity in both species. Exceptions were positive correlations of HCB and heptachlor epoxide with respiratory burst activity in largemouth bass, and HCB with respiratory burst activity in bullhead and ΣBHC for all three functional assays in bullhead. Data here provide additional support that organochlorine contamination is associated with immunomodulation, and that species differences exist within sites.
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Papaleo, Elena; Renzetti, Giulia; Tiberti, Matteo
2012-01-01
Protein dynamics and the underlying networks of intramolecular interactions and communicating residues within the three-dimensional (3D) structure are known to influence protein function and stability, as well as to modulate conformational changes and allostery. Acylaminoacyl peptidase (AAP) subfamily of enzymes belongs to a unique class of serine proteases, the prolyl oligopeptidase (POP) family, which has not been thoroughly investigated yet. POPs have a characteristic multidomain three-dimensional architecture with the active site at the interface of the C-terminal catalytic domain and a β-propeller domain, whose N-terminal region acts as a bridge to the hydrolase domain. In the present contribution, protein dynamics signatures of a hyperthermophilic acylaminoacyl peptidase (AAP) of the prolyl oligopeptidase (POP) family, as well as of a deletion variant and alanine mutants (I12A, V13A, V16A, L19A, I20A) are reported. In particular, we aimed at identifying crucial residues for long range communications to the catalytic site or promoting the conformational changes to switch from closed to open ApAAP conformations. Our investigation shows that the N-terminal α1-helix mediates structural intramolecular communication to the catalytic site, concurring to the maintenance of a proper functional architecture of the catalytic triad. Main determinants of the effects induced by α1-helix are a subset of hydrophobic residues (V16, L19 and I20). Moreover, a subset of residues characterized by relevant interaction networks or coupled motions have been identified, which are likely to modulate the conformational properties at the interdomain interface. PMID:22558199
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Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James; Hermida, Leandro; Primig, Michael
2007-01-01
We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at http://www.germonline.org/.
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Chemotaxing and haptotaxing random walkers having directional persistence
NASA Astrophysics Data System (ADS)
Kwon, Tae Goo; Kyoungjin Lee Team; Taeseok Daniel Yang Team
2015-03-01
Biological cell crawling is a rather complex process involving various bio-chemical and bio-mechanical processes, many of which are still not well understood. The difficulties in understanding the crawling are originating not just from cell-intrinsic factors but from their complex social interactions, cell-to-substrate interactions and nonlinear responses toward extrinsic factors. Here, in this report we investigate chemotactic behavior of mathematical model cells that naturally have directional persistence. A cell density is measured as a function of time and space, then the resulting steady state is compared with that of the well-known Keller-Segal model, which describes a population of chemotactic random walker. Then, we add a cell-to-cell interaction, mimicking a ``haptotaxis'' mediated interaction, to the model and access its role as for altering the steady-state cell density profile. This mathematical model system, which we have developed and considered in this work, can be quite relevant to the chemotactic responses of interacting immune cells, like microglia, moving toward and around a site of wound, as for an example. We conclude by discussing some relevant recent experimental findings.
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González-Alvarez, I; Fernández-Teruel, C; Garrigues, T M; Casabo, V G; Ruiz-García, A; Bermejo, M
2005-12-01
The purpose was to develop a general mathematical model for estimating passive permeability and efflux transport parameters from in vitro cell culture experiments. The procedure is applicable for linear and non-linear transport of drug with time, <10 or >10% of drug transport, negligible or relevant back flow, and would allow the adequate correction in the case of relevant mass balance problems. A compartmental kinetic approach was used and the transport barriers were described quantitatively in terms of apical and basolateral clearances. The method can be applied when sink conditions are not achieved and it allows the evaluation of the location of the transporter and its binding site. In this work it was possible to demonstrate, from a functional point of view, the higher efflux capacity of the TC7 clone and to identify the apical membrane as the main resistance for the xenobiotic transport. This methodology can be extremely useful as a complementary tool for molecular biology approaches in order to establish meaningful hypotheses about transport mechanisms.
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Yu, Yi-Kuo; Capra, John A.; Stojmirović, Aleksandar; Landsman, David; Altschul, Stephen F.
2015-01-01
Motivation: DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. Results: We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column’s observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. Availability and implementation: Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. Contact: altschul@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25294922
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DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1996-10-01
This document contains the appendixes for the remedial investigation and feasibility study for the David Witherspoon, Inc., 901 site in Knoxville, Tennessee. The following topics are covered in the appendixes: (A) David Witherspoon, Inc., 901 Site Historical Data, (B) Fieldwork Plans for the David Witherspoon, Inc., 901 Site, (C) Risk Assessment, (D) Remediation Technology Discussion, (E) Engineering Support Documentation, (F) Applicable or Relevant and Appropriate Requirements, and (G) Cost Estimate Documentation.
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POPcorn: A PrOject Portal for corn
USDA-ARS?s Scientific Manuscript database
The rapidly increasing quantity of maize data available on the Internet means that locating and searching for relevant data and information is increasingly difficult for maize researchers. Finding appropriate sites and then learning how to navigate the sites can be difficult and time-consuming. Find...
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10 CFR 503.33 - Site limitations.
Code of Federal Regulations, 2011 CFR
2011-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... types of site limitations to which a petitioner may certify in order to qualify for this exemption include: (i) Inaccessibility of alternate fuels as a result of a specific physical limitation; (ii...
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10 CFR 503.33 - Site limitations.
Code of Federal Regulations, 2013 CFR
2013-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... types of site limitations to which a petitioner may certify in order to qualify for this exemption include: (i) Inaccessibility of alternate fuels as a result of a specific physical limitation; (ii...
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10 CFR 503.33 - Site limitations.
Code of Federal Regulations, 2014 CFR
2014-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... types of site limitations to which a petitioner may certify in order to qualify for this exemption include: (i) Inaccessibility of alternate fuels as a result of a specific physical limitation; (ii...
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10 CFR 503.33 - Site limitations.
Code of Federal Regulations, 2012 CFR
2012-01-01
... more specific physical limitations relevant to the location or operation of the proposed facility exist... types of site limitations to which a petitioner may certify in order to qualify for this exemption include: (i) Inaccessibility of alternate fuels as a result of a specific physical limitation; (ii...
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40 CFR 60.1115 - What is a siting analysis?
Code of Federal Regulations, 2010 CFR
2010-07-01
... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What is a siting analysis? 60.1115 Section 60.1115 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS... unit affects ambient air quality, visibility, soils, vegetation, and other relevant factors. The...
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A Vision for the Future: Site-Based Strategic Planning.
ERIC Educational Resources Information Center
Herman, Jerry J.
1989-01-01
Presents a model to help principals with strategic planning. Success hinges on involving stakeholders, scanning for relevant data, identifying critical success factors, developing vision and mission statements, analyzing the site manager's supports and constraints, creating strategic goals and objectives, developing action plans, allocating…
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COSTS AND ISSUES RELATED TO REMEDIATION OF PETROLEUM-CONTAMINATED SITES
The remediation costs required at sites contaminated with petroleum-derived compounds remains a relevant issue because of the large number of existing underground storage tanks the United States and the presence of benzene, MTBE, and TBA in some drinking water supplies. Cost inf...
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Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.
Edlefsen, Paul T; Rolland, Morgane; Hertz, Tomer; Tovanabutra, Sodsai; Gartland, Andrew J; deCamp, Allan C; Magaret, Craig A; Ahmed, Hasan; Gottardo, Raphael; Juraska, Michal; McCoy, Connor; Larsen, Brendan B; Sanders-Buell, Eric; Carrico, Chris; Menis, Sergey; Kijak, Gustavo H; Bose, Meera; Arroyo, Miguel A; O'Connell, Robert J; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Rerks-Ngarm, Supachai; Robb, Merlin L; Kirys, Tatsiana; Georgiev, Ivelin S; Kwong, Peter D; Scheffler, Konrad; Pond, Sergei L Kosakovsky; Carlson, Jonathan M; Michael, Nelson L; Schief, William R; Mullins, James I; Kim, Jerome H; Gilbert, Peter B
2015-02-01
The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or "signatures" and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens.
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Comprehensive Sieve Analysis of Breakthrough HIV-1 Sequences in the RV144 Vaccine Efficacy Trial
Edlefsen, Paul T.; Rolland, Morgane; Hertz, Tomer; Tovanabutra, Sodsai; Gartland, Andrew J.; deCamp, Allan C.; Magaret, Craig A.; Ahmed, Hasan; Gottardo, Raphael; Juraska, Michal; McCoy, Connor; Larsen, Brendan B.; Sanders-Buell, Eric; Carrico, Chris; Menis, Sergey; Bose, Meera; Arroyo, Miguel A.; O’Connell, Robert J.; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Rerks-Ngarm, Supachai; Robb, Merlin L.; Kirys, Tatsiana; Georgiev, Ivelin S.; Kwong, Peter D.; Scheffler, Konrad; Pond, Sergei L. Kosakovsky; Carlson, Jonathan M.; Michael, Nelson L.; Schief, William R.; Mullins, James I.; Kim, Jerome H.; Gilbert, Peter B.
2015-01-01
The RV144 clinical trial showed the partial efficacy of a vaccine regimen with an estimated vaccine efficacy (VE) of 31% for protecting low-risk Thai volunteers against acquisition of HIV-1. The impact of vaccine-induced immune responses can be investigated through sieve analysis of HIV-1 breakthrough infections (infected vaccine and placebo recipients). A V1/V2-targeted comparison of the genomes of HIV-1 breakthrough viruses identified two V2 amino acid sites that differed between the vaccine and placebo groups. Here we extended the V1/V2 analysis to the entire HIV-1 genome using an array of methods based on individual sites, k-mers and genes/proteins. We identified 56 amino acid sites or “signatures” and 119 k-mers that differed between the vaccine and placebo groups. Of those, 19 sites and 38 k-mers were located in the regions comprising the RV144 vaccine (Env-gp120, Gag, and Pro). The nine signature sites in Env-gp120 were significantly enriched for known antibody-associated sites (p = 0.0021). In particular, site 317 in the third variable loop (V3) overlapped with a hotspot of antibody recognition, and sites 369 and 424 were linked to CD4 binding site neutralization. The identified signature sites significantly covaried with other sites across the genome (mean = 32.1) more than did non-signature sites (mean = 0.9) (p < 0.0001), suggesting functional and/or structural relevance of the signature sites. Since signature sites were not preferentially restricted to the vaccine immunogens and because most of the associations were insignificant following correction for multiple testing, we predict that few of the genetic differences are strongly linked to the RV144 vaccine-induced immune pressure. In addition to presenting results of the first complete-genome analysis of the breakthrough infections in the RV144 trial, this work describes a set of statistical methods and tools applicable to analysis of breakthrough infection genomes in general vaccine efficacy trials for diverse pathogens. PMID:25646817
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Portable bioreactor for perfusion and electrical stimulation of engineered cardiac tissue.
Tandon, Nina; Taubman, Alanna; Cimetta, Elisa; Saccenti, Laetitia; Vunjak-Novakovic, Gordana
2013-01-01
Cardiac tissue engineering aims to create functional tissue constructs that can reestablish the structure and function of injured myocardium. Although bioreactors have facilitated the engineering of cardiac patches of clinically relevant size in vitro, a major drawback remains the transportation of the engineered tissues from a production facility to a medical operation facility while maintaining tissue viability and preventing contamination. Furthermore, after implantation, most of the cells are endangered by hypoxic conditions that exist before vascular flow is established. We developed a portable device that provides the perfusion and electrical stimulation necessary to engineer cardiac tissue in vitro, and to transport it to the site where it will be implantated. The micropump-powered perfusion apparatus may additionally function as an extracorporeal active pumping system providing nutrients and oxygen supply to the graft post-implantation. Such a system, through perfusion of oxygenated media and bioactive molecules (e.g. growth factors), could transiently support the tissue construct until it connects to the host vasculature and heart muscle, after which it could be taken away or let biodegrade.
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The Genetics of the Thyroid Stimulating Hormone Receptor: History and Relevance
Yin, Xiaoming; Latif, Rauf
2010-01-01
Background The thyroid stimulating hormone receptor (TSHR) is the key regulator of thyrocyte function. The gene for the TSHR on chromosome 14q31 has been implicated as coding for the major autoantigen in the autoimmune hyperthyroidism of Graves' disease (GD) to which T cells and autoantibodies are directed. Summary The TSHR is a seven-transmembrane domain receptor that undergoes complex posttranslational processing. In this brief review, we look at the genetics of this important autoantigen and its influence on a variety of tissue functions in addition to its role in the induction of GD. Conclusions There is convincing evidence that the TSH receptor gene confers increased susceptibility for GD, but not Hashimoto's thyroiditis. GD is associated with polymorphisms in the intron 1 gene region. How such noncoding nucleotide changes influence disease susceptibility remains uncertain, but is likely to involve TSHR splicing variants and/or microRNAs arising from this gene region. Whether such influences are confined to the thyroid gland or whether they influence cell function in the many extrathyroidal sites of TSHR expression remains unknown. PMID:20578897
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NASA Astrophysics Data System (ADS)
Korotana, R.; Mallia, G.; Gercsi, Z.; Liborio, L.; Harrison, N. M.
2014-05-01
Hybrid-exchange density functional theory calculations are carried out to determine the effects of A-site doping on the electronic and magnetic properties of the manganite series La1-xCaxMnO3. This study focuses on the ground state of an ordered Ca occupancy in a periodic structure. It is shown that the hybrid-exchange functional, Becke three-parameter Lee-Yang-Parr (B3LYP), provides an accurate and consistent description of the electronic structure for LaMnO3, CaMnO3, and La0.75Ca0.25MnO3. We have quantified the relevant structural, magnetic, and electronic energy contributions to the stability of the doped compound. An insight into the exchange coupling mechanism for the low hole density region of the phase diagram, where a polaron (anti-Jahn-Teller) forms, is also provided. This study completes a microscopic description of the lightly doped insulator with an antiferromagnetic-to-ferromagnetic and metal-to-insulator transition.
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Monoamine oxidases as sources of oxidants in the heart
Kaludercic, Nina; Mialet-Perez, Jeanne; Paolocci, Nazareno; Parini, Angelo; Di Lisa, Fabio
2014-01-01
Oxidative stress can be generated at several sites within the mitochondria. Among these, monoamine oxidases (MAO) have been described as a prominent source. MAO are mitochondrial flavoenzymes responsible for the oxidative deamination of catecholamines, serotonin and biogenic amines, and during this process they generate H2O2 and aldehyde intermediates. The role of MAO in cardiovascular pathophysiology has only recently gathered some attention since it has been demonstrated that both H2O2 and aldehydes may target mitochondrial function and consequently affect function and viability of the myocardium. In the present review, we will discuss the role of MAO in catecholamine and serotonin clearance and cycling in relation to cardiac structure and function. The relevant contribution of each MAO isoform (MAO-A or -B) will be discussed in relation to mitochondrial dysfunction and myocardial injury. Finally, we will examine both beneficial effects of their pharmacological or genetic inhibition along with potential adverse effects observed at baseline in MAO knockout mice, as well as the deleterious effects following their over-expression specifically at cardiomyocyte level. PMID:24412580
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Hellmann, Christine; Große-Stoltenberg, André; Thiele, Jan; Oldeland, Jens; Werner, Christiane
2017-06-23
Spatial heterogeneity of ecosystems crucially influences plant performance, while in return plant feedbacks on their environment may increase heterogeneous patterns. This is of particular relevance for exotic plant invaders that transform native ecosystems, yet, approaches integrating geospatial information of environmental heterogeneity and plant-plant interaction are lacking. Here, we combined remotely sensed information of site topography and vegetation cover with a functional tracer of the N cycle, δ 15 N. Based on the case study of the invasion of an N 2 -fixing acacia in a nutrient-poor dune ecosystem, we present the first model that can successfully predict (R 2 = 0.6) small-scale spatial variation of foliar δ 15 N in a non-fixing native species from observed geospatial data. Thereby, the generalized additive mixed model revealed modulating effects of heterogeneous environments on invader impacts. Hence, linking remote sensing techniques with tracers of biological processes will advance our understanding of the dynamics and functioning of spatially structured heterogeneous systems from small to large spatial scales.
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Towards identifying the next generation of superfund and hazardous waste site contaminants
Ela, Wendell P.; Sedlak, David L.; Barlaz, Morton A.; Henry, Heather F.; Muir, Derek C.G.; Swackhamer, Deborah L.; Weber, Eric J.; Arnold, Robert G.; Ferguson, P. Lee; Field, Jennifer A.; Furlong, Edward T.; Giesy, John P.; Halden, Rolf U.; Henry, Tala; Hites, Ronald A.; Hornbuckle, Keri C.; Howard, Philip H.; Luthy, Richard G.; Meyer, Anita K.; Saez, A. Eduardo; vom Saal, Frederick S.; Vulpe, Chris D.; Wiesner, Mark R.
2011-01-01
Conclusions A need exists for a carefully considered and orchestrated expansion of programmatic and research efforts to identify, evaluate, and manage CECs of hazardous waste site relevance, including developing an evolving list of priority CECs, intensifying the identification and monitoring of likely sites of present or future accumulation of CECs, and implementing efforts that focus on a holistic approach to prevention.
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Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.
Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A
2015-01-01
Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity.
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ERIC Educational Resources Information Center
Lowrie, Anthony
2008-01-01
Purpose: The purpose of this paper is to illustrate how language functions to construct relevance at moments of articulation and how language functions as an aggressive marketing practice to promote a self-regulated (production-oriented) system of accreditation. Design/methodology/approach: Drawing on the political theory of Laclau and Lacanian…
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Structure of Drosophila Oskar reveals a novel RNA binding protein
Yang, Na; Yu, Zhenyu; Hu, Menglong; Wang, Mingzhu; Lehmann, Ruth; Xu, Rui-Ming
2015-01-01
Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix–fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3′UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3′UTRs, and provide structural insights into a novel protein–RNA interaction motif involving a hydrolase-related domain. PMID:26324911
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Shenoy, Dinesh; Fu, Wei; Li, Jane; Crasto, Curtis; Jones, Graham; DiMarzio, Charles; Sridhar, Srinivas; Amiji, Mansoor
2006-01-01
For the development of surface-functionalized gold nanoparticles as cellular probes and delivery agents, we have synthesized hetero-bifunctional poly(ethylene glycol) (PEG, MW 1500) having a thiol group on one terminus and a reactive functional group on the other for use as a flexible spacer. Coumarin, a model fluorescent dye, was conjugated to one end of the PEG spacer and gold nanoparticles were modified with coumarin-PEG-thiol. Surface attachment of coumarin through the PEG spacer decreased the fluorescence quenching effect of gold nanoparticles. The results of cellular cytotoxicity and fluorescence confocal analyses showed that the PEG spacer-modified nanoparticles were essentially non-toxic and could be efficiently internalized in the cells within 1 hour of incubation. Intracellular particle tracking using a Keck 3-D Fusion Microscope System showed that the functionalized gold nanoparticles were rapidly internalized in the cells and localized in the peri-nuclear region. Using the PEG spacer, the gold nano-platform can be conjugated with a variety of biologically relevant ligands such as fluorescent dyes, antibodies, etc in order to target, probe, and induce a stimulus at the target site. PMID:16467923
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Puttini, Stefania; Ouvrard-Pascaud, Antoine; Palais, Gael; Beggah, Ahmed T; Gascard, Philippe; Cohen-Tannoudji, Michel; Babinet, Charles; Blot-Chabaud, Marcel; Jaisser, Frederic
2005-03-16
Functional genomic analysis is a challenging step in the so-called post-genomic field. Identification of potential targets using large-scale gene expression analysis requires functional validation to identify those that are physiologically relevant. Genetically modified cell models are often used for this purpose allowing up- or down-expression of selected targets in a well-defined and if possible highly differentiated cell type. However, the generation of such models remains time-consuming and expensive. In order to alleviate this step, we developed a strategy aimed at the rapid and efficient generation of genetically modified cell lines with conditional, inducible expression of various target genes. Efficient knock-in of various constructs, called targeted transgenesis, in a locus selected for its permissibility to the tet inducible system, was obtained through the stimulation of site-specific homologous recombination by the meganuclease I-SceI. Our results demonstrate that targeted transgenesis in a reference inducible locus greatly facilitated the functional analysis of the selected recombinant cells. The efficient screening strategy we have designed makes possible automation of the transfection and selection steps. Furthermore, this strategy could be applied to a variety of highly differentiated cells.
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Callard, G V; Tchoudakova, A V; Kishida, M; Wood, E
2001-12-01
Teleost fish are characterized by exceptionally high levels of brain estrogen biosynthesis when compared to the brains of other vertebrates or to the ovaries of the same fish. Goldfish (Carassius auratus) and zebrafish (Danio rerio) have utility as complementary models for understanding the molecular basis and functional significance of exaggerated neural estrogen biosynthesis. Multiple cytochrome P450 aromatase (P450arom) cDNAs that derive from separate gene loci (cyp19a and cyp19b) are differentially expressed in brain (P450aromB>A) and ovary (P450aromA>B) and have a different developmental program (B>A) and response to estrogen upregulation (B only). As measured by increased P450aromB mRNA, a functional estrogen response system is first detected 24-48 h post-fertilization (hpf), consistent with the onset of estrogen receptor (ER) expression (alpha, beta, and gamma). The 5'-flanking region of the cyp19b gene has a TATA box, two estrogen response elements (EREs), an ERE half-site (ERE1/2), a nerve growth factor inducible-B protein (NGFI-B)/Nur77 responsive element (NBRE) binding site, and a sequence identical to the zebrafish GATA-2 gene neural specific enhancer. The cyp19a promoter region has TATA and CAAT boxes, a steroidogenic factor-1 (SF-1) binding site, and two aryl hydrocarbon receptor (AhR)/AhR nuclear translocator factor (ARNT) binding motifs. Both genes have multiple potential SRY/SOX binding sites (16 and 8 in cyp19b and cyp19a, respectively). Luciferase reporters have basal promoter activity in GH3 cells, but differences (a>b) are opposite to fish pituitary (b>a). When microinjected into fertilized zebrafish eggs, a cyp19b promoter-driven green fluorescent protein (GFP) reporter (but not cyp19a) is expressed in neurons of 30-48 hpf embryos, most prominently in retinal ganglion cells (RGCs) and their projections to optic tectum. Further studies are required to identify functionally relevant cis-elements and cellular factors, and to determine the regulatory role of estrogen in neurodevelopment.
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Cady, Sarah; Wang, Tuo; Hong, Mei
2011-01-01
The influenza A M2 protein forms a proton channel for virus infection and also mediates virus assembly and budding. The minimum protein length that encodes both functions contains the transmembrane (TM) domain (roughly residues 22 to 46) for the amantadine-sensitive proton-channel activity and an amphipathic cytoplasmic helix (roughly residues 45 to 62) for curvature induction and virus budding. However, structural studies involving the TM domain with or without the amphipathic helix differed on the drug-binding site. Here we use solid-state NMR spectroscopy to determine the amantadine binding site in the cytoplasmic-helix-containing M2(21–61). 13C-2H distance measurements of 13C-labeled protein and 2H-labeled amantadine showed that in DMPC bilayers, the first equivalent of drug bound S31 inside the M2(21–61) pore, similar to the behavior of M2TM in DMPC bilayers. The non-specific surface site of D44 observed in M2TM is disfavored in the longer peptide. Thus, the pharmacologically relevant drug-binding site in the fully functional M2(21–61) is S31 in the TM pore. Interestingly, when M2(21–61) was reconstituted into a virus-mimetic membrane containing 30% cholesterol, no chemical shift perturbation was observed for pore-lining residues, while M2TM in the same membrane exhibited drug-induced chemical shift changes. Reduction of the cholesterol level and the use of unsaturated phospholipids shifted the conformational equilibrium of M2TM fully to the bound state, but did not rescue drug binding to M2(21–61). These results suggest that the amphipathic helix, together with cholesterol, modulates the ability of the TM helices to bind amantadine. Thus, the M2 protein interacts with the lipid membrane and small-molecule inhibitors in a complex fashion, and a careful examination of the environmental dependence of the protein conformation is required to fully understand the structure-function relation of this protein. PMID:21661724
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MONITORING FOR POLICY-RELEVANT REGIONAL TRENDS OVER TIME
The term trend describes the continuing directional change in the value of an indicator, generally upward or generally downward. Many policy questions concern trend across a number of sites, such as lakes in a region, rather than trend at a single site. Power to detect regional t...
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Proactively Teaching Technology Ethics
ERIC Educational Resources Information Center
Johnson, Doug
2004-01-01
This article presents certain advice to librarians on online ethical conduct. It is very important for librarians to talk to their students and clear the permissible limit of what is allowed and what is not. Librarians should teach some strategies about using clues in search results to discriminate between relevant and non-relevant Web sites.…
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Human germline and pan-cancer variomes and their distinct functional profiles
Pan, Yang; Karagiannis, Konstantinos; Zhang, Haichen; Dingerdissen, Hayley; Shamsaddini, Amirhossein; Wan, Quan; Simonyan, Vahan; Mazumder, Raja
2014-01-01
Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially increased due to advances in Next-Generation Sequencing technologies. The functional impacts of these variations have been difficult to ascertain because the corresponding knowledge about sequence functional sites is quite fragmented. It is clear that mapping of variations to sequence functional features can help us better understand the pathophysiological role of variations. In this study, we investigated the effect of nsSNVs on more than 17 common types of post-translational modification (PTM) sites, active sites and binding sites. Out of 1 705 285 distinct nsSNVs on 259 216 functional sites we identified 38 549 variations that significantly affect 10 major functional sites. Furthermore, we found distinct patterns of site disruptions due to germline and somatic nsSNVs. Pan-cancer analysis across 12 different cancer types led to the identification of 51 genes with 106 nsSNV affected functional sites found in 3 or more cancer types. 13 of the 51 genes overlap with previously identified Significantly Mutated Genes (Nature. 2013 Oct 17;502(7471)). 62 mutations in these 13 genes affecting functional sites such as DNA, ATP binding and various PTM sites occur across several cancers and can be prioritized for additional validation and investigations. PMID:25232094
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Negative Emotion Weakens the Degree of Self-Reference Effect: Evidence from ERPs
Fan, Wei; Zhong, Yiping; Li, Jin; Yang, Zilu; Zhan, Youlong; Cai, Ronghua; Fu, Xiaolan
2016-01-01
We investigated the influence of negative emotion on the degree of self-reference effect using event-related potentials (ERPs). We presented emotional pictures and self-referential stimuli (stimuli that accelerate and improve processing and improve memory of information related to an individual’s self-concept) in sequence. Participants judged the color of the target stimulus (self-referential stimuli). ERP results showed that the target stimuli elicited larger P2 amplitudes under neutral conditions than under negative emotional conditions. Under neutral conditions, N2 amplitudes for highly self-relevant names (target stimulus) were smaller than those for any other names. Under negative emotional conditions, highly and moderately self-referential stimuli activated smaller N2 amplitudes. P3 amplitudes activated by self-referential processing under negative emotional conditions were smaller than neutral conditions. In the left and central sites, highly self-relevant names activated larger P3 amplitudes than any other names. But in the central sites, moderately self-relevant names activated larger P3 amplitudes than non-self-relevant names. The findings indicate that negative emotional processing could weaken the degree of self-reference effect. PMID:27733836
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White, David J.; Congedo, Marco; Ciorciari, Joseph
2014-01-01
A developing literature explores the use of neurofeedback in the treatment of a range of clinical conditions, particularly ADHD and epilepsy, whilst neurofeedback also provides an experimental tool for studying the functional significance of endogenous brain activity. A critical component of any neurofeedback method is the underlying physiological signal which forms the basis for the feedback. While the past decade has seen the emergence of fMRI-based protocols training spatially confined BOLD activity, traditional neurofeedback has utilized a small number of electrode sites on the scalp. As scalp EEG at a given electrode site reflects a linear mixture of activity from multiple brain sources and artifacts, efforts to successfully acquire some level of control over the signal may be confounded by these extraneous sources. Further, in the event of successful training, these traditional neurofeedback methods are likely influencing multiple brain regions and processes. The present work describes the use of source-based signal processing methods in EEG neurofeedback. The feasibility and potential utility of such methods were explored in an experiment training increased theta oscillatory activity in a source derived from Blind Source Separation (BSS) of EEG data obtained during completion of a complex cognitive task (spatial navigation). Learned increases in theta activity were observed in two of the four participants to complete 20 sessions of neurofeedback targeting this individually defined functional brain source. Source-based EEG neurofeedback methods using BSS may offer important advantages over traditional neurofeedback, by targeting the desired physiological signal in a more functionally and spatially specific manner. Having provided preliminary evidence of the feasibility of these methods, future work may study a range of clinically and experimentally relevant brain processes where individual brain sources may be targeted by source-based EEG neurofeedback. PMID:25374520
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Theory and methods in cultural neuroscience
Hariri, Ahmad R.; Harada, Tokiko; Mano, Yoko; Sadato, Norihiro; Parrish, Todd B.; Iidaka, Tetsuya
2010-01-01
Cultural neuroscience is an emerging research discipline that investigates cultural variation in psychological, neural and genomic processes as a means of articulating the bidirectional relationship of these processes and their emergent properties. Research in cultural neuroscience integrates theory and methods from anthropology, cultural psychology, neuroscience and neurogenetics. Here, we review a set of core theoretical and methodological challenges facing researchers when planning and conducting cultural neuroscience studies, and provide suggestions for overcoming these challenges. In particular, we focus on the problems of defining culture and culturally appropriate experimental tasks, comparing neuroimaging data acquired from different populations and scanner sites and identifying functional genetic polymorphisms relevant to culture. Implications of cultural neuroscience research for addressing current issues in population health disparities are discussed. PMID:20592044
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Vitamin D: Implications for Ocular Disease and Therapeutic Potential
Reins, Rose Y.; McDermott, Alison M.
2015-01-01
Vitamin D is a multifunctional hormone that is now known to play a significant role in a variety of biological functions in addition to its traditional role in regulating calcium homeostasis. There are a large number of studies demonstrating that adequate vitamin D levels are important in maintaining health and show that vitamin D is able to be utilized at local tissue sites. In the eye, we have increasing evidence of the association between disease and vitamin D. In this narrative review, we summarize recent findings on vitamin D and its relationship to various ocular pathologies and the therapeutic potential for some of these, as well as examine the basic science studies that demonstrate that vitamin D is biologically relevant in the eye. PMID:25724179
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The presence of Ti(II) centers in doped nanoscale TiO2 and TiO2-xNx
NASA Astrophysics Data System (ADS)
Mikulas, Tanya; Fang, Zongtang; Gole, James L.; White, Mark G.; Dixon, David A.
2012-06-01
Unusual trends are observed in the Ti (2s, 2p) XPS spectra of Fe(II) doped TiO2 and TiO2-xNx. The binding energy of Ti (2s, 2p) initially decreases with increasing Fe(II) concentration, as expected, but increases at higher Fe(II) doping levels. Density functional theory is used to analyze the results. The observed VB-XPS and core level XPS spectra are consistent with the facile charge transfer sequence Ti(IV) + Fe(II) → Ti(III) + Fe(III) followed by Ti(III) + Fe(II) → Ti(II) + Fe(III). The formed Ti(II) sites may be relevant to nanoparticle catalysis on TiO2 surfaces.
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Friendly Home and Inhabitants' Morality: Mutual Relationships.
Nartova-Bochaver, Sofya K; Kuznetsova, Valeriya B
2017-01-01
The study is aimed at investigating the connection between the friendliness of the home environment and the moral motives' level. The friendliness of the home environment includes two aspects: the number of functions provided by home (functionality) and the congruence of these functions with inhabitants' needs (relevance). The theoretical framework of the study was formed by research and ideas emphasizing the interplay between people and their environments. We hypothesized that the friendliness of the home environment and inhabitants' moral motives would have a reciprocal relationship: the friendlier the home the higher the inhabitants' moral motives' level, and, vice versa, the higher the person's moral motives' level the more positive home image. The respondents were 550 students (25% male). The Home Environment Functionality Questionnaire, the Home Environment Relevance Questionnaire, and the Moral Motivation Model Scale were used. As expected, it was found that the friendliness of the home environment and the inhabitants' moral motives are in reciprocal synergetic relationships. Relevance formed more nuanced correlation patterns with moral motives than functionality did. Functionality predicted moral motives poorly whereas moral motives predicted functionality strongly. Finally, relevance and moral motives were found to be in mutual relationships whereas the perceived functionality was predicted by moral motives only.
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Friendly Home and Inhabitants' Morality: Mutual Relationships
Nartova-Bochaver, Sofya K.; Kuznetsova, Valeriya B.
2018-01-01
The study is aimed at investigating the connection between the friendliness of the home environment and the moral motives' level. The friendliness of the home environment includes two aspects: the number of functions provided by home (functionality) and the congruence of these functions with inhabitants' needs (relevance). The theoretical framework of the study was formed by research and ideas emphasizing the interplay between people and their environments. We hypothesized that the friendliness of the home environment and inhabitants' moral motives would have a reciprocal relationship: the friendlier the home the higher the inhabitants' moral motives' level, and, vice versa, the higher the person's moral motives' level the more positive home image. The respondents were 550 students (25% male). The Home Environment Functionality Questionnaire, the Home Environment Relevance Questionnaire, and the Moral Motivation Model Scale were used. As expected, it was found that the friendliness of the home environment and the inhabitants' moral motives are in reciprocal synergetic relationships. Relevance formed more nuanced correlation patterns with moral motives than functionality did. Functionality predicted moral motives poorly whereas moral motives predicted functionality strongly. Finally, relevance and moral motives were found to be in mutual relationships whereas the perceived functionality was predicted by moral motives only. PMID:29375450
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Qiu, Ying-Hua; Deng, Fei-Yan; Tang, Zai-Xiang; Jiang, Zhen-Huan; Lei, Shu-Feng
2015-10-01
Type 1 diabetes mellitus (type 1 DM) is an autoimmune disease. Although genome-wide association studies (GWAS) and meta-analyses have successfully identified numerous type 1 DM-associated susceptibility loci, the underlying mechanisms for these susceptibility loci are currently largely unclear. Based on publicly available datasets, we performed integrative analyses (i.e., integrated gene relationships among implicated loci, differential gene expression analysis, functional prediction and functional annotation clustering analysis) and combined with expression quantitative trait loci (eQTL) results to further explore function mechanisms underlying the associations between genetic variants and type 1 DM. Among a total of 183 type 1 DM-associated SNPs, eQTL analysis showed that 17 SNPs with cis-regulated eQTL effects on 9 genes. All the 9 eQTL genes enrich in immune-related pathways or Gene Ontology (GO) terms. Functional prediction analysis identified 5 SNPs located in transcription factor (TF) binding sites. Of the 9 eQTL genes, 6 (TAP2, HLA-DOB, HLA-DQB1, HLA-DQA1, HLA-DRB5 and CTSH) were differentially expressed in type 1 DM-associated related cells. Especially, rs3825932 in CTSH has integrative functional evidence supporting the association with type 1 DM. These findings indicated that integrative analyses can yield important functional information to link genetic variants and type 1 DM. Copyright © 2015 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.
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Integrating abundance and functional traits reveals new global hotspots of fish diversity.
Stuart-Smith, Rick D; Bates, Amanda E; Lefcheck, Jonathan S; Duffy, J Emmett; Baker, Susan C; Thomson, Russell J; Stuart-Smith, Jemina F; Hill, Nicole A; Kininmonth, Stuart J; Airoldi, Laura; Becerro, Mikel A; Campbell, Stuart J; Dawson, Terence P; Navarrete, Sergio A; Soler, German A; Strain, Elisabeth M A; Willis, Trevor J; Edgar, Graham J
2013-09-26
Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.
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Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites.
Chojnacki, Matthew; Banks, Maria; Urso, Anna
2018-02-01
Aeolian processes have likely been the predominant geomorphic agent for most of Mars' history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low.
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Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites
Chojnacki, Matthew; Banks, Maria; Urso, Anna
2018-01-01
Aeolian processes have likely been the predominant geomorphic agent for most of Mars’ history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low. PMID:29568719
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Wind-Driven Erosion and Exposure Potential at Mars 2020 Rover Candidate-Landing Sites
NASA Astrophysics Data System (ADS)
Chojnacki, Matthew; Banks, Maria; Urso, Anna
2018-02-01
Aeolian processes have likely been the predominant geomorphic agent for most of Mars' history and have the potential to produce relatively young exposure ages for geologic units. Thus, identifying local evidence for aeolian erosion is highly relevant to the selection of landing sites for future missions, such as the Mars 2020 Rover mission that aims to explore astrobiologically relevant ancient environments. Here we investigate wind-driven activity at eight Mars 2020 candidate-landing sites to constrain erosion potential at these locations. To demonstrate our methods, we found that contemporary dune-derived abrasion rates were in agreement with rover-derived exhumation rates at Gale crater and could be employed elsewhere. The Holden crater candidate site was interpreted to have low contemporary erosion rates, based on the presence of a thick sand coverage of static ripples. Active ripples at the Eberswalde and southwest Melas sites may account for local erosion and the dearth of small craters. Moderate-flux regional dunes near Mawrth Vallis were deemed unrepresentative of the candidate site, which is interpreted to currently be experiencing low levels of erosion. The Nili Fossae site displayed the most unambiguous evidence for local sand transport and erosion, likely yielding relatively young exposure ages. The downselected Jezero crater and northeast Syrtis sites had high-flux neighboring dunes and exhibited substantial evidence for sediment pathways across their ellipses. Both sites had relatively high estimated abrasion rates, which would yield young exposure ages. The downselected Columbia Hills site lacked evidence for sand movement, and contemporary local erosion rates are estimated to be relatively low.
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The challenges of applying benefit transfer models to policy sites are often underestimated. Analysts commonly need to estimate site-specific effects for areas that lack data on the number of people who use the resource, intensity of use, and other relevant variables. Yet, the be...
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Optimising Web Site Designs for People with Learning Disabilities
ERIC Educational Resources Information Center
Williams, Peter; Hennig, Christian
2015-01-01
Much relevant internet-mediated information is inaccessible to people with learning disabilities because of difficulties in navigating the web. This paper reports on the methods undertaken to determine how information can be optimally presented for this cohort. Qualitative work is outlined where attributes relating to site layout affecting…
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10 CFR 765.20 - Procedures for submitting reimbursement claims.
Code of Federal Regulations, 2011 CFR
2011-01-01
... Section 765.20 Energy DEPARTMENT OF ENERGY REIMBURSEMENT FOR COSTS OF REMEDIAL ACTION AT ACTIVE URANIUM... reimbursement ceiling for any active uranium or thorium processing site; (5) Any revision in the per dry short ton limit on reimbursement for all active uranium processing sites; and (6) Any other relevant...
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10 CFR 765.20 - Procedures for submitting reimbursement claims.
Code of Federal Regulations, 2013 CFR
2013-01-01
... Section 765.20 Energy DEPARTMENT OF ENERGY REIMBURSEMENT FOR COSTS OF REMEDIAL ACTION AT ACTIVE URANIUM... reimbursement ceiling for any active uranium or thorium processing site; (5) Any revision in the per dry short ton limit on reimbursement for all active uranium processing sites; and (6) Any other relevant...
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10 CFR 765.20 - Procedures for submitting reimbursement claims.
Code of Federal Regulations, 2012 CFR
2012-01-01
... Section 765.20 Energy DEPARTMENT OF ENERGY REIMBURSEMENT FOR COSTS OF REMEDIAL ACTION AT ACTIVE URANIUM... reimbursement ceiling for any active uranium or thorium processing site; (5) Any revision in the per dry short ton limit on reimbursement for all active uranium processing sites; and (6) Any other relevant...
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10 CFR 765.20 - Procedures for submitting reimbursement claims.
Code of Federal Regulations, 2014 CFR
2014-01-01
... Section 765.20 Energy DEPARTMENT OF ENERGY REIMBURSEMENT FOR COSTS OF REMEDIAL ACTION AT ACTIVE URANIUM... reimbursement ceiling for any active uranium or thorium processing site; (5) Any revision in the per dry short ton limit on reimbursement for all active uranium processing sites; and (6) Any other relevant...
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COSTS AND ISSUES RELATED TO REMEDIATION OF PETROLEUM-CONTAMINATED SITES (NEW ORLEANS, LA)
The remediation costs required at sites contaminated with petroleum-derived compounds remains a relevant issue because of the large number of existing underground storage tanks the United States and the presence of benzene, MTBE, and TBA in some drinking water supplies. Cost inf...
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Stockburger, Carola; Miano, Davide; Pallas, Thea; Friedland, Kristina; Müller, Walter E
2016-01-01
The mitochondrial cascade hypothesis of dementia assumes mitochondrial dysfunction leading to reduced energy supply, impaired neuroplasticity, and finally cell death as one major pathomechanism underlying the continuum from brain aging over mild cognitive impairment to initial and advanced late onset Alzheimer's disease. Accordingly, improving mitochondrial function has become an important strategy to treat the early stages of this continuum. The metabolic enhancer piracetam has been proposed as possible prototype for those compounds by increasing impaired mitochondrial function and related aspects like mechanisms of neuroplasticity. We here report that piracetam at therapeutically relevant concentrations improves neuritogenesis in the human cell line SH-SY5Y over conditions mirroring the whole spectrum of age-associated cognitive decline. These effects go parallel with improvement of impaired mitochondrial dynamics shifting back fission and fusion balance to the energetically more favorable fusion site. Impaired fission and fusion balance can also be induced by a reduction of the mitochondrial permeability transition pore (mPTP) function as atractyloside which indicates the mPTP has similar effects on mitochondrial dynamics. These changes are also reduced by piracetam. These findings suggest the mPTP as an important target for the beneficial effects of piracetam on mitochondrial function.
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Stockburger, Carola; Miano, Davide; Pallas, Thea; Müller, Walter E.
2016-01-01
The mitochondrial cascade hypothesis of dementia assumes mitochondrial dysfunction leading to reduced energy supply, impaired neuroplasticity, and finally cell death as one major pathomechanism underlying the continuum from brain aging over mild cognitive impairment to initial and advanced late onset Alzheimer's disease. Accordingly, improving mitochondrial function has become an important strategy to treat the early stages of this continuum. The metabolic enhancer piracetam has been proposed as possible prototype for those compounds by increasing impaired mitochondrial function and related aspects like mechanisms of neuroplasticity. We here report that piracetam at therapeutically relevant concentrations improves neuritogenesis in the human cell line SH-SY5Y over conditions mirroring the whole spectrum of age-associated cognitive decline. These effects go parallel with improvement of impaired mitochondrial dynamics shifting back fission and fusion balance to the energetically more favorable fusion site. Impaired fission and fusion balance can also be induced by a reduction of the mitochondrial permeability transition pore (mPTP) function as atractyloside which indicates the mPTP has similar effects on mitochondrial dynamics. These changes are also reduced by piracetam. These findings suggest the mPTP as an important target for the beneficial effects of piracetam on mitochondrial function. PMID:27747106
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Verma, Anjali; Rajagopalan, Pavithra; Lotke, Rishikesh; Varghese, Rebu; Selvam, Deepak; Kundu, Tapas K.
2016-01-01
ABSTRACT Of the various genetic subtypes of human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) and simian immunodeficiency virus (SIV), only in subtype C of HIV-1 is a genetically variant NF-κB binding site found at the core of the viral promoter in association with a subtype-specific Sp1III motif. How the subtype-associated variations in the core transcription factor binding sites (TFBS) influence gene expression from the viral promoter has not been examined previously. Using panels of infectious viral molecular clones, we demonstrate that subtype-specific NF-κB and Sp1III motifs have evolved for optimal gene expression, and neither of the motifs can be replaced by a corresponding TFBS variant. The variant NF-κB motif binds NF-κB with an affinity 2-fold higher than that of the generic NF-κB site. Importantly, in the context of an infectious virus, the subtype-specific Sp1III motif demonstrates a profound loss of function in association with the generic NF-κB motif. An additional substitution of the Sp1III motif fully restores viral replication, suggesting that the subtype C-specific Sp1III has evolved to function with the variant, but not generic, NF-κB motif. A change of only two base pairs in the central NF-κB motif completely suppresses viral transcription from the provirus and converts the promoter into heterochromatin refractory to tumor necrosis factor alpha (TNF-α) induction. The present work represents the first demonstration of functional incompatibility between an otherwise functional NF-κB motif and a unique Sp1 site in the context of an HIV-1 promoter. Our work provides important leads as to the evolution of the HIV-1 subtype C viral promoter with relevance for gene expression regulation and viral latency. IMPORTANCE Subtype-specific genetic variations provide a powerful tool to examine how these variations offer a replication advantage to specific viral subtypes, if any. Only in subtype C of HIV-1 are two genetically distinct transcription factor binding sites positioned at the most critical location of the viral promoter. Since a single promoter regulates viral gene expression, the promoter variations can play a critical role in determining the replication fitness of the viral strains. Our work for the first time provides a scientific explanation for the presence of a unique NF-κB binding motif in subtype C, a major HIV-1 genetic family responsible for half of the global HIV-1 infections. The results offer compelling evidence that the subtype C viral promoter not only is stronger but also is endowed with a qualitative gain-of-function advantage. The genetically variant NF-κB and the Sp1III motifs may be respond differently to specific cell signal pathways, and these mechanisms must be examined. PMID:27194770
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Bruegger, Joel J; Smith, Brian C; Wynia-Smith, Sarah L; Marletta, Michael A
2018-04-27
Cysteine S -nitrosation is a reversible post-translational modification mediated by nitric oxide ( • NO)-derived agents. S -Nitrosation participates in cellular signaling and is associated with several diseases such as cancer, cardiovascular diseases, and neuronal disorders. Despite the physiological importance of this nonclassical • NO-signaling pathway, little is understood about how much S -nitrosation affects protein function. Moreover, identifying physiologically relevant targets of S -nitrosation is difficult because of the dynamics of transnitrosation and a limited understanding of the physiological mechanisms leading to selective protein S -nitrosation. To identify proteins whose activities are modulated by S -nitrosation, we performed a metabolomics study comparing WT and endothelial nitric-oxide synthase knockout mice. We integrated our results with those of a previous proteomics study that identified physiologically relevant S -nitrosated cysteines, and we found that the activity of at least 21 metabolic enzymes might be regulated by S -nitrosation. We cloned, expressed, and purified four of these enzymes and observed that S -nitrosation inhibits the metabolic enzymes 6-phosphogluconate dehydrogenase, Δ1-pyrroline-5-carboxylate dehydrogenase, catechol- O -methyltransferase, and d-3-phosphoglycerate dehydrogenase. Furthermore, using site-directed mutagenesis, we identified the predominant cysteine residue influencing the observed activity changes in each enzyme. In summary, using an integrated metabolomics approach, we have identified several physiologically relevant S -nitrosation targets, including metabolic enzymes, which are inhibited by this modification, and we have found the cysteines modified by S -nitrosation in each enzyme. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
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2017-01-01
ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation. The first challenge can be overcome by applying orthogonal structural biology techniques that are capable of observing alternative, biologically relevant conformations. The second challenge can be addressed by determining the structure in the same biological state with two independent techniques under different experimental conditions. If both techniques converge to the same structural model, the confidence that an unperturbed biologically relevant conformation is observed increases. To this end, we determine the structure of the C-terminal domain of the effector protein, ExoU, from data obtained by electron paramagnetic resonance spectroscopy in conjunction with site-directed spin labeling and in silico de novo structure determination. Our protocol encompasses a multimodule approach, consisting of low-resolution topology sampling, clustering, and high-resolution refinement. The resulting model was compared with an ExoU model in complex with its chaperone SpcU obtained previously by X-ray crystallography. The two models converged to a minimal RMSD100 of 3.2 Å, providing evidence that the unbound structure of ExoU matches the fold observed in complex with SpcU. PMID:28691114
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Solution of the effective Hamiltonian of impurity hopping between two sites in a metal
NASA Astrophysics Data System (ADS)
Ye, Jinwu
1997-07-01
We analyze in detail all the possible fixed points of the effective Hamiltonian of a nonmagnetic impurity hopping between two sites in a metal obtained by Moustakas and Fisher (MF). We find a line of non-Fermi liquid fixed points which continuously interpolates between the two-channel Kondo fixed point (2CK) and the one-channel, two-impurity Kondo (2IK) fixed point. There is one relevant direction with scaling dimension 12 and one leading irrelevant operator with dimension 32. There is also one marginal operator in the spin sector moving along this line. The marginal operator, combined with the leading irrelevant operator, will generate the relevant operator. For the general position on this line, the leading low-temperature exponents of the specific heat, the hopping susceptibility and the electron conductivity Cimp,χhimp,σ(T) are the same as those of the 2CK, but the finite-size spectrum depends on the position on the line. No universal ratios can be formed from the amplitudes of the three quantities except at the 2CK point on this line where the universal ratios can be formed. At the 2IK point on this line, σ(T)~2σu(1+aT3/2), no universal ratio can be formed either. The additional non-Fermi-liquid fixed point found by MF has the same symmetry as the 2IK, it has two relevant directions with scaling dimension 12, and is therefore also unstable. The leading low-temperature behaviors are Cimp~T,χhimp~lnT,σ(T)~2σu(1+aT3/2) no universal ratios can be formed. The system is shown to flow to a line of Fermi-liquid fixed points which continuously interpolates between the noninteracting fixed point and the two-channel spin-flavor Kondo fixed point discussed by the author previously. The effect of particle-hole symmetry breaking is discussed. The effective Hamiltonian in the external magnetic field is analyzed. The scaling functions for the physical measurable quantities are derived in the different regimes; their predictions for the experiments are given. Finally the implications are given for a nonmagnetic impurity hopping around three sites with triangular symmetry discussed by MF.
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e-Health and new moms: Contextual factors associated with sources of health information.
Walker, Lorraine O; Mackert, Michael S; Ahn, Jisoo; Vaughan, Misha W; Sterling, Bobbie S; Guy, Sarah; Hendrickson, Sherry
2017-11-01
Guided by the Uses and Gratifications approach, to examine mothers' use and preference of e-Health media, and associated contextual factors. Cross-sectional survey of 165 mothers (White, African-American, and Hispanic) from a stratified random sample. Use of online media about mother-baby care; favorite websites about motherhood and best-liked features of Web sites; channel preferences (Web site, postal mail, text) for receiving three types of health information; and contextual factors, e.g., education. Media use ranged from 96% for health information searches about babies to 46% for YouTube viewing about mother-baby topics. Contextual factors, such as education, were associated with media use. Babycenter was the most frequently reported favorite Web site and rich, relevant information was the best-liked feature. Across three health topics (weight, stress/depression, parenting) mothers preferred receiving information by Web site, followed by postal mail and least by text messaging (χ 2 statistics, p < .001). Stress and race/ethnicity were among factors associated with preferences. Mothers widely used e-Health related media, but use was associated with contextual factors. In public health efforts to reach new mothers, partnering with mother-favored Web sites, focusing on audience-relevant media, and adopting attributes of successful sites are recommended strategies. © 2017 Wiley Periodicals, Inc.
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Toward identifying the next generation of superfund and hazardous waste site contaminants.
Ela, Wendell P; Sedlak, David L; Barlaz, Morton A; Henry, Heather F; Muir, Derek C G; Swackhamer, Deborah L; Weber, Eric J; Arnold, Robert G; Ferguson, P Lee; Field, Jennifer A; Furlong, Edward T; Giesy, John P; Halden, Rolf U; Henry, Tala; Hites, Ronald A; Hornbuckle, Keri C; Howard, Philip H; Luthy, Richard G; Meyer, Anita K; Sáez, A Eduardo; Vom Saal, Frederick S; Vulpe, Chris D; Wiesner, Mark R
2011-01-01
This commentary evolved from a workshop sponsored by the National Institute of Environmental Health Sciences titled "Superfund Contaminants: The Next Generation" held in Tucson, Arizona, in August 2009. All the authors were workshop participants. Our aim was to initiate a dynamic, adaptable process for identifying contaminants of emerging concern (CECs) that are likely to be found in future hazardous waste sites, and to identify the gaps in primary research that cause uncertainty in determining future hazardous waste site contaminants. Superfund-relevant CECs can be characterized by specific attributes: They are persistent, bioaccumulative, toxic, occur in large quantities, and have localized accumulation with a likelihood of exposure. Although still under development and incompletely applied, methods to quantify these attributes can assist in winnowing down the list of candidates from the universe of potential CECs. Unfortunately, significant research gaps exist in detection and quantification, environmental fate and transport, health and risk assessment, and site exploration and remediation for CECs. Addressing these gaps is prerequisite to a preventive approach to generating and managing hazardous waste sites. A need exists for a carefully considered and orchestrated expansion of programmatic and research efforts to identify, evaluate, and manage CECs of hazardous waste site relevance, including developing an evolving list of priority CECs, intensifying the identification and monitoring of likely sites of present or future accumulation of CECs, and implementing efforts that focus on a holistic approach to prevention.
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Adaptive evolution of the STRA6 genes in mammalian.
Wu, Jianghong; Xiang, Hui; Qi, Yunxia; Yang, Ding; Wang, Xiaojuan; Sun, Hailian; Wang, Feng; Liu, Bin
2014-01-01
Stimulated by retinoic acid 6 (STRA6) is the receptor for retinol binding protein and is relevant for the transport of retinol to specific sites such as the eye. The adaptive evolution mechanism that vertebrates have occupied nearly every habitat available on earth and adopted various lifestyles associated with different light conditions and visual challenges, as well as their role in development and adaptation is thus far unknown. In this work, we have investigated different aspects of vertebrate STRA6 evolution and used molecular evolutionary analyses to detect evidence of vertebrate adaptation to the lightless habitat. Free-ratio model revealed significant rate shifts immediately after the species divergence. The amino acid sites detected to be under positive selection are within the extracellular loops of STRA6 protein. Branch-site model A test revealed that STRA6 has undergone positive selection in the different phyla of mammalian except for the branch of rodent. The results suggest that interactions between different light environments and host may be driving adaptive change in STRA6 by competition between species. In support of this, we found that altered functional constraints may take place at some amino acid residues after speciation. We suggest that STRA6 has undergone adaptive evolution in different branch of vertebrate relation to habitat environment.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Fuchs, G.; Mobassaleh, M.; Donohue-Rolfe, A.
This study examined the binding of purified /sup 125/I-labeled shigella toxin to rabbit jejunal microvillus membranes (MVMs). Toxin binding was concentration dependent, saturable, reversible, and specifically inhibited by unlabeled toxin. The calculated number of toxin molecules bound at 4/sup 0/C was 7.9 X 10(10) (3 X 10(10) to 2 X 10(11))/micrograms of MVM protein or 1.2 X 10(6) per enterocyte. Scatchard analysis showed the binding site to be of a single class with an equilibrium association constant, K, of 4.7 X 10(9) M-1 at 4/sup 0/C. Binding was inversely related to the temperature of incubation. A total of 80% ofmore » the labeled toxin binding at 4/sup 0/C dissociated from MVM when the temperature was raised to 37/sup 0/C, but reassociated when the temperature was again brought to 4/sup 0/C. There was no structural or functional change of MVM due to toxin as monitored by electron microscopy or assay of MVM sucrase activity. These studies demonstrate a specific binding site for shigella toxin on rabbit MVMs. The physiological relevance of this receptor remains to be determined.« less
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Sacristán-Reviriego, Almudena; Madrid, Marisa; Cansado, José; Martín, Humberto; Molina, María
2014-01-01
Dual-specificity MAPK phosphatases (MKPs) are essential for the negative regulation of MAPK pathways. Similar to other MAPK-interacting proteins, most MKPs bind MAPKs through specific docking domains known as D-motifs. However, we found that the Saccharomyces cerevisiae MKP Msg5 binds the MAPK Slt2 within the cell wall integrity (CWI) pathway through a distinct motif (IYT). Here, we demonstrate that the IYT motif mediates binding of the Msg5 paralogue Sdp1 to Slt2 as well as of the MKP Pmp1 to its CWI MAPK counterpart Pmk1 in the evolutionarily distant yeast Schizosaccharomyces pombe. As a consequence, removal of the IYT site in Msg5, Sdp1 and Pmp1 reduces MAPK trapping caused by the overexpression of catalytically inactive versions of these phosphatases. Accordingly, an intact IYT site is necessary for inactive Sdp1 to prevent nuclear accumulation of Slt2. We also show that both Ile and Tyr but not Thr are essential for the functionality of the IYT motif. These results provide mechanistic insight into MKP-MAPK interplay and stress the relevance of this conserved non-canonical docking site in the regulation of the CWI pathway in fungi. PMID:24465549
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NASA Astrophysics Data System (ADS)
Soundararajan, Venky; Aravamudan, Murali
2014-12-01
The efficacy and mechanisms of therapeutic action are largely described by atomic bonds and interactions local to drug binding sites. Here we introduce global connectivity analysis as a high-throughput computational assay of therapeutic action - inspired by the Google page rank algorithm that unearths most ``globally connected'' websites from the information-dense world wide web (WWW). We execute short timescale (30 ps) molecular dynamics simulations with high sampling frequency (0.01 ps), to identify amino acid residue hubs whose global connectivity dynamics are characteristic of the ligand or mutation associated with the target protein. We find that unexpected allosteric hubs - up to 20Å from the ATP binding site, but within 5Å of the phosphorylation site - encode the Gibbs free energy of inhibition (ΔGinhibition) for select protein kinase-targeted cancer therapeutics. We further find that clinically relevant somatic cancer mutations implicated in both drug resistance and personalized drug sensitivity can be predicted in a high-throughput fashion. Our results establish global connectivity analysis as a potent assay of protein functional modulation. This sets the stage for unearthing disease-causal exome mutations and motivates forecast of clinical drug response on a patient-by-patient basis. We suggest incorporation of structure-guided genetic inference assays into pharmaceutical and healthcare Oncology workflows.
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FY94 CAG trip reports, CAG memos and other products: Volume 2. Final report
DOE Office of Scientific and Technical Information (OSTI.GOV)
NONE
1994-12-15
The Yucca Mountain Site Characterization Project (YMP) of the US DOE is tasked with designing, constructing, and operating an Exploratory Studies Facility (ESF) at Yucca Mountain, Nevada. The purpose of the YMP is to provide detailed characterization of the Yucca Mountain site for the potential mined geologic repository for permanent disposal of high-level radioactive waste. Detailed characterization of properties of the site are to be conducted through a wide variety of short-term and long-term in-situ tests. Testing methods require the installation of a large number of test instruments and sensors with a variety of functions. These instruments produce analog andmore » digital data that must be collected, processed, stored, and evaluated in an attempt to predict performance of the repository. The Integrated Data and Control System (IDCS) is envisioned as a distributed data acquisition that electronically acquires and stores data from these test instruments. IDCS designers are responsible for designing and overseeing the procurement of the system, IDCS Operation and Maintenance operates and maintains the installed system, and the IDCS Data Manager is responsible for distribution of IDCS data to participants. This report is a compilation of trip reports, interoffice memos, and other memos relevant to Computer Applications Group, Inc., work on this project.« less
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Heat shock protein 27 regulates human prostate cancer cell motility and metastatic progression
Voll, Eric A; Ogden, Irene M; Pavese, Janet M; Huang, XiaoKe; Xu, Li; Jovanovic, Borko D; Bergan, Raymond C
2014-01-01
Prostate cancer (PCa) is the most common form of cancer in American men. Mortality from PCa is caused by the movement of cancer cells from the primary organ to form metastatic tumors at distant sites. Heat shock protein 27 (HSP27) is known to increase human PCa cell invasion and its overexpression is associated with metastatic disease. The role of HSP27 in driving PCa cell movement from the prostate to distant metastatic sites is unknown. Increased HSP27 expression increased metastasis as well as primary tumor mass. In vitro studies further examined the mechanism of HSP27-induced metastatic behavior. HSP27 did not affect cell detachment, adhesion, or migration, but did increase cell invasion. Cell invasion was dependent upon matrix metalloproteinase 2 (MMP-2), whose expression was increased by HSP27. In vivo, HSP27 induced commensurate changes in MMP-2 expression in tumors. These findings demonstrate that HSP27 drives metastatic spread of cancer cells from the prostate to distant sites, does so across a continuum of expression levels, and identifies HSP27-driven increases in MMP-2 expression as functionally relevant. These findings add to prior studies demonstrating that HSP27 increases PCa cell motility, growth and survival. Together, they demonstrate that HSP27 plays an important role in PCa progression. PMID:24798191
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NASA Astrophysics Data System (ADS)
Marquardt, W.; Ihle, P.
At two sites in the north of the G.D.R. 80-100 km distant from industry rain from individual precipitation events was collected by automatic samplers and relevant ionic species were analyzed. The sampler is described. The cloud routes at the 850 hPa level were traced back 1 day and then seven sectors were formed for each collection site taking into consideration geographical aspects and features of the emission pattern for the rea concerned. Investigating the precipitation components as a function of the emission pattern knowledge of meteorological input parameters are required. The influence of these parameters is reported. Contrary to the combustion of other fossil fuels, in the case of brown coal combustion a considerable emission of neutralizing components (especially CaO) occurs, counteracting the formation of "acid rain". This effect is clearly proven by means of individual examples and average considerations, i.e. the formation of acid rain does not only depend on the SO 2 and NO x emissions. The wet deposition of all types of ions at the measuring site for every emission sector was calculated by means of precipitation statistics. Using these investigations reference points with regard to border crossing transport are given.
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Tang, Tao; Stevenson, R Jan; Infante, Dana M
2016-10-15
Regional variation in both natural environment and human disturbance can influence performance of ecological assessments. In this study we calculated 5 types of benthic diatom multimetric indices (MMIs) with 3 different approaches to account for variation in ecological assessments. We used: site groups defined by ecoregions or diatom typologies; the same or different sets of metrics among site groups; and unmodeled or modeled MMIs, where models accounted for natural variation in metrics within site groups by calculating an expected reference condition for each metric and each site. We used data from the USEPA's National Rivers and Streams Assessment to calculate the MMIs and evaluate changes in MMI performance. MMI performance was evaluated with indices of precision, bias, responsiveness, sensitivity and relevancy which were respectively measured as MMI variation among reference sites, effects of natural variables on MMIs, difference between MMIs at reference and highly disturbed sites, percent of highly disturbed sites properly classified, and relation of MMIs to human disturbance and stressors. All 5 types of MMIs showed considerable discrimination ability. Using different metrics among ecoregions sometimes reduced precision, but it consistently increased responsiveness, sensitivity, and relevancy. Site specific metric modeling reduced bias and increased responsiveness. Combined use of different metrics among site groups and site specific modeling significantly improved MMI performance irrespective of site grouping approach. Compared to ecoregion site classification, grouping sites based on diatom typologies improved precision, but did not improve overall performance of MMIs if we accounted for natural variation in metrics with site specific models. We conclude that using different metrics among ecoregions and site specific metric modeling improve MMI performance, particularly when used together. Applications of these MMI approaches in ecological assessments introduced a tradeoff with assessment consistency when metrics differed across site groups, but they justified the convenient and consistent use of ecoregions. Copyright © 2016 Elsevier B.V. All rights reserved.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Sabyrov, Kairat; Musselwhite, Nathan; Melaet, Gérôme
As the impact of acids on catalytically driven chemical transformations is tremendous, fundamental understanding of catalytically relevant factors is essential for the design of more efficient solid acid catalysts. In this work, we employed a post-synthetic doping method to synthesize a highly selective hydroisomerization catalyst and to demonstrate the effect of acid strength and density, catalyst microstructure, and platinum nanoparticle size on the reaction rate and selectivity. Aluminum doped mesoporous silica catalyzed gas-phase n-hexadecane isomerization with remarkably high selectivity to monobranched isomers (~95%), producing a substantially higher amount of isomers than traditional zeolite catalysts. Mildly acidic sites generated by post-syntheticmore » aluminum grafting were found to be the main reason for its high selectivity. The flexibility of the post-synthetic doping method enabled us to systematically explore the effect of the acid site density on the reaction rate and selectivity, which has been extremely difficult to achieve with zeolite catalysts. We found that a higher density of Brønsted acid sites leads to higher cracking of n-hexadecane presumably due to an increased surface residence time. Furthermore, regardless of pore size and microstructure, hydroisomerization turnover frequency linearly increased as a function of Brønsted acid site density. In addition to strength and density of acid sites, platinum nanoparticle size affected catalytic activity and selectivity. The smallest platinum nanoparticles produced the most effective bifunctional catalyst presumably because of higher percolation into aluminum doped mesoporous silica, generating more 'intimate' metallic and acidic sites. Finally, the aluminum doped silica catalyst was shown to retain its remarkable selectivity towards isomers even at increased reaction conversions.« less
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Dagnino, Alessandro; Sforzini, Susanna; Dondero, Francesco; Fenoglio, Stefano; Bona, Elisa; Jensen, John; Viarengo, Aldo
2008-07-01
A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C).
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Sabyrov, Kairat; Musselwhite, Nathan; Melaet, Gérôme; ...
2017-01-01
As the impact of acids on catalytically driven chemical transformations is tremendous, fundamental understanding of catalytically relevant factors is essential for the design of more efficient solid acid catalysts. In this work, we employed a post-synthetic doping method to synthesize a highly selective hydroisomerization catalyst and to demonstrate the effect of acid strength and density, catalyst microstructure, and platinum nanoparticle size on the reaction rate and selectivity. Aluminum doped mesoporous silica catalyzed gas-phase n-hexadecane isomerization with remarkably high selectivity to monobranched isomers (~95%), producing a substantially higher amount of isomers than traditional zeolite catalysts. Mildly acidic sites generated by post-syntheticmore » aluminum grafting were found to be the main reason for its high selectivity. The flexibility of the post-synthetic doping method enabled us to systematically explore the effect of the acid site density on the reaction rate and selectivity, which has been extremely difficult to achieve with zeolite catalysts. We found that a higher density of Brønsted acid sites leads to higher cracking of n-hexadecane presumably due to an increased surface residence time. Furthermore, regardless of pore size and microstructure, hydroisomerization turnover frequency linearly increased as a function of Brønsted acid site density. In addition to strength and density of acid sites, platinum nanoparticle size affected catalytic activity and selectivity. The smallest platinum nanoparticles produced the most effective bifunctional catalyst presumably because of higher percolation into aluminum doped mesoporous silica, generating more 'intimate' metallic and acidic sites. Finally, the aluminum doped silica catalyst was shown to retain its remarkable selectivity towards isomers even at increased reaction conversions.« less
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NASA Astrophysics Data System (ADS)
Yu, Qiang; Fein, Jeremy B.
2015-10-01
The adsorption and desorption of Cd onto Shewanella oneidensis bacterial cells with and without blocking of sulfhydryl sites was measured in order to determine the effect of metal loading and to understand the role of sulfhydryl sites in the adsorption reactions. The observed adsorption/desorption behaviors display strong dependence on metal loading. Under a high loading of 40 μmol Cd/g bacterial cells, blocking the sulfhydryl sites within the cell envelope by exposure of the biomass to monobromo(trimethylammonio)bimane bromide (qBBr) does not significantly affect the extent of Cd adsorption, and we observed fully reversible adsorption under this condition. In contrast, under a low metal loading of 1.3 μmol Cd/g bacterial cells, the extent of Cd adsorption onto sulfhydryl-blocked S. oneidensis cells was significantly lower than that onto untreated cells, and only approximately 50-60% of the adsorbed Cd desorbed from the cells upon acidification. In conjunction with previous EXAFS results, our findings demonstrate that Cd adsorption onto S. oneidensis under low metal loading conditions is dominated by sulfhydryl binding, and thus is controlled by a distinct adsorption mechanism from the non-sulfhydryl site binding which controls Cd adsorption under high metal loading conditions. We use the data to develop a surface complexation model that constrains the values of the stability constants for individual Cd-sulfhydryl and Cd-non-sulfhydryl bacterial complexes, and we use this approach to account for the Cd adsorption behavior as a function of both pH and metal loading. This approach is crucial in order to predict metal adsorption onto bacteria under environmentally relevant metal loading conditions where sulfhydryl binding sites can dominate the adsorption reaction.
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Allosteric Regulation of Mammalian Pantothenate Kinase*
Subramanian, Chitra; Yun, Mi-Kyung; Yao, Jiangwei; Sharma, Lalit Kumar; Lee, Richard E.; White, Stephen W.; Jackowski, Suzanne; Rock, Charles O.
2016-01-01
Pantothenate kinase is the master regulator of CoA biosynthesis and is feedback-inhibited by acetyl-CoA. Comparison of the human PANK3·acetyl-CoA complex to the structures of PANK3 in four catalytically relevant complexes, 5′-adenylyl-β,γ-imidodiphosphate (AMPPNP)·Mg2+, AMPPNP·Mg2+·pantothenate, ADP·Mg2+·phosphopantothenate, and AMP phosphoramidate (AMPPN)·Mg2+, revealed a large conformational change in the dimeric enzyme. The amino-terminal nucleotide binding domain rotates to close the active site, and this allows the P-loop to engage ATP and facilitates required substrate/product interactions at the active site. Biochemical analyses showed that the transition between the inactive and active conformations, as assessed by the binding of either ATP·Mg2+ or acyl-CoA to PANK3, is highly cooperative indicating that both protomers move in concert. PANK3(G19V) cannot bind ATP, and biochemical analyses of an engineered PANK3/PANK3(G19V) heterodimer confirmed that the two active sites are functionally coupled. The communication between the two protomers is mediated by an α-helix that interacts with the ATP-binding site at its amino terminus and with the substrate/inhibitor-binding site of the opposite protomer at its carboxyl terminus. The two α-helices within the dimer together with the bound ligands create a ring that stabilizes the assembly in either the active closed conformation or the inactive open conformation. Thus, both active sites of the dimeric mammalian pantothenate kinases coordinately switch between the on and off states in response to intracellular concentrations of ATP and its key negative regulators, acetyl(acyl)-CoA. PMID:27555321
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Recognition of functional sites in protein structures.
Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J
2004-06-04
Recognition of regions on the surface of one protein, that are similar to a binding site of another is crucial for the prediction of molecular interactions and for functional classifications. We first describe a novel method, SiteEngine, that assumes no sequence or fold similarities and is able to recognize proteins that have similar binding sites and may perform similar functions. We achieve high efficiency and speed by introducing a low-resolution surface representation via chemically important surface points, by hashing triangles of physico-chemical properties and by application of hierarchical scoring schemes for a thorough exploration of global and local similarities. We proceed to rigorously apply this method to functional site recognition in three possible ways: first, we search a given functional site on a large set of complete protein structures. Second, a potential functional site on a protein of interest is compared with known binding sites, to recognize similar features. Third, a complete protein structure is searched for the presence of an a priori unknown functional site, similar to known sites. Our method is robust and efficient enough to allow computationally demanding applications such as the first and the third. From the biological standpoint, the first application may identify secondary binding sites of drugs that may lead to side-effects. The third application finds new potential sites on the protein that may provide targets for drug design. Each of the three applications may aid in assigning a function and in classification of binding patterns. We highlight the advantages and disadvantages of each type of search, provide examples of large-scale searches of the entire Protein Data Base and make functional predictions.
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DOE Office of Scientific and Technical Information (OSTI.GOV)
Schaller, A.; Skanata, D.
1995-12-31
Site selection approach to radioactive waste disposal facility, which is under way in Croatia, is presented in the paper. This approach is based on application of certain relevant terrestrial and technical criteria in the site selection process. Basic documentation used for this purpose are regional planning documents prepared by the Regional Planning Institute of Croatia. The basic result of research described in the paper is the proposal of several potential areas which are suitable for siting a radioactive waste repository. All relevant conclusions are based on both data groups -- generic and on-field experienced (measured). Out of a dozen potentialmore » areas, four have been chosen as representative by the authors. The presented comparative analysis was made by means of the VISA II computer code, developed by the V. Belton and SPV Software Products. The code was donated to the APO by the IAEA. The main objective of the paper is to initiate and facilitate further discussions on possible ways of evaluation and comparison of potential areas for sitting of radioactive waste repository in this country, as well as to provide additional contributions to the current site selection process in the Republic of Croatia.« less
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Crystal Structure of Thrombin Bound to the Uncleaved Extracellular Fragment of PAR1
DOE Office of Scientific and Technical Information (OSTI.GOV)
Gandhi, Prafull S.; Chen, Zhiwei; Di Cera, Enrico
2010-05-11
Abundant structural information exists on how thrombin recognizes ligands at the active site or at exosites separate from the active site region, but remarkably little is known about how thrombin recognizes substrates that bridge both the active site and exosite I. The case of the protease-activated receptor PAR1 is particularly relevant in view of the plethora of biological effects associated with its activation by thrombin. Here, we present the 1.8 {angstrom} resolution structure of thrombin S195A in complex with a 30-residue long uncleaved extracellular fragment of PAR1 that documents for the first time a productive binding mode bridging the activemore » site and exosite I. The structure reveals two unexpected features of the thrombin-PAR1 interaction. The acidic P3 residue of PAR1, Asp{sup 39}, does not hinder binding to the active site and actually makes favorable interactions with Gly{sup 219} of thrombin. The tethered ligand domain shows a considerable degree of disorder even when bound to thrombin. The results fill a significant gap in our understanding of the molecular mechanisms of recognition by thrombin in ways that are relevant to other physiological substrates.« less
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Computer analysis of protein functional sites projection on exon structure of genes in Metazoa
2015-01-01
Background Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. Results One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. Conclusions These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and allow a better understanding of the emergence of biological diversity. PMID:26693737
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Plant functional traits and diversity in sand dune ecosystems across different biogeographic regions
NASA Astrophysics Data System (ADS)
Mahdavi, P.; Bergmeier, E.
2016-07-01
Plant species of a functional group respond similarly to environmental pressures and may be expected to act similarly on ecosystem processes and habitat properties. However, feasibility and applicability of functional groups in ecosystems across very different climatic regions have not yet been studied. In our approach we specified the functional groups in sand dune ecosystems of the Mediterranean, Hyrcanian and Irano-Turanian phytogeographic regions. We examined whether functional groups are more influenced by region or rather by habitat characteristics, and identified trait syndromes associated with common habitat types in sand dunes (mobile dunes, stabilized dunes, salt marshes, semi-wet sands, disturbed habitats). A database of 14 traits, 309 species and 314 relevés was examined and trait-species, trait-plot and species-plot matrices were built. Cluster analysis revealed similar plant functional groups in sand dune ecosystems across regions of very different species composition and climate. Specifically, our study showed that plant traits in sand dune ecosystems are grouped reflecting habitat affiliation rather than region and species pool. Environmental factors and constraints such as sand mobility, soil salinity, water availability, nutrient status and disturbance are more important for the occurrence and distribution of plant functional groups than regional belonging. Each habitat is shown to be equipped with specific functional groups and can be described by specific sets of traits. In restoration ecology the completeness of functional groups and traits in a site may serve as a guideline for maintaining or restoring the habitat.
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Thoemmes, Stephen F; Stutzke, Crystal A; Du, Yanmei; Browning, Michael D; Buttrick, Peter M; Walker, Lori A
2014-01-31
Phosphorylation of cardiac troponin I is a well established mechanism by which cardiac contractility is modulated. However, there are a number of phosphorylation sites on TnI which contribute singly or in combination to influence cardiac function. Accordingly, methods for accurately measuring site-specific TnI phosphorylation are needed. Currently, two strategies are employed: mass spectrometry, which is costly, difficult and has a low throughput; and Western blotting using phospho-specific antibodies, which is limited by the availability of reagents. In this report, we describe a cohort of new site-specific TnI phosphoantibodies, generated against physiologically relevant phosphorylation sites, that are superior to the current commercially available antibodies: to phospho-serine 22/23 which shows a >5-fold phospho-specificity for phosphorylated TnI; to phospho-serine 43, which has >3-fold phospho-specificity for phosphorylated TnI; and phospho-serine 150 which has >2-fold phospho-specificity for phosphorylated TnI. These new antibodies demonstrated greater sensitivity and specificity for the phosphorylated TnI than the most widely used commercially available reagents. For example, at a protein load of 20 μg of total cardiac extract, a commercially available antibody recognized both phosphorylated and dephosphorylated TnI to the same degree. At the same protein load our phospho-serine 22/23 antibody exhibited no cross-reactivity with dephosphorylated TnI. These new tools should allow a more accurate assessment and a better understanding of the role of TnI phosphorylation in the response of the heart to pathologic stress. Copyright © 2013 Elsevier B.V. All rights reserved.
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Distributed Observing Networks of the Past: Using Archaeological Sites to Study Global Change
NASA Astrophysics Data System (ADS)
Jensen, A. M.
2015-12-01
The Arctic is changing rapidly, and there is much concern over what the effects of those changes might be. Although changes of considerable magnitude have happened in the past, current understanding of Arctic systems is not yet sufficient to enable useful predictions. Scientific observations span a very limited period in the Arctic, and do not encompass even fairly recent (Little Ice Age, Medieval Climate Anomaly) periods of climate change. One way to address this would be to extend the period of observation, but the situation is urgent. As an alternative, various types of proxy data can serve a similar function. It is suggested that archaeological sites with good organic preservation are not only sources of data on past human behavior and cultural organization, but also valuable resources for paleoenvironmental reconstruction, with potential similar to other paleoenvironmental proxy records. The sites tend to be located at or near places that are still occupied today, thus providing locally relevant data. They also tend to incorporate the same range of species that are important for subsistence and food security today, so that one can examine how changes affected those species in the past in a fairly direct manner. Yet, just as new methods increase our ability to retrieve and study this information, global climate change poses a dire threat, both to the wealth of organic data in such sites, and to many of the sites themselves. Global change-related threats including increased coastal erosion and the warming and thawing of permafrost are major and imminent threats to the archaeological and paleoecological record.
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Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.
Righetti, Francesco; Nuss, Aaron M; Twittenhoff, Christian; Beele, Sascha; Urban, Kristina; Will, Sebastian; Bernhart, Stephan H; Stadler, Peter F; Dersch, Petra; Narberhaus, Franz
2016-06-28
RNA structures are fundamentally important for RNA function. Dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and RNA thermometers. By parallel analysis of RNA structures, we mapped the RNA structurome of Yersinia pseudotuberculosis at three different temperatures. This human pathogen is exquisitely responsive to host body temperature (37 °C), which induces a major metabolic transition. Our analysis profiles the structure of more than 1,750 RNAs at 25 °C, 37 °C, and 42 °C. Average mRNAs tend to be unstructured around the ribosome binding site. We searched for 5'-UTRs that are folded at low temperature and identified novel thermoresponsive RNA structures from diverse gene categories. The regulatory potential of 16 candidates was validated. In summary, we present a dynamic bacterial RNA structurome and find that the expression of virulence-relevant functions in Y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mRNAs.
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CLASP2 interacts with p120-catenin and governs microtubule dynamics at adherens junctions
Shahbazi, Marta N.; Megias, Diego; Epifano, Carolina; Akhmanova, Anna; Gundersen, Gregg G.; Fuchs, Elaine
2013-01-01
Classical cadherins and their connections with microtubules (MTs) are emerging as important determinants of cell adhesion. However, the functional relevance of such interactions and the molecular players that contribute to tissue architecture are still emerging. In this paper, we report that the MT plus end–binding protein CLASP2 localizes to adherens junctions (AJs) via direct interaction with p120-catenin (p120) in primary basal mouse keratinocytes. Reductions in the levels of p120 or CLASP2 decreased the localization of the other protein to cell–cell contacts and altered AJ dynamics and stability. These features were accompanied by decreased MT density and altered MT dynamics at intercellular junction sites. Interestingly, CLASP2 was enriched at the cortex of basal progenitor keratinocytes, in close localization to p120. Our findings suggest the existence of a new mechanism of MT targeting to AJs with potential functional implications in the maintenance of proper cell–cell adhesion in epidermal stem cells. PMID:24368809
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Synoptic reporting in tumor pathology: advantages of a web-based system.
Qu, Zhenhong; Ninan, Shibu; Almosa, Ahmed; Chang, K G; Kuruvilla, Supriya; Nguyen, Nghia
2007-06-01
The American College of Surgeons Commission on Cancer (ACS-CoC) mandates that pathology reports at ACS-CoC-approved cancer programs include all scientifically validated data elements for each site and tumor specimen. The College of American Pathologists (CAP) has produced cancer checklists in static text formats to assist reporting. To be inclusive, the CAP checklists are pages long, requiring extensive text editing and multiple intermediate steps. We created a set of dynamic tumor-reporting templates, using Microsoft Active Server Page (ASP.NET), with drop-down list and data-compile features, and added a reminder function to indicate missing information. Users can access this system on the Internet, prepare the tumor report by selecting relevant data from drop-down lists with an embedded tumor staging scheme, and directly transfer the final report into a laboratory information system by using the copy-and-paste function. By minimizing extensive text editing and eliminating intermediate steps, this system can reduce reporting errors, improve work efficiency, and increase compliance.
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Descriptive and experimental analyses of variables maintaining self-injurious behavior.
Lerman, D C; Iwata, B A
1993-01-01
Independent descriptive (correlational) and functional (experimental) analyses were conducted to determine the extent to which the two methods would yield data supporting similar conclusions about variables maintaining the self-injurious behavior (SIB) of 6 subjects. For the descriptive analyses, subjects were observed in their residences and at training sites at various times each day while observers recorded naturally occurring sequences of specified subject and staff behaviors. The subjects also participated in a day program for the assessment and treatment of SIB, in which they were exposed to functional analyses that manipulated potential maintaining variables in multielement designs. Both sets of data were analyzed via conditional probabilities to identify relevant antecedent and consequent events for subjects' SIB. Using outcomes of the experimental analysis as the standard for comparison, results indicated that the descriptive analysis was useful in identifying the extent to which SIB was related to social versus nonsocial contingencies, but was limited in its ability to distinguish between positive and negative reinforcement (i.e., attention versus escape). PMID:8407680
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Regulation of the Drosophila Hypoxia-Inducible Factor α Sima by CRM1-Dependent Nuclear Export ▿
Romero, Nuria M.; Irisarri, Maximiliano; Roth, Peggy; Cauerhff, Ana; Samakovlis, Christos; Wappner, Pablo
2008-01-01
Hypoxia-inducible factor α (HIF-α) proteins are regulated by oxygen levels through several different mechanisms that include protein stability, transcriptional coactivator recruitment, and subcellular localization. It was previously reported that these transcription factors are mainly nuclear in hypoxia and cytoplasmic in normoxia, but so far the molecular basis of this regulation is unclear. We show here that the Drosophila melanogaster HIF-α protein Sima shuttles continuously between the nucleus and the cytoplasm. We identified the relevant nuclear localization signal and two functional nuclear export signals (NESs). These NESs are in the Sima basic helix-loop-helix (bHLH) domain and promote CRM1-dependent nuclear export. Site-directed mutagenesis of either NES provoked Sima nuclear retention and increased transcriptional activity, suggesting that nuclear export contributes to Sima regulation. The identified NESs are conserved and probably functional in the bHLH domains of several bHLH-PAS proteins. We propose that rapid nuclear export of Sima regulates the duration of cellular responses to hypoxia. PMID:18332128
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Tight Junction Proteins and Oxidative Stress in Heavy Metals-Induced Nephrotoxicity
Reyes, José L.; Molina-Jijón, Eduardo; Rodríguez-Muñoz, Rafael; Bautista-García, Pablo; Debray-García, Yazmin; Namorado, María del Carmen
2013-01-01
Kidney is a target organ for heavy metals. They accumulate in several segments of the nephron and cause profound alterations in morphology and function. Acute intoxication frequently causes acute renal failure. The effects of chronic exposure have not been fully disclosed. In recent years increasing awareness of the consequences of their presence in the kidney has evolved. In this review we focus on the alterations induced by heavy metals on the intercellular junctions of the kidney. We describe that in addition to the proximal tubule, which has been recognized as the main site of accumulation and injury, other segments of the nephron, such as glomeruli, vessels, and distal nephron, show also deleterious effects. We also emphasize the participation of oxidative stress as a relevant component of the renal damage induced by heavy metals and the beneficial effect that some antioxidant drugs, such as vitamin A (all-trans-retinoic acid) and vitamin E (α-tocopherol), depict on the morphological and functional alterations induced by heavy metals. PMID:23710457
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Inverted-U Function Relating Cortical Plasticity and Task Difficulty
Engineer, Navzer D.; Engineer, Crystal T.; Reed, Amanda C.; Pandya, Pritesh K.; Jakkamsetti, Vikram; Moucha, Raluca; Kilgard, Michael P.
2012-01-01
Many psychological and physiological studies with simple stimuli have suggested that perceptual learning specifically enhances the response of primary sensory cortex to task-relevant stimuli. The aim of this study was to determine whether auditory discrimination training on complex tasks enhances primary auditory cortex responses to a target sequence relative to non-target and novel sequences. We collected responses from more than 2,000 sites in 31 rats trained on one of six discrimination tasks that differed primarily in the similarity of the target and distractor sequences. Unlike training with simple stimuli, long-term training with complex stimuli did not generate target specific enhancement in any of the groups. Instead, cortical receptive field size decreased, latency decreased, and paired pulse depression decreased in rats trained on the tasks of intermediate difficulty while tasks that were too easy or too difficult either did not alter or degraded cortical responses. These results suggest an inverted-U function relating neural plasticity and task difficulty. PMID:22249158
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Chialvo, Ariel A.; Vlcek, Lukas
2014-12-16
We explore the deconvolution of the water-nitrate correlations by the first-order difference approach involving neutron diffraction of heavy- and null-aqueous solutions of KNO 3 under 14N 15N and natON 18ON substitutions to achieve a full characterization of the first water coordination around the nitrate ion. For that purpose we performed isobaric-isothermal simulations of 3.5m KNO 3 aqueous solutions at ambient conditions to generate the relevant radial distribution functions (RDF) required in the analysis (a) to identify the individual partial contributions to the total neutron weighted distribution function, (b) to isolate and assess the contribution of NO 3 -!K + pairmore » formation, (c) to test the accuracy of the NDIS-based coordination calculations and XRDbased assumptions, and (d) to describe the water coordination around both the nitrogen and oxygen sites of the nitrate ion.« less
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MEF2 responds to multiple calcium-regulated signals in the control of skeletal muscle fiber type
Wu, Hai; Naya, Francisco J.; McKinsey, Timothy A.; Mercer, Brian; Shelton, John M.; Chin, Eva R.; Simard, Alain R.; Michel, Robin N.; Bassel-Duby, Rhonda; Olson, Eric N.; Williams, R. Sanders
2000-01-01
Different patterns of motor nerve activity drive distinctive programs of gene transcription in skeletal muscles, thereby establishing a high degree of metabolic and physiological specialization among myofiber subtypes. Recently, we proposed that the influence of motor nerve activity on skeletal muscle fiber type is transduced to the relevant genes by calcineurin, which controls the functional activity of NFAT (nuclear family of activated T cell) proteins. Here we demonstrate that calcineurin-dependent gene regulation in skeletal myocytes is mediated also by MEF2 transcription factors, and is integrated with additional calcium-regulated signaling inputs, specifically calmodulin-dependent protein kinase activity. In skeletal muscles of transgenic mice, both NFAT and MEF2 binding sites are necessary for properly regulated function of a slow fiber-specific enhancer, and either forced expression of activated calcineurin or motor nerve stimulation up-regulates a MEF2-dependent reporter gene. These results provide new insights into the molecular mechanisms by which specialized characteristics of skeletal myofiber subtypes are established and maintained. PMID:10790363
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Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65
Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K.; Zhu, Hu; Chen, Xin; Moy, Sheryl S.; Saddoris, Kara A.; Nikolova, Viktoriya; Farrell, Martilias S.; Wang, Sheng; Mangano, Thomas J.; Deshpande, Deepak A.; Jiang, Alice; Penn, Raymond B.; Jin, Jian; Koller, Beverly H.; Kenakin, Terry; Shoichet, Brian K.; Roth, Bryan L.
2016-01-01
At least 120 non-olfactory G protein-coupled receptors in the human genome are ”orphans” for which endogenous ligands are unknown, and many have no selective ligands, hindering elucidation of their biological functions and clinical relevance. Among these is GPR68, a proton receptor that lacks small molecule modulators for probing its biology. Yeast-based screens against GPR68 identified the benzodiazepine drug lorazepam as a non-selective GPR68 positive allosteric modulator. Over 3000 GPR68 homology models were refined to recognize lorazepam in a putative allosteric site. Docking 3.1 million molecules predicted new GPR68 modulators many of which were confirmed in functional assays. One potent GPR68 modulator—ogerin– suppressed recall in fear conditioning in wild-type, but not in GPR68 knockout mice. The same approach led to the discovery of allosteric agonists and negative allosteric modulators for GPR65. Combining physical and structure-based screening may be broadly useful for ligand discovery for understudied and orphan GPCRs. PMID:26550826
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Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.
Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim
2014-07-08
Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.
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No evidence for a local renin-angiotensin system in liver mitochondria
Astin, Ronan; Bentham, Robert; Djafarzadeh, Siamak; Horscroft, James A.; Kuc, Rhoda E.; Leung, Po Sing; Skipworth, James R. A.; Vicencio, Jose M.; Davenport, Anthony P.; Murray, Andrew J.; Takala, Jukka; Jakob, Stephan M.; Montgomery, Hugh; Szabadkai, Gyorgy
2013-01-01
The circulating, endocrine renin-angiotensin system (RAS) is important to circulatory homeostasis, while ubiquitous tissue and cellular RAS play diverse roles, including metabolic regulation. Indeed, inhibition of RAS is associated with improved cellular oxidative capacity. Recently it has been suggested that an intra-mitochondrial RAS directly impacts on metabolism. Here we sought to rigorously explore this hypothesis. Radiolabelled ligand-binding and unbiased proteomic approaches were applied to purified mitochondrial sub-fractions from rat liver, and the impact of AngII on mitochondrial function assessed. Whilst high-affinity AngII binding sites were found in the mitochondria-associated membrane (MAM) fraction, no RAS components could be detected in purified mitochondria. Moreover, AngII had no effect on the function of isolated mitochondria at physiologically relevant concentrations. We thus found no evidence of endogenous mitochondrial AngII production, and conclude that the effects of AngII on cellular energy metabolism are not mediated through its direct binding to mitochondrial targets. PMID:23959064
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Androgens and the male reproductive tract: an overview of classical roles and current perspectives.
Patrão, Marilia T C C; Silva, Erick J R; Avellar, Maria Christina W
2009-11-01
Androgens are steroid hormones that play key roles in the development and maintenance of male phenotype and reproductive function. These hormones also affect the function of several non-reproductive organs, such as bone and skeletal muscle. Endogenous androgens exert most of their effects by genomic mechanisms, which involve hormone binding to the androgen receptor (AR), a ligand-activated transcription factor, resulting in the modulation of gene expression. AR-induced non-genomic mechanisms have also been reported. A large number of steroidal and non-steroidal AR-ligands have been developed for therapeutic use, including the treatment of male hypogonadism (AR agonists) and prostate diseases (AR antagonists), among other pathological conditions. Here, the AR gene and protein structure, mechanism of action and AR gene homologous regulation were reviewed. The AR expression pattern, its in vivo regulation and physiological relevance in the developing and adult testis and epididymis, which are sites of sperm production and maturation, respectively, were also presented.
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Inflammation, vitamin B6 and related pathways.
Ueland, Per Magne; McCann, Adrian; Midttun, Øivind; Ulvik, Arve
2017-02-01
The active form of vitamin B6, pyridoxal 5'-phosphate (PLP), serves as a co-factor in more than 150 enzymatic reactions. Plasma PLP has consistently been shown to be low in inflammatory conditions; there is a parallel reduction in liver PLP, but minor changes in erythrocyte and muscle PLP and in functional vitamin B6 biomarkers. Plasma PLP also predicts the risk of chronic diseases like cardiovascular disease and some cancers, and is inversely associated with numerous inflammatory markers in clinical and population-based studies. Vitamin B6 intake and supplementation improve some immune functions in vitamin B6-deficient humans and experimental animals. A possible mechanism involved is mobilization of vitamin B6 to the sites of inflammation where it may serve as a co-factor in pathways producing metabolites with immunomodulating effects. Relevant vitamin B6-dependent inflammatory pathways include vitamin B6 catabolism, the kynurenine pathway, sphingosine 1-phosphate metabolism, the transsulfuration pathway, and serine and glycine metabolism. Copyright © 2016 Elsevier Ltd. All rights reserved.
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Wiehe, Kevin; Bradley, Todd; Meyerhoff, R Ryan; Hart, Connor; Williams, Wilton B; Easterhoff, David; Faison, William J; Kepler, Thomas B; Saunders, Kevin O; Alam, S Munir; Bonsignori, Mattia; Haynes, Barton F
2018-06-13
HIV-1 broadly neutralizing antibodies (bnAbs) require high levels of activation-induced cytidine deaminase (AID)-catalyzed somatic mutations for optimal neutralization potency. Probable mutations occur at sites of frequent AID activity, while improbable mutations occur where AID activity is infrequent. One bottleneck for induction of bnAbs is the evolution of viral envelopes (Envs) that can select bnAb B cell receptors (BCR) with improbable mutations. Here we define the probability of bnAb mutations and demonstrate the functional significance of key improbable mutations in three bnAb B cell lineages. We show that bnAbs are enriched for improbable mutations, which implies that their elicitation will be critical for successful vaccine induction of potent bnAb B cell lineages. We discuss a mutation-guided vaccine strategy for identification of Envs that can select B cells with BCRs that have key improbable mutations required for bnAb development. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.
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PDT dose dosimetry for Photofrin-mediated pleural photodynamic therapy (pPDT)
NASA Astrophysics Data System (ADS)
Ong, Yi Hong; Kim, Michele M.; Finlay, Jarod C.; Dimofte, Andreea; Singhal, Sunil; Glatstein, Eli; Cengel, Keith A.; Zhu, Timothy C.
2018-01-01
Photosensitizer fluorescence excited by photodynamic therapy (PDT) treatment light can be used to monitor the in vivo concentration of the photosensitizer and its photobleaching. The temporal integral of the product of in vivo photosensitizer concentration and light fluence is called PDT dose, which is an important dosimetry quantity for PDT. However, the detected photosensitizer fluorescence may be distorted by variations in the absorption and scattering of both excitation and fluorescence light in tissue. Therefore, correction of the measured fluorescence for distortion due to variable optical properties is required for absolute quantification of photosensitizer concentration. In this study, we have developed a four-channel PDT dose dosimetry system to simultaneously acquire light dosimetry and photosensitizer fluorescence data. We measured PDT dose at four sites in the pleural cavity during pleural PDT. We have determined an empirical optical property correction function using Monte Carlo simulations of fluorescence for a range of physiologically relevant tissue optical properties. Parameters of the optical property correction function for Photofrin fluorescence were determined experimentally using tissue-simulating phantoms. In vivo measurements of photosensitizer fluorescence showed negligible photobleaching of Photofrin during the PDT treatment, but large intra- and inter-patient heterogeneities of in vivo Photofrin concentration are observed. PDT doses delivered to 22 sites in the pleural cavity of 8 patients were different by 2.9 times intra-patient and 8.3 times inter-patient.
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Trends in Culturally Relevant Interface Design Features for Latino Web Site Users
ERIC Educational Resources Information Center
Sachau, Lori L.; Hutchinson, Susan R.
2012-01-01
There is a lack of published research on designing Web-based instruction for the adult U.S. Latino population. Instructional designers need guidance on how to design culturally relevant learning environments for this audience, particularly for Latino people from Mexican heritage. The authors used content analysis to investigate the extent to which…
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ERIC Educational Resources Information Center
Jaffee, Ashley Taylor
2016-01-01
This study examines how teachers in 4 urban newcomer high schools conceptualized and implemented social studies education for Latino/a newcomer youth through an emerging framework of culturally and linguistically relevant citizenship education. Through a multi-site, collective case study design, the perspectives and decision making of social…
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Mendoza, Brian J; Trinh, Cong T
2018-01-01
Genetic diversity of non-model organisms offers a repertoire of unique phenotypic features for exploration and cultivation for synthetic biology and metabolic engineering applications. To realize this enormous potential, it is critical to have an efficient genome editing tool for rapid strain engineering of these organisms to perform novel programmed functions. To accommodate the use of CRISPR/Cas systems for genome editing across organisms, we have developed a novel method, named CRISPR Associated Software for Pathway Engineering and Research (CASPER), for identifying on- and off-targets with enhanced predictability coupled with an analysis of non-unique (repeated) targets to assist in editing any organism with various endonucleases. Utilizing CASPER, we demonstrated a modest 2.4% and significant 30.2% improvement (F-test, P < 0.05) over the conventional methods for predicting on- and off-target activities, respectively. Further we used CASPER to develop novel applications in genome editing: multitargeting analysis (i.e. simultaneous multiple-site modification on a target genome with a sole guide-RNA requirement) and multispecies population analysis (i.e. guide-RNA design for genome editing across a consortium of organisms). Our analysis on a selection of industrially relevant organisms revealed a number of non-unique target sites associated with genes and transposable elements that can be used as potential sites for multitargeting. The analysis also identified shared and unshared targets that enable genome editing of single or multiple genomes in a consortium of interest. We envision CASPER as a useful platform to enhance the precise CRISPR genome editing for metabolic engineering and synthetic biology applications. https://github.com/TrinhLab/CASPER. ctrinh@utk.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com
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Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies
NASA Astrophysics Data System (ADS)
Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo
2011-06-01
The identification of BACE-1, a key enzyme in the production of Amyloid-β (Aβ) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of Aβ peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus dispersion energies.
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Quantum mechanics study of the hydroxyethylamines-BACE-1 active site interaction energies.
Gueto-Tettay, Carlos; Drosos, Juan Carlos; Vivas-Reyes, Ricardo
2011-06-01
The identification of BACE-1, a key enzyme in the production of Amyloid-β (Aβ) peptides, generated by the proteolytic processing of amyloid precursor protein, was a major advance in the field of Alzheimer's disease as this pathology is characterized by the presence of extracellular senile plaques, mainly comprised of Aβ peptides. Hydroxyethylamines have demonstrated a remarkable potential, like candidate drugs, for this disease using BACE-1 as target. Density Functional Theory calculations were employed to estimate interaction energies for the complexes formed between the hydroxyethylamine derivated inhibitors and 24 residues in the BACE-1 active site. The collected data offered not only a general but a particular quantitative description that gives a deep insight of the interactions in the active site, showing at the same time how ligand structural variations affect them. Polar interactions are the major energetic contributors for complex stabilization and those ones with charged aspartate residues are highlighted, as they contribute over 90% of the total attractive interaction energy. Ligand-ARG296 residue interaction reports the most repulsive value and decreasing of the magnitude of this repulsion can be a key feature for the design of novel and more potent BACE-1 inhibitors. Also it was explained why sultam derivated BACE-1 inhibitors are better ones than lactam based. Hydrophobic interactions concentrated at S1 zone and other relevant repulsions and attractions were also evaluated. The comparison of two different theory levels (X3LYP and M062X) allowed to confirm the relevance of the detected interactions as each theory level has its own strength to depict the forces involved, as is the case of M062X which is better describing the hydrophobic interactions. Those facts were also evaluated and confirmed by comparing the quantitative trend, of selected ligand-residue interactions, with MP2 theory level as reference standard method for electrostatic plus dispersion energies.