Energy Technology Data Exchange (ETDEWEB)
Sofia, Heidi J.; Chen, Guang; Hetzler, Elizabeth G.; Reyes Spindola, Jorge F.; Miller, Nancy E.
2001-03-01
A large protein superfamily with over 500 members has been discovered and analyzed using powerful new bioinformatics and information visualization methods. Evidence exists that these proteins generate a 5?-deoxyadenosyl radical by reductive cleavage of S-adenosylmethionine (SAM) through an unusual Fe-S center. Radical SAM superfamily proteins function in DNA precursor, vitamin, cofactor, antibiotic, and herbicide biosynthesis in a collection of basic and familiar pathways. One of the members is interferon-inducible and is considered a candidate drug target for osteoporosis. The identification of this superfamily suggests that radical-based catalysis is important in a number of previously well-studied but unresolved biochemical pathways.
Inference of functional properties from large-scale analysis of enzyme superfamilies.
Brown, Shoshana D; Babbitt, Patricia C
2012-01-02
As increasingly large amounts of data from genome and other sequencing projects become available, new approaches are needed to determine the functions of the proteins these genes encode. We show how large-scale computational analysis can help to address this challenge by linking functional information to sequence and structural similarities using protein similarity networks. Network analyses using three functionally diverse enzyme superfamilies illustrate the use of these approaches for facile updating and comparison of available structures for a large superfamily, for creation of functional hypotheses for metagenomic sequences, and to summarize the limits of our functional knowledge about even well studied superfamilies.
Inference of Functional Properties from Large-scale Analysis of Enzyme Superfamilies*
Brown, Shoshana D.; Babbitt, Patricia C.
2012-01-01
As increasingly large amounts of data from genome and other sequencing projects become available, new approaches are needed to determine the functions of the proteins these genes encode. We show how large-scale computational analysis can help to address this challenge by linking functional information to sequence and structural similarities using protein similarity networks. Network analyses using three functionally diverse enzyme superfamilies illustrate the use of these approaches for facile updating and comparison of available structures for a large superfamily, for creation of functional hypotheses for metagenomic sequences, and to summarize the limits of our functional knowledge about even well studied superfamilies. PMID:22069325
The aldo-keto reductase superfamily homepage.
Hyndman, David; Bauman, David R; Heredia, Vladi V; Penning, Trevor M
2003-02-01
The aldo-keto reductases (AKRs) are one of the three enzyme superfamilies that perform oxidoreduction on a wide variety of natural and foreign substrates. A systematic nomenclature for the AKR superfamily was adopted in 1996 and was updated in September 2000 (visit www.med.upenn.edu/akr). Investigators have been diligent in submitting sequences of functional proteins to the Web site. With the new additions, the superfamily contains 114 proteins expressed in prokaryotes and eukaryotes that are distributed over 14 families (AKR1-AKR14). The AKR1 family contains the aldose reductases, the aldehyde reductases, the hydroxysteroid dehydrogenases and steroid 5beta-reductases, and is the largest. Other families of interest include AKR6, which includes potassium channel beta-subunits, and AKR7 the aflatoxin aldehyde reductases. Two new families include AKR13 (yeast aldose reductase) and AKR14 (Escherichia coli aldehyde reductase). Crystal structures of many AKRs and their complexes with ligands are available in the PDB and accessible through the Web site. Each structure has the characteristic (alpha/beta)(8)-barrel motif of the superfamily, a conserved cofactor binding site and a catalytic tetrad, and variable loop structures that define substrate specificity. Although the majority of AKRs are monomeric proteins of about 320 amino acids in length, the AKR2, AKR6 and AKR7 family may form multimers. To expand the nomenclature to accommodate multimers, we recommend that the composition and stoichiometry be listed. For example, AKR7A1:AKR7A4 (1:3) would designate a tetramer of the composition indicated. The current nomenclature is recognized by the Human Genome Project (HUGO) and the Web site provides a link to genomic information including chromosomal localization, gene boundaries, human ESTs and SNPs and much more.
Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A
2016-01-29
Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.
Spatial and temporal expression of immunoglobulin superfamily member 1 in the rat
Joustra, Sjoerd D.; Meijer, Onno C.; Heinen, Charlotte A.; Mol, Isabel M.; Laghmani, El Houari; Sengers, Rozemarijn M. A.; Carreno, Gabriela; van Trotsenburg, A. S. Paul; Biermasz, Nienke R.; Bernard, Daniel J.; Wit, Jan M.; Oostdijk, Wilma; van Pelt, Ans M. M.; Hamer, Geert; Wagenaar, Gerry T. M.
2015-01-01
Loss-of-function mutations in the immunoglobulin superfamily member 1 (IGSF1) gene cause an X-linked syndrome of central hypothyroidism, macroorchidism, variable prolactin and GH deficiency, delayed pubertal testosterone rise, and obesity. To understand the pathophysiology of this syndrome,
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
Hu, H.; Haas, S.A.; Chelly, J.; Van Esch, H.; Raynaud, M.; de Brouwer, A.P.M.; Weinert, S.; Froyen, G.; Frints, S.G.M.; Laumonnier, F.; Zemojtel, T.; Love, M.I.; Richard, H.; Emde, A.K.; Bienek, M.
2016-01-01
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of ...
CD147 Immunoglobulin Superfamily Receptor Function and Role in Pathology
Iacono, Kathryn T.; Brown, Amy L.; Greene, Mark I.; Saouaf, Sandra J.
2007-01-01
The immunoglobulin superfamily member CD147 plays an important role in fetal, neuronal, lymphocyte and extracellular matrix development. Here we review the current understanding of CD147 expression and protein interactions with regard to CD147 function and its role in pathologic conditions including heart disease, Alzheimer’s disease, stroke and cancer. A model linking hypoxic conditions found within the tumor microenvironment to up-regulation of CD147 expression and tumor progression is intr...
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
Hu, H; Haas, S.A.; Chelly, J.; Esch, H. Van; Raynaud, M.; Brouwer, A.P. de; Weinert, S.; Froyen, G.; Frints, S.G.; Laumonnier, F.; Zemojtel, T.; Love, M.I.; Richard, H.; Emde, A.K.; Bienek, M.; Jensen, C.; Hambrock, M.; Fischer, U.; Langnick, C.; Feldkamp, M.; Wissink-Lindhout, W.; Lebrun, N.; Castelnau, L.; Rucci, J.; Montjean, R.; Dorseuil, O.; Billuart, P.; Stuhlmann, T.; Shaw, M.; Corbett, M.A.; Gardner, A.; Willis-Owen, S.; Tan, C.; Friend, K.L.; Belet, S.; Roozendaal, K.E. van; Jimenez-Pocquet, M.; Moizard, M.P.; Ronce, N.; Sun, R.; O'Keeffe, S.; Chenna, R.; Bommel, A. van; Goke, J.; Hackett, A.; Field, M.; Christie, L.; Boyle, J.; Haan, E.; Nelson, J.; Turner, G.; Baynam, G.; Gillessen-Kaesbach, G.; Muller, U.; Steinberger, D.; Budny, B.; Badura-Stronka, M.; Latos-Bielenska, A.; Ousager, L.B.; Wieacker, P.; Rodriguez Criado, G.; Bondeson, M.L.; Anneren, G.; Dufke, A.; Cohen, M.; Maldergem, L. Van; Vincent-Delorme, C.; Echenne, B.; Simon-Bouy, B.; Kleefstra, T.; Willemsen, M.H.; Fryns, J.P.; Devriendt, K.; Ullmann, R.; Vingron, M.; Wrogemann, K.; Wienker, T.F.; Tzschach, A.; Bokhoven, H. van; Gecz, J.; Jentsch, T.J.; Chen, W.; Ropers, H.H.; Kalscheuer, V.M.
2016-01-01
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
DEFF Research Database (Denmark)
Hu, H; Haas, S A; Chelly, J
2016-01-01
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes...
Unresolved mourning, supernatural beliefs and dissociation: a mediation analysis.
Thomson, Paula; Jaque, S Victoria
2014-01-01
Unresolved mourning is marked by disorganized behavior and states of mind. In this study, we speculated that pathological dissociation would mediate the effects of unresolved mourning on supernatural beliefs. This hypothesis was determined based on findings that indicate an association between higher levels of dissociation, stronger beliefs in the supernatural and unresolved mourning. We examined two groups of participants, one classified as non-unresolved (non-U) (n = 56) and the other as unresolved (n = 26) (U) with respect to past loss/trauma as measured by the Adult Attachment Interview (AAI). Two self-report instruments were administered to measure supernatural beliefs and dissociation. As hypothesized, the multivariate analysis of variance indicated mean differences between the two groups. The unresolved group had greater belief in the supernatural and more pathological dissociative processes. The mediation analysis demonstrated that pathological dissociation fully mediated the effects of unresolved mourning on supernatural beliefs.
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
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Ranyee A Chiang
2008-08-01
Full Text Available The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.
Chiang, Ranyee A; Sali, Andrej; Babbitt, Patricia C
2008-08-01
The evolution of enzymes affects how well a species can adapt to new environmental conditions. During enzyme evolution, certain aspects of molecular function are conserved while other aspects can vary. Aspects of function that are more difficult to change or that need to be reused in multiple contexts are often conserved, while those that vary may indicate functions that are more easily changed or that are no longer required. In analogy to the study of conservation patterns in enzyme sequences and structures, we have examined the patterns of conservation and variation in enzyme function by analyzing graph isomorphisms among enzyme substrates of a large number of enzyme superfamilies. This systematic analysis of substrate substructures establishes the conservation patterns that typify individual superfamilies. Specifically, we determined the chemical substructures that are conserved among all known substrates of a superfamily and the substructures that are reacting in these substrates and then examined the relationship between the two. Across the 42 superfamilies that were analyzed, substantial variation was found in how much of the conserved substructure is reacting, suggesting that superfamilies may not be easily grouped into discrete and separable categories. Instead, our results suggest that many superfamilies may need to be treated individually for analyses of evolution, function prediction, and guiding enzyme engineering strategies. Annotating superfamilies with these conserved and reacting substructure patterns provides information that is orthogonal to information provided by studies of conservation in superfamily sequences and structures, thereby improving the precision with which we can predict the functions of enzymes of unknown function and direct studies in enzyme engineering. Because the method is automated, it is suitable for large-scale characterization and comparison of fundamental functional capabilities of both characterized and uncharacterized
Main trends of karyotype evolution in the superfamily Chalcidoidea (Hymenoptera
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Vladimir Gokhman
2009-08-01
Full Text Available An overview of karyotype evolution in the superfamily Chalcidoidea is given. Structural types of chromosome sets in the superfamily are listed. Main pathways of karyotypic change in the Chalcidoidea are outlined. The chromosome set containing eleven subtelo- or acrocentrics is considered as an ancestral karyotype for the superfamily. Multiple independent reductions in n values through chromosomal fusions presumably occurred in various groups of chalcid families.
Phylogenomic analysis of the GIY-YIG nuclease superfamily
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Bujnicki Janusz M
2006-04-01
Full Text Available Abstract Background The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported. Results We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for extending the GIY-YIG superfamily to include members of COG3680 and a number of proteins not classified in COGs and to predict that these proteins may function as nucleases, potentially involved in DNA recombination and/or repair. Finally, all old and new members of the GIY-YIG superfamily were compared and analyzed to infer the phylogenetic tree. Conclusion An evolutionary classification of the GIY-YIG superfamily is presented for the very first time, along with the structural annotation of all (subfamilies. It provides a comprehensive picture of sequence-structure-function relationships in this superfamily of nucleases, which will help to design experiments to study the mechanism of action of known members (especially the uncharacterized ones and will facilitate the prediction of function for the newly discovered ones.
Two different groups of signal sequence in M-superfamily conotoxins.
Wang, Qi; Jiang, Hui; Han, Yu-Hong; Yuan, Duo-Duo; Chi, Cheng-Wu
2008-04-01
M-superfamily conotoxins can be divided into four branches (M-1, M-2, M-3 and M-4) according to the number of amino acid residues in the third Cys loop. In general, it is widely accepted that the conotoxin signal peptides of each superfamily are strictly conserved. Recently, we cloned six cDNAs of novel M-superfamily conotoxins from Conus leopardus, Conus marmoreus and Conus quercinus, belonging to either M-1 or M-3 branch. These conotoxins, judging from the putative peptide sequences deducted from cDNAs, are rich in acidic residues and share highly conserved signal and pro-peptide region. However, they are quite different from the reported conotoxins of M-2 and M-4 branches even in their signal peptides, which in general are considered highly conserved for each superfamily of conotoxins. The signal sequences of M-1 and M-3 conotoxins composed of 24 residues start with MLKMGVVL-, while those of M-2 and M-4 conotoxins composed of 25 residues start with MMSKLGVL-. It is another example that different types of signal peptides can exist within a superfamily besides the I-conotoxin superfamily. In addition to the different disulfide connectivity of M-1 conotoxins from that of M-4 or M-2 conotoxins, the sequence alignment, preferential Cys codon usage and phylogenetic tree analysis suggest that M-1 and M-3 conotoxins have much closer relationship, being different from the conotoxins of other two branches (M-4 and M-2) of M-superfamily.
A global view of structure-function relationships in the tautomerase superfamily.
Davidson, Rebecca; Baas, Bert-Jan; Akiva, Eyal; Holliday, Gemma L; Polacco, Benjamin J; LeVieux, Jake A; Pullara, Collin R; Zhang, Yan Jessie; Whitman, Christian P; Babbitt, Patricia C
2018-02-16
The tautomerase superfamily (TSF) consists of more than 11,000 nonredundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure-function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence similarity network to guide classification into distinct subgroups. Our results indicate that TSF members are found in all domains of life, with most being present in bacteria. The eukaryotic members of the cis -3-chloroacrylic acid dehalogenase subgroup are limited to fungal species, whereas the macrophage migration inhibitory factor subgroup has wide eukaryotic representation (including mammals). Unexpectedly, we found that 346 TSF sequences lack Pro-1, of which 85% are present in the malonate semialdehyde decarboxylase subgroup. The computed network also enabled the identification of similarity paths, namely sequences that link functionally diverse subgroups and exhibit transitional structural features that may help explain reaction divergence. A structure-guided comparison of these linker proteins identified conserved transitions between them, and kinetic analysis paralleled these observations. Phylogenetic reconstruction of the linker set was consistent with these findings. Our results also suggest that contemporary TSF members may have evolved from a short 4-oxalocrotonate tautomerase-like ancestor followed by gene duplication and fusion. Our new linker-guided strategy can be used to enrich the discovery of sequence/structure/function transitions in other enzyme superfamilies. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.
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Holly J Atkinson
Full Text Available The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.
Atkinson, Holly J; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C
2009-01-01
The dramatic increase in heterogeneous types of biological data--in particular, the abundance of new protein sequences--requires fast and user-friendly methods for organizing this information in a way that enables functional inference. The most widely used strategy to link sequence or structure to function, homology-based function prediction, relies on the fundamental assumption that sequence or structural similarity implies functional similarity. New tools that extend this approach are still urgently needed to associate sequence data with biological information in ways that accommodate the real complexity of the problem, while being accessible to experimental as well as computational biologists. To address this, we have examined the application of sequence similarity networks for visualizing functional trends across protein superfamilies from the context of sequence similarity. Using three large groups of homologous proteins of varying types of structural and functional diversity--GPCRs and kinases from humans, and the crotonase superfamily of enzymes--we show that overlaying networks with orthogonal information is a powerful approach for observing functional themes and revealing outliers. In comparison to other primary methods, networks provide both a good representation of group-wise sequence similarity relationships and a strong visual and quantitative correlation with phylogenetic trees, while enabling analysis and visualization of much larger sets of sequences than trees or multiple sequence alignments can easily accommodate. We also define important limitations and caveats in the application of these networks. As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships.
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals.
Nishihara, Hidenori; Plazzi, Federico; Passamonti, Marco; Okada, Norihiro
2016-02-12
SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we describe 15 SINEs, among which 13 are novel, that have a similar 66-bp central region and therefore constitute a new SINE superfamily, MetaSINEs. MetaSINEs are distributed from fish to cnidarians, suggesting their common evolutionary origin at least 640 Ma. Because the 3' tails of MetaSINEs are variable, these SINEs most likely survived by changing their partner long interspersed elements for retrotransposition during evolution. Furthermore, we examined the presence of members of other SINE superfamilies in bivalve genomes and characterized eight new SINEs belonging to the CORE-SINEs, V-SINEs, and DeuSINEs, in addition to the MetaSINEs. The broad distribution of bivalve SINEs suggests that at least three SINEs originated in the common ancestor of Bivalvia. Our comparative analysis of the central domains of the SINEs revealed that, in each superfamily, only a restricted region is shared among all of its members. Because the functions of the central domains of the SINE superfamilies remain unknown, such structural information of SINE superfamilies will be useful for future experimental and comparative analyses to reveal why they have been retained in metazoan genomes during evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Unresolved safety issues summary: aqua book
International Nuclear Information System (INIS)
1982-06-01
The unresolved safety issues summary is designed to provide the management of the Nuclear Regulatory Commission with a quarterly overview of the progress and plans for completion of generic tasks addressing unresolved safety issues reported to Congress pursuant to Section 210 of the Energy Reorganization Act of 1974 as amended. This summary utilizes data collected from the Office of Nuclear Reactor Regulation, Office of Nuclear Regulatory Research, and the National Laboratories and is prepared by the Office of Resource Management. The schedules in this book include a milestone at the end of each action plan which represents the initiation of the implementation process both with respect to incorporation of the technical resolution in the NRC official guidance or requirements and also the application of changes to individual operating plants. The progress and status for implementation of unresolved safety issues for which a technical resolution has been completed are reported specifically in a separate table provided in this summary
Heinz, Eva; Lithgow, Trevor
2014-01-01
Members of the Omp85/TpsB protein superfamily are ubiquitously distributed in Gram-negative bacteria, and function in protein translocation (e.g., FhaC) or the assembly of outer membrane proteins (e.g., BamA). Several recent findings are suggestive of a further level of variation in the superfamily, including the identification of the novel membrane protein assembly factor TamA and protein translocase PlpD. To investigate the diversity and the causal evolutionary events, we undertook a comprehensive comparative sequence analysis of the Omp85/TpsB proteins. A total of 10 protein subfamilies were apparent, distinguished in their domain structure and sequence signatures. In addition to the proteins FhaC, BamA, and TamA, for which structural and functional information is available, are families of proteins with so far undescribed domain architectures linked to the Omp85 β-barrel domain. This study brings a classification structure to a dynamic protein superfamily of high interest given its essential function for Gram-negative bacteria as well as its diverse domain architecture, and we discuss several scenarios of putative functions of these so far undescribed proteins. PMID:25101071
MetaSINEs: Broad Distribution of a Novel SINE Superfamily in Animals
Nishihara, Hidenori; Plazzi, Federico; Passamonti, Marco; Okada, Norihiro
2016-01-01
SINEs (short interspersed elements) are transposable elements that typically originate independently in each taxonomic clade (order/family). However, some SINE families share a highly similar central sequence and are thus categorized as a SINE superfamily. Although only four SINE superfamilies (CORE-SINEs, V-SINEs, DeuSINEs, and Ceph-SINEs) have been reported so far, it is expected that new SINE superfamilies would be discovered by deep exploration of new SINEs in metazoan genomes. Here we de...
Unresolved safety issues summary: aqua book
International Nuclear Information System (INIS)
1983-06-01
The unresolved safety issues summary is designed to provide the management of the nuclear regulatory commission with a quarterly overview of the progress and plans for completion of generic tasks addressing unresolved safety issues reported to congress pursuant to section 210 of the Energy Reorganization Act of 1974 as amended. The schedules in this book include a milestone at the end of each action plan which represents the initiation of the implementation process both with respect to incorporation of the technical resolution in the NRC official guidance or requirements and also the application of changes to individual operating plants. The schedule for implementation will not normally be included in the task action plan(s) for the resolution of a USI since the nature and extent of the activities necessary to accomplish the implementation cannot normally be reasonably determined prior to the determination of a technical resolution. The progress and status for implementation of unresolved safety issues for which a technical resolution has been completed are reported specifically in a separate table provided in this summary
Self-shielding effect in unresolved resonance data in JENDL-4.0
International Nuclear Information System (INIS)
Konno, Chikara; Takakura, Kosuke; Ochiai, Kentaro; Sato, Satoshi; Kato, Yoshinari
2012-01-01
At International Conference on Nuclear Data for Science and Technology in 2007 we pointed out that most of unresolved resonance data in JENDL-3.3 have a problem related to self-shielding correction. Here with a simple calculation model we have investigated whether the latest JENDL, JENDL-4.0, was improved for the problem or not. The results suggest that unresolved resonance data in JENDL-4.0 have no problem, but it seems that self-shielding effects for the unresolved resonance data in JENDL-4.0 are too large. New benchmark experiments for unresolved resonance data are strongly recommended in order to verify unresolved resonance data. (author)
Keanekaragaman Jenis Kupu-Kupu Superfamili Papilionoidae di Banyuwindu, Limbangan Kendal
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Ratna Oqtafiana
2013-03-01
Full Text Available Kupu-kupu turut memberi andil dalam mempertahankan keseimbangan ekosistem dan memperkaya keanekaragaman hayati. Tujuan dari penelitian ini adalah untuk mengetahui keanekaragaman jenis kupu-kupu superfamili Papilionoidae di Dukuh Banyuwindu Desa Limbangan Kecamatan Limbangan Kabupaten Kendal khususnya di habitat hutan sekunder, permukiman, Daerah Aliran Sungai (DAS dan persawahan.Populasi dalam penelitian ini adalah semua jenis kupu-kupu superfamili Papilionoidae yang ada di Banyuwindu, Limbangan Kendal. Sampel penelitian ini adalah jenis kupu-kupu superfamili Papilionoidae yang teramati di Banyuwindu Limbangan Kendal khususnya di habitat hutan sekunder, permukiman, DAS dan persawahan. Penelitian dilakukan dengan metode Indeks Point Abudance (IPA atau metode titik hitung.Hasil penelitian ditemukan sebanyak 62 jenis kupu-kupu superfamili Papilionoidae yang terdiri dari 737 individu yang tergolong kedalam empat famili yaitu Papilionidae, Pieridae, Lycaenidae dan Nymphalidae. Hasil analisis indeks keanekaragaman jenis berkisar antara 2,74-3,09, indeks kemerataan jenis berkisar antara 0,86-0,87 dan memiliki dominansi berkisar antara 0,07-0,09. Indeks keanekaragaman jenis dan indeks kemerataan jenis tertinggi tercatat pada habitat permukiman yaitu 3,09 dan 0,87 dan memiliki dominansi 0,07 sedangkan terendah tercatat pada habitat persawahan yaitu 2,74 dan 0,86 dan memiliki dominansi 0,07.Butterfly also contribute in maintaining the ecological balance and enrich biodiversity. The aim of this research was to determine the diversity of butterflies’ superfamily Papilionoidae in Banyuwindu Hamlet Limbangan Sub district Kendal Regency, especially in the secondary forest habitat, settlements, river flow area (RFA and rice field. The population in this research were all kinds of butterflies’ Papilionoidae superfamily in Banyuwindu, Limbangan Kendal. The sample was kind of butterfly superfamily Papilionoidae that observed in Banyuwindu Limbangan Kendal
Designer TGFβ superfamily ligands with diversified functionality.
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George P Allendorph
Full Text Available Transforming Growth Factor--beta (TGFβ superfamily ligands, including Activins, Growth and Differentiation Factors (GDFs, and Bone Morphogenetic Proteins (BMPs, are excellent targets for protein-based therapeutics because of their pervasiveness in numerous developmental and cellular processes. We developed a strategy termed RASCH (Random Assembly of Segmental Chimera and Heteromer, to engineer chemically-refoldable TGFβ superfamily ligands with unique signaling properties. One of these engineered ligands, AB208, created from Activin-βA and BMP-2 sequences, exhibits the refolding characteristics of BMP-2 while possessing Activin-like signaling attributes. Further, we find several additional ligands, AB204, AB211, and AB215, which initiate the intracellular Smad1-mediated signaling pathways more strongly than BMP-2 but show no sensitivity to the natural BMP antagonist Noggin unlike natural BMP-2. In another design, incorporation of a short N-terminal segment from BMP-2 was sufficient to enable chemical refolding of BMP-9, without which was never produced nor refolded. Our studies show that the RASCH strategy enables us to expand the functional repertoire of TGFβ superfamily ligands through development of novel chimeric TGFβ ligands with diverse biological and clinical values.
McBride, Carolyn S.; Arguello, J. Roman
2007-01-01
The insect chemoreceptor superfamily comprises the olfactory receptor (Or) and gustatory receptor (Gr) multigene families. These families give insects the ability to smell and taste chemicals in the environment and are thus rich resources for linking molecular evolutionary and ecological processes. Although dramatic differences in family size among distant species and high divergence among paralogs have led to the belief that the two families evolve rapidly, a lack of evolutionary data over s...
Unresolved safety issues: where do we go from here
International Nuclear Information System (INIS)
Aycock, M.B.
1980-01-01
Section 210 of the Energy reorganization Act of 1974, as amended requires the NRC to develop a program for resolving Unresolved Safety Issues related to nuclear power plants. Seventeen Unresolved Safety Issues were identified by the NRC in 1978 and by early 1979 the NRC Unresolved Safety Issues Program was quickly becoming a well defined and manageable effort. Although, the Three Mile Island accident caused the momentum developed in early 1979 to be lost, efforts on ongoing generic tasks were continued by a special NRC Task Force established in June 1979. The momentum that was lost must be regained, however, if the Congressional mandate in Section 210 is to be met. With increased industry involvement and the marriage of the Unresolved Safety Issues Program with the improved and broader safety program development, audit and evaluation activities of the new NRR Division of Safety Technology, this should be possible
Transmission access raises unresolved economic issues
International Nuclear Information System (INIS)
Happ, H.H.
1994-01-01
The electric utility industry is in the process of gradual change from a fully regulated industry to one of partial deregulation. Instead of relying on regulation to achieve a fair and equitable price to the consumer for electric energy, the reliance is placed more and more on market forces, through competition, to provide wholesale energy at the best market price. Clearly, open transmission access is required to create a viable competitive wholesale market for new generation resources. This article describes four unresolved, or at least partially unresolved, issues associated with transmission access for wholesale wheeling. Wheeling has been defined as the use of a utility's transmission facilities to transmit power for other buyers and sellers. At least three parties are involved in a wheeling transaction: a seller, a buyer, and one or more wheeling utilities that transmit the power from the seller to the buyer. This article considers wholesale or bulk wheeling only, and does not consider retail wheeling. The four unresolved economic issues described in this article pertain to transmission access: Actual cost of providing transmission services, Methodology or methodologies used in evaluating the cost of wheeling, Contract path versus the actual power flows of the wheel, Issues associated with the formation of transmission regions
Diversity, classification and function of the plant protein kinase superfamily
Lehti-Shiu, Melissa D.; Shiu, Shin-Han
2012-01-01
Eukaryotic protein kinases belong to a large superfamily with hundreds to thousands of copies and are components of essentially all cellular functions. The goals of this study are to classify protein kinases from 25 plant species and to assess their evolutionary history in conjunction with consideration of their molecular functions. The protein kinase superfamily has expanded in the flowering plant lineage, in part through recent duplications. As a result, the flowering plant protein kinase r...
Detecting unresolved binary stars in Euclid VIS images
Kuntzer, T.; Courbin, F.
2017-10-01
Measuring a weak gravitational lensing signal to the level required by the next generation of space-based surveys demands exquisite reconstruction of the point-spread function (PSF). However, unresolved binary stars can significantly distort the PSF shape. In an effort to mitigate this bias, we aim at detecting unresolved binaries in realistic Euclid stellar populations. We tested methods in numerical experiments where (I) the PSF shape is known to Euclid requirements across the field of view; and (II) the PSF shape is unknown. We drew simulated catalogues of PSF shapes for this proof-of-concept paper. Following the Euclid survey plan, the objects were observed four times. We propose three methods to detect unresolved binary stars. The detection is based on the systematic and correlated biases between exposures of the same object. One method is a simple correlation analysis, while the two others use supervised machine-learning algorithms (random forest and artificial neural network). In both experiments, we demonstrate the ability of our methods to detect unresolved binary stars in simulated catalogues. The performance depends on the level of prior knowledge of the PSF shape and the shape measurement errors. Good detection performances are observed in both experiments. Full complexity, in terms of the images and the survey design, is not included, but key aspects of a more mature pipeline are discussed. Finding unresolved binaries in objects used for PSF reconstruction increases the quality of the PSF determination at arbitrary positions. We show, using different approaches, that we are able to detect at least binary stars that are most damaging for the PSF reconstruction process. The code corresponding to the algorithms used in this work and all scripts to reproduce the results are publicly available from a GitHub repository accessible via http://lastro.epfl.ch/software
Akiva, Eyal; Copp, Janine N; Tokuriki, Nobuhiko; Babbitt, Patricia C
2017-11-07
Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold. Copyright © 2017 the Author(s). Published by PNAS.
Systematic classification of the His-Me finger superfamily.
Jablonska, Jagoda; Matelska, Dorota; Steczkiewicz, Kamil; Ginalski, Krzysztof
2017-11-16
The His-Me finger endonucleases, also known as HNH or ββα-metal endonucleases, form a large and diverse protein superfamily. The His-Me finger domain can be found in proteins that play an essential role in cells, including genome maintenance, intron homing, host defense and target offense. Its overall structural compactness and non-specificity make it a perfectly-tailored pathogenic module that participates on both sides of inter- and intra-organismal competition. An extremely low sequence similarity across the superfamily makes it difficult to identify and classify new His-Me fingers. Using state-of-the-art distant homology detection methods, we provide an updated and systematic classification of His-Me finger proteins. In this work, we identified over 100 000 proteins and clustered them into 38 groups, of which three groups are new and cannot be found in any existing public domain database of protein families. Based on an analysis of sequences, structures, domain architectures, and genomic contexts, we provide a careful functional annotation of the poorly characterized members of this superfamily. Our results may inspire further experimental investigations that should address the predicted activity and clarify the potential substrates, to provide more detailed insights into the fundamental biological roles of these proteins. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.
Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies
Directory of Open Access Journals (Sweden)
R. Shyama Prasad Rao
2010-02-01
Full Text Available Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline which are the potential sites of asparagine (N linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average, but the sequon density was significantly lower owing to the increase in protein size and decrease in sequon specific amino acids. However, mammalian ABC proteins have significantly higher sequon density, and both serine and threonine containing sequons (NXS and NXT have been positively selected—against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly higher than expected in plant ABC proteins which have the lowest number of NXS/T sequons. Accord- ingly, compared to overall proteins, N-glycosylation sequons in ABC protein superfamilies have a distinct pattern of occurrence, and the results are discussed in an evolutionary perspective.
Can temporal fine structure represent the fundamental frequency of unresolved harmonics?
Oxenham, Andrew J; Micheyl, Christophe; Keebler, Michael V
2009-04-01
At least two modes of pitch perception exist: in one, the fundamental frequency (F0) of harmonic complex tones is estimated using the temporal fine structure (TFS) of individual low-order resolved harmonics; in the other, F0 is derived from the temporal envelope of high-order unresolved harmonics that interact in the auditory periphery. Pitch is typically more accurate in the former than in the latter mode. Another possibility is that pitch can sometimes be coded via the TFS from unresolved harmonics. A recent study supporting this third possibility [Moore et al. (2006a). J. Acoust. Soc. Am. 119, 480-490] based its conclusion on a condition where phase interaction effects (implying unresolved harmonics) accompanied accurate F0 discrimination (implying TFS processing). The present study tests whether these results were influenced by audible distortion products. Experiment 1 replicated the original results, obtained using a low-level background noise. However, experiments 2-4 found no evidence for the use of TFS cues with unresolved harmonics when the background noise level was raised, or the stimulus level was lowered, to render distortion inaudible. Experiment 5 measured the presence and phase dependence of audible distortion products. The results provide no evidence that TFS cues are used to code the F0 of unresolved harmonics.
Transient receptor potential channel superfamily: Role in lower urinary tract function.
Ogawa, Teruyuki; Imamura, Tetsuya; Nakazawa, Masaki; Hiragata, Shiro; Nagai, Takashi; Minagawa, Tomonori; Yokoyama, Hitoshi; Ishikawa, Masakuni; Domen, Takahisa; Ishizuka, Osamu
2015-11-01
Lower urinary tract symptoms associated with neurogenic bladder and overactive bladder syndrome are mediated in part by members of the transient receptor potential channel superfamily. The best studied member of this superfamily is the vanilloid receptor. Other transient receptor potential channels, such as the melastatin receptor and the ankyrin receptor, are also active in the pathogenesis of lower urinary tract dysfunction. However, the detailed mechanisms by which the transient receptor potential channels contribute to lower urinary tract symptoms are still not clear, and the therapeutic benefits of modulating transient receptor potential channel activity have not been proved in the clinical setting. In the present review, to better understand the pathophysiology and therapeutic potential for lower urinary tract symptoms, we summarize the presence and role of different members of the transient receptor potential channel superfamily in the lower urinary tract. © 2015 The Japanese Urological Association.
A Structural Approach to Unresolved Mourning in Single Parent Family Systems.
Fulmer, Richard H.
1983-01-01
Considers the mother's depression as a special problem in therapy of single-parent families, resulting from unresolved mourning maintained by the family system. Offers reasons why the single-parent family's structure seems inherently vulnerable to unresolved mourning. Suggests techniques of Structural Family Therapy to facilitate mourning in such…
Unresolved trauma in mothers: intergenerational effects and the role of reorganization
Iyengar, Udita; Kim, Sohye; Martinez, Sheila; Fonagy, Peter; Strathearn, Lane
2014-01-01
A mother's unresolved trauma may interfere with her ability to sensitively respond to her infant, thus affecting the development of attachment in her own child, and potentially contributing to the intergenerational transmission of trauma. One novel construct within the Dynamic Maturational Model of Attachment and Adaptation (DMM) coding of the Adult Attachment Interview (AAI) is “reorganization,” a process whereby speakers are actively changing their understanding of past and present experiences and moving toward attachment security. We conducted a study of mothers with unresolved trauma, exploring their own attachment classification, attachment outcomes of their children, and the potential effects of reorganization on child attachment. Forty-seven first-time mothers participated in the AAI during pregnancy, and returned with their child at 11 months to assess child attachment using the Strange Situation Procedure. Mothers with and without unresolved trauma were compared. We found that mothers with unresolved trauma had insecure attachment themselves and were more likely to have infants with insecure attachment. However, the one exception was that all of the mothers with unresolved trauma who were reorganizing toward secure attachment had infants with secure attachment. These preliminary findings suggest that mothers who are reorganizing may be able to more sensitively respond to their child's cues, contributing to the development of secure attachment. While our results need to be replicated in a larger cohort, this study is the first to explore the construct of reorganization and its potential relationship with child attachment. If confirmed in future studies, it may provide clinical insight into the intergenerational transmission of insecure attachment within the context of unresolved trauma. PMID:25225490
Functional diversity of the superfamily of K⁺ transporters to meet various requirements.
Diskowski, Marina; Mikusevic, Vedrana; Stock, Charlott; Hänelt, Inga
2015-09-01
The superfamily of K+ transporters unites proteins from plants, fungi, bacteria, and archaea that translocate K+ and/or Na+ across membranes. These proteins are key components in osmotic regulation, pH homeostasis, and resistance to high salinity and dryness. The members of the superfamily are closely related to K+ channels such as KcsA but also show several striking differences that are attributed to their altered functions. This review highlights these functional differences, focusing on the bacterial superfamily members KtrB, TrkH, and KdpA. The functional variations within the family and comparison to MPM-type K+ channels are discussed in light of the recently solved structures of the Ktr and Trk systems.
Preterm birth, an unresolved issue
Beliz?n, Jose M; Hofmeyr, Justus; Buekens, Pierre; Salaria, Natasha
2013-01-01
Premature birth is the world?s leading cause of neonatal mortality with worldwide estimates indicating 11.1% of all live births were preterm in 2010. Preterm birth rates are increasing in most countries with continual differences in survival rates amongst rich and poor countries. Preterm birth is currently an important unresolved global issue with research efforts focusing on uterine quiescence and activation, the ?omics? approaches and implementation science in order to reduce the incidence ...
Error due to unresolved scales in estimation problems for atmospheric data assimilation
Janjic, Tijana
The error arising due to unresolved scales in data assimilation procedures is examined. The problem of estimating the projection of the state of a passive scalar undergoing advection at a sequence of times is considered. The projection belongs to a finite- dimensional function space and is defined on the continuum. Using the continuum projection of the state of a passive scalar, a mathematical definition is obtained for the error arising due to the presence, in the continuum system, of scales unresolved by the discrete dynamical model. This error affects the estimation procedure through point observations that include the unresolved scales. In this work, two approximate methods for taking into account the error due to unresolved scales and the resulting correlations are developed and employed in the estimation procedure. The resulting formulas resemble the Schmidt-Kalman filter and the usual discrete Kalman filter, respectively. For this reason, the newly developed filters are called the Schmidt-Kalman filter and the traditional filter. In order to test the assimilation methods, a two- dimensional advection model with nonstationary spectrum was developed for passive scalar transport in the atmosphere. An analytical solution on the sphere was found depicting the model dynamics evolution. Using this analytical solution the model error is avoided, and the error due to unresolved scales is the only error left in the estimation problem. It is demonstrated that the traditional and the Schmidt- Kalman filter work well provided the exact covariance function of the unresolved scales is known. However, this requirement is not satisfied in practice, and the covariance function must be modeled. The Schmidt-Kalman filter cannot be computed in practice without further approximations. Therefore, the traditional filter is better suited for practical use. Also, the traditional filter does not require modeling of the full covariance function of the unresolved scales, but only
Molecular evolution of the insect chemoreceptor gene superfamily in Drosophila melanogaster
Robertson, Hugh M.; Warr, Coral G.; Carlson, John R.
2003-01-01
The insect chemoreceptor superfamily in Drosophila melanogaster is predicted to consist of 62 odorant receptor (Or) and 68 gustatory receptor (Gr) proteins, encoded by families of 60 Or and 60 Gr genes through alternative splicing. We include two previously undescribed Or genes and two previously undescribed Gr genes; two previously predicted Or genes are shown to be alternative splice forms. Three polymorphic pseudogenes and one highly defective pseudogene are recognized. Phylogenetic analysis reveals deep branches connecting multiple highly divergent clades within the Gr family, and the Or family appears to be a single highly expanded lineage within the superfamily. The genes are spread throughout the Drosophila genome, with some relatively recently diverged genes still clustered in the genome. The Gr5a gene on the X chromosome, which encodes a receptor for the sugar trehalose, has transposed from one such tandem cluster of six genes at cytological location 64, as has Gr61a, and all eight of these receptors might bind sugars. Analysis of intron evolution suggests that the common ancestor consisted of a long N-terminal exon encoding transmembrane domains 1-5 followed by three exons encoding transmembrane domains 6-7. As many as 57 additional introns have been acquired idiosyncratically during the evolution of the superfamily, whereas the ancestral introns and some of the older idiosyncratic introns have been lost at least 48 times independently. Altogether, these patterns of molecular evolution suggest that this is an ancient superfamily of chemoreceptors, probably dating back at least to the origin of the arthropods. PMID:14608037
Unresolved safety issues summary. Aqua Book. Volume 6, No. 3
International Nuclear Information System (INIS)
Butts, J.
1984-01-01
The unresolved safety issues summary is designed to provide the management of the Nuclear Regulatory Commission with a quarterly overview of the progress and plans for completion of generic tasks addressing unresolved safety issues reported to Congress pursuant to Section 210 of the Energy Reorganization Act of 1974 as amended. This summary utilizes data collected from the Office of Nuclear Reactor Regulation, Office of Nuclear Regulatory Research, and the national laboratories and is prepared by the Office of Nuclear Reactor Regulation
A Short History of ENDF/B Unresolved Resonance Parameters
Energy Technology Data Exchange (ETDEWEB)
Cullen, Dermott E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2010-10-31
This paper is designed to address two topics relating to ENDF/B data in the unresolved resonance region, Part 1: For years code users have pointed out and complained that various ENDF data processing codes, in particular PREPRO and NJOY, produce different answers from one another for the cross sections in unresolved resonance region. First I assure code users that NJOY has now been updated to agree with PREPRO, so that this problem has now been solved. Part 2: Next, this paper documents why we saw these differences; the emphasis here is on explaining what my own codes do, but I will also try to briefly outline what other codes do, so the reader can understand why we were producing different answers. The first topic should be of general interest to all readers, particularly users of our codes, whereas the second topic will be of more limited interest only to those readers who are interested in the details of our calculations in the unresolved resonance region. Now that our PREPRO and NJOY results agree we consider this problem solved and no further action is necessary.
New O-superfamily conotoxins from Conus striatus inhabited near Chinese Hainan Island
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Conotoxins are short peptide-toxins with specific targets and large diversity.They are useful in analgesia,neuroprotection,detection of some kinds of deseases,and receptor and ion channel study.In order to explore the conotoxin resourses of Chinese oceans,rapid amplification of 3' cDNA ends (RACE) method was utilized to systemically analyze the O-superfamily conotoxin content of Conus striatus inhabited near Chinese Hainan Island.Six new O-superfamily conopeptides were identified,one of which is highly homologous to MVIIA,an N-type calcium channel antagonist.
Bacterial Multidrug Efflux Pumps of the Major Facilitator Superfamily as Targets for Modulation.
Kumar, Sanath; He, Guixin; Kakarla, Prathusha; Shrestha, Ugina; Ranjana, K C; Ranaweera, Indrika; Willmon, T Mark; Barr, Sharla R; Hernandez, Alberto J; Varela, Manuel F
2016-01-01
Causative agents of infectious disease that are multidrug resistant bacterial pathogens represent a serious public health concern due to the increasingly difficult nature of achieving efficacious clinical treatments. Of the various acquired and intrinsic antimicrobial agent resistance determinants, integral-membrane multidrug efflux pumps of the major facilitator superfamily constitute a major mechanism of bacterial resistance. The major facilitator superfamily (MFS) encompasses thousands of known related secondary active and passive solute transporters, including multidrug efflux pumps, from bacteria to humans. This review article addresses recent developments involving the targeting by various modulators of bacterial multidrug efflux pumps from the major facilitator superfamily. It is currently of tremendous interest to modulate bacterial multidrug efflux pumps in order to eventually restore the clinical efficacy of therapeutic agents against recalcitrant bacterial infections. Such MFS multidrug efflux pumps are good targets for modulation.
Interactions among resonances in the unresolved region
International Nuclear Information System (INIS)
Queiroz Bogado Leite, S. de.
1982-11-01
The theory on resonance absorption in the unresolved region is reviewed and a subroutine is presented, optional to UNRES in MC 2 code. Comparisons with the isolated resonance model suggest the necessity, in some cases, of considering interference and overlapping effects among resonances of the system. (Author) [pt
Biodiversity and systematics in cephalopods: Unresolved problems ...
African Journals Online (AJOL)
Some problems of cephalopod biodiversity are discussed. Many squid species are represented by 2–4 intraspecies groupings that may be wholly or partly sympatric, but differ in spawning season and size at maturity. They may be genetically distinct stock units, but their taxonomic status remains unresolved. Discovery of a ...
Nuclear Receptors in atherosclerosis: a superfamily with many 'Goodfellas'
Kurakula, Kondababu; Hamers, Anouk A. J.; de Waard, Vivian; de Vries, Carlie J. M.
2013-01-01
Nuclear Receptors form a superfamily of 48 transcription factors that exhibit a plethora of functions in steroid hormone signaling, regulation of metabolism, circadian rhythm and cellular differentiation. In this review, we describe our current knowledge on the role of Nuclear Receptors in
Relationship between Apolipoprotein Superfamily and Parkinson's Disease
Directory of Open Access Journals (Sweden)
Lin Li
2017-01-01
Conclusions: The Apo superfamily has been proved to be closely involved in the initiation, progression, and prognosis of PD. Apos and their genes are of great value in predicting the susceptibility of PD and hopeful to become the target of medical intervention to prevent the onset of PD or slow down the progress. Therefore, further large-scale studies are warranted to elucidate the precise mechanisms of Apos in PD.
Stochasticity effects on derivation of physical parameters of unresolved star clusters
de Meulenaer, Philippe; Narbutis, Donatas; Mineikis, Tadas; Vansevičius, Vladas
2013-01-01
We developed a method for a fast modeling of broad-band UBVRI integrated magnitudes of unresolved star clusters and used it to derive their physical parameters (age, mass, and extinction). The method was applied on M33 galaxy cluster sample and consistency of ages and masses derived from unresolved observations with the values derived from resolved stellar photometry was demonstrated. We found that interstellar extinction causes minor age-extinction degeneracy for the studied sample due to a ...
Unresolved safety issues summary. Volume 3, Number 3. Aqua book
International Nuclear Information System (INIS)
1981-01-01
The 'Unresolved Safety Issues' summary is designed to provide the management of the Nuclear Regulatory Commission with a quarterly overview of the progress and plans for completion of generic tasks addressing Unresolved Safety Issues reported to Congress pursuant to section 210 of The Energy Reorganization Act of 1974 as amended. This summary utilizes data collected from the Office of Nuclear Reactor Regulation, Office of Nuclear Regulatory Research, and the National Laboratories and is prepared by the office of Management and Program Analysis. The definition of what constitutes completion of an unresolved safety issue (USI) has recently been expanded to include the implementation of the technical resolution. This is in acknowledgement of the fact that real safety benefits occur only after the implementation has taken place. The schedules in this book include a milestone at the end of each action plan which represents the initiation of the implementation process both with respect to incorporation of the technical resolution in the NRC official guidance or requirements and also the application of changes to individual operating plants. The schedule for implementation will not normally be included in the task action plan(s) for the resolution of a USI since the nature and extent of the activities necessary to accomplish the implementation cannot normally be reasonably determined prior to the determination of a technical resolution. The progress and status for implementation of unresolved safety issues for which a technical resolution has been completed are reported specifically in a separate table provided in this summary
Contribution to the study of the unresolved resonance range of the neutrons cross sections
International Nuclear Information System (INIS)
Noguere, Gilles
2014-01-01
This document presents the statistical description of neutron cross sections in the unresolved resonance range. The modeling of the total cross section and of the 'shape - elastic' cross section is based on the 'average R-Matrix' formalism. The partial cross sections describing the radiative capture, elastic scattering, inelastic scattering and fission process are calculated using the Hauser-Feshbach formalism with width fluctuation corrections. In the unresolved resonance range, these models depend on the average resonance parameters (neutron strength function Sc, mean level spacing D c , average partial reaction widths Γ c , channel radius a c , effective radius R' and distant level parameter R-bar c ∞ ). The codes (NJOY, CALENDF...) dedicated to the processing of nuclear data libraries (JEFF, ENDF/B, JENDL, CENDL, BROND... ) use the average parameters to take into account the self-shielding phenomenon for the simulation of the neutron transport in Monte-Carlo (MCNP, TRIPOLI... ) and deterministic (APOLLO, ERANOS...) codes. The evaluation work consists in establishing a consistent set of average parameters as a function of the total angular momentum J of the system and of the orbital moment of the incident neutron l. The work presented in this paper aims to describe the links between the S-Matrix and the 'average R-Matrix' formalism for the calculation of Sc, R-bar c ∞ , ac and R'. (author) [fr
The Nature of the Unresolved Extragalactic Cosmic Soft X-Ray Background
Cappelluti, N.; Ranalli, P.; Roncarelli, M.; Arevalo, P.; Zamorani, G.; Comastri, A.; Gilli, R.; Rovilos, E.; Vignali, C.; Allevato, V.;
2013-01-01
In this paper we investigate the power spectrum of the unresolved 0.5-2 keV cosmic X-ray background (CXB) with deep Chandra 4-Msec (Ms) observations in the Chandra Deep Field South (CDFS). We measured a signal that, on scales >30 arcsec, is significantly higher than the shot noise and is increasing with angular scale. We interpreted this signal as the joint contribution of clustered undetected sources like active galactic nuclei (AGN), galaxies and the intergalactic medium (IGM). The power of unresolved cosmic source fluctuations accounts for approximately 12 per cent of the 0.5-2 keV extragalactic CXB. Overall, our modelling predicts that approximately 20 per cent of the unresolved CXB flux is produced by low-luminosity AGN, approximately 25 per cent by galaxies and approximately 55 per cent by the IGM. We do not find any direct evidence of the so-called 'warm hot intergalactic medium' (i.e. matter with 10(exp 5) less than T less than 10(exp 7) K and density contrast delta less than 1000), but we estimated that it could produce about 1/7 of the unresolved CXB. We placed an upper limit on the space density of postulated X-ray-emitting early black holes at z greater than 7.5 and compared it with supermassive black hole evolution models.
Directory of Open Access Journals (Sweden)
Ying Liu
2016-01-01
Full Text Available Expansins are important components of plant cell walls, which are involved in the process of cell wall loosening under low extracellular pH. By using a combinational method for homology search and protein domain analysis, a total of 42 expansin genes were identified from Medicago truncatula genome in this study. They were divided into four families, based on sequence alignment and phylogenetic analysis. Gene duplication events were identified in the expansins superfamily, especially in the extension of α-expansin family. By analysis of RNA-sequencing data from National Center for Biotechnology Information, the expansin (EXP genes expressed during tissues development were characterized. Meanwhile, lots of cis-acting regulatory DNA elements in the EXP superfamily were identified, which were mainly related to plant growth and development processes. The results presented in this study are expected to facilitate further research works on this gene superfamily and provide new insights about the molecular mechanisms of expansins in M. truncatula.
Self-Assembly in the Ferritin Nano-Cage Protein Superfamily
Directory of Open Access Journals (Sweden)
Yu Zhang
2011-08-01
Full Text Available Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.
Assessment method to predict the rate of unresolved false alarms
International Nuclear Information System (INIS)
Reardon, P.T.; Eggers, R.F.; Heaberlin, S.W.
1982-06-01
A method has been developed to predict the rate of unresolved false alarms of material loss in a nuclear facility. The computer program DETRES-1 was developed. The program first assigns the true values of control unit components receipts, shipments, beginning and ending inventories. A normal random number generator is used to generate measured values of each component. A loss estimator is calculated from the control unit's measured values. If the loss estimator triggers a detection alarm, a response is simulated. The response simulation is divided into two phases. The first phase is to simulate remeasurement of the components of the detection loss estimator using the same or better measurement methods or inferences from surrounding control units. If this phase of response continues to indicate a material loss, phase of response simulating a production shutdown and comprehensive cleanout is initiated. A new loss estimator is found, and tested against the alarm thresholds. If the estimator value is below the threshold, the original detection alarm is considered resolved; if above the threshold, an unresolved alarm has occurred. A tally is kept of valid alarms, unresolved false alarms, and failure to alarm upon a true loss
Perception of the pitch of unresolved harmonics by 3- and 7-month-old human infants.
Lau, Bonnie K; Werner, Lynne A
2014-08-01
Three-month-olds discriminate resolved harmonic complexes on the basis of missing fundamental (MF) pitch. In view of reported difficulty in discriminating unresolved complexes at 7 months and striking changes in the organization of the auditory system during early infancy, infants' ability to discriminate unresolved complexes is of some interest. This study investigated the ability of 3-month-olds, 7-month-olds, and adults to discriminate the pitch of unresolved harmonic complexes using an observer-based method. Stimuli were MF complexes bandpass filtered with a -12 dB/octave slope, combined in random phase, presented at 70 dB sound pressure level (SPL) for 650 ms with a 50 ms rise/fall with a pink noise at 65 dB SPL. The conditions were (1) "LOW" unresolved harmonics (2500-4500 Hz) based on MFs of 160 and 200 Hz and (2) "HIGH" unresolved harmonics (4000-6000 Hz) based on MFs of 190 and 200 Hz. To demonstrate MF discrimination, participants had to ignore spectral changes in complexes with the same fundamental and respond only when the fundamental changed. Nearly all infants tested categorized complexes by MF pitch suggesting discrimination of pitch extracted from unresolved harmonics by 3 months. Adults also categorized the complexes by MF pitch, although musically trained adults were more successful than musically untrained adults.
Anantharaman, Vivek; Aravind, L
2003-01-01
Peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. The N1pC/P60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages. Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. In addition to the well characterized P60-like proteins, this superfamily includes the AcmB/LytN and YaeF/YiiX families of bacterial proteins, the amidase domain of bacterial and kinetoplastid glutathionylspermidine synthases (GSPSs), and several proteins from eukaryotes, phages, poxviruses, positive-strand RNA viruses, and certain archaea. The eukaryotic members include lecithin retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, and candidate tumor suppressor H-rev107. These eukaryotic proteins, along with the bacterial YaeF/poxviral G6R family, show a circular permutation of the catalytic domain. We identified three conserved residues, namely a cysteine, a histidine and a polar residue, that are involved in the catalytic activities of this superfamily. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them. Several related, but distinct, catalytic activities, such as murein degradation, acyl transfer and amide hydrolysis, have emerged in the N1pC/P60 superfamily. The three conserved catalytic residues of this superfamily are shown to be equivalent to the catalytic triad of the papain-like thiol peptidases. The predicted structural features indicate that the N1pC/P60 enzymes contain a fold similar to the papain-like peptidases, transglutaminases and arylamine acetyltransferases.
Efficacy of Artemether in Unresolving Plasmodium Falciparum Malaria
African Journals Online (AJOL)
The emergence of possible resistant Plasmodium falciparum malaria to artemisinin known for its immense benefit in malaria chemotherapy is worrisome. We report a case of unresolving Plasmodium falciparum malaria to Artesunate treatment in a 29- year old man in Enugu Nigeria. Plasmodium falciparum count of Giemsa ...
Kazmierczak, Marcin; Zhang, Xiaofei; Chen, Bihan; Mulkey, Daniel K.; Shi, Yingtang; Wagner, Paul G.; Pivaroff-Ward, Kendra; Sassic, Jessica K.; Bayliss, Douglas A.
2013-01-01
The Ether-a-go-go (EAG) superfamily of voltage-gated K+ channels consists of three functionally distinct gene families (Eag, Elk, and Erg) encoding a diverse set of low-threshold K+ currents that regulate excitability in neurons and muscle. Previous studies indicate that external acidification inhibits activation of three EAG superfamily K+ channels, Kv10.1 (Eag1), Kv11.1 (Erg1), and Kv12.1 (Elk1). We show here that Kv10.2, Kv12.2, and Kv12.3 are similarly inhibited by external protons, suggesting that high sensitivity to physiological pH changes is a general property of EAG superfamily channels. External acidification depolarizes the conductance–voltage (GV) curves of these channels, reducing low threshold activation. We explored the mechanism of this high pH sensitivity in Kv12.1, Kv10.2, and Kv11.1. We first examined the role of acidic voltage sensor residues that mediate divalent cation block of voltage activation in EAG superfamily channels because protons reduce the sensitivity of Kv12.1 to Zn2+. Low pH similarly reduces Mg2+ sensitivity of Kv10.1, and we found that the pH sensitivity of Kv11.1 was greatly attenuated at 1 mM Ca2+. Individual neutralizations of a pair of EAG-specific acidic residues that have previously been implicated in divalent block of diverse EAG superfamily channels greatly reduced the pH response in Kv12.1, Kv10.2, and Kv11.1. Our results therefore suggest a common mechanism for pH-sensitive voltage activation in EAG superfamily channels. The EAG-specific acidic residues may form the proton-binding site or alternatively are required to hold the voltage sensor in a pH-sensitive conformation. The high pH sensitivity of EAG superfamily channels suggests that they could contribute to pH-sensitive K+ currents observed in vivo. PMID:23712551
Kazmierczak, Marcin; Zhang, Xiaofei; Chen, Bihan; Mulkey, Daniel K; Shi, Yingtang; Wagner, Paul G; Pivaroff-Ward, Kendra; Sassic, Jessica K; Bayliss, Douglas A; Jegla, Timothy
2013-06-01
The Ether-a-go-go (EAG) superfamily of voltage-gated K(+) channels consists of three functionally distinct gene families (Eag, Elk, and Erg) encoding a diverse set of low-threshold K(+) currents that regulate excitability in neurons and muscle. Previous studies indicate that external acidification inhibits activation of three EAG superfamily K(+) channels, Kv10.1 (Eag1), Kv11.1 (Erg1), and Kv12.1 (Elk1). We show here that Kv10.2, Kv12.2, and Kv12.3 are similarly inhibited by external protons, suggesting that high sensitivity to physiological pH changes is a general property of EAG superfamily channels. External acidification depolarizes the conductance-voltage (GV) curves of these channels, reducing low threshold activation. We explored the mechanism of this high pH sensitivity in Kv12.1, Kv10.2, and Kv11.1. We first examined the role of acidic voltage sensor residues that mediate divalent cation block of voltage activation in EAG superfamily channels because protons reduce the sensitivity of Kv12.1 to Zn(2+). Low pH similarly reduces Mg(2+) sensitivity of Kv10.1, and we found that the pH sensitivity of Kv11.1 was greatly attenuated at 1 mM Ca(2+). Individual neutralizations of a pair of EAG-specific acidic residues that have previously been implicated in divalent block of diverse EAG superfamily channels greatly reduced the pH response in Kv12.1, Kv10.2, and Kv11.1. Our results therefore suggest a common mechanism for pH-sensitive voltage activation in EAG superfamily channels. The EAG-specific acidic residues may form the proton-binding site or alternatively are required to hold the voltage sensor in a pH-sensitive conformation. The high pH sensitivity of EAG superfamily channels suggests that they could contribute to pH-sensitive K(+) currents observed in vivo.
The American Indian Holocaust: Healing Historical Unresolved Grief.
Brave Heart, Maria Yellow Horse; DeBruyn, Lemyra M.
1998-01-01
Argues for the existence of historical unresolved grief among American Indians. Outlines the historical legacy of war, genocide, and boarding schools resulting in intergenerational trauma and a host of associated social problems. Suggests healing strategies that integrate modern and traditional approaches to healing at the individual, family, and…
Unresolved resonance range cross section, probability tables and self shielding factor
International Nuclear Information System (INIS)
Sublet, J.Ch.; Blomquist, R.N.; Goluoglu, S.; Mac Farlane, R.E.
2009-07-01
The performance and methodology of 4 processing codes have been compared in the unresolved resonance range of a selected set of isotopes. Those isotopes have been chosen to encompass most cases encountered in the unresolved energy range contained in major libraries like Endf/B-7 or Jeff-3.1.1. The code results comparison is accompanied by data format and formalism examinations and processing code fine-interpretation study. After some improvements, the results showed generally good agreement, although not perfect with infinite dilute cross-sections. However, much larger differences occur when shelf-shielded effective cross-sections are compared. The infinitely dilute cross-section are often plot checked but it is the probability table derived and shelf-shielded cross sections that are used and interpreted in criticality and transport calculations. This suggests that the current evaluation data format and formalism, in the unresolved resonance range should be tightened up, ambiguities removed. In addition production of the shelf shielded cross-sections should be converged to a much greater accuracy. (author)
RASOnD - A comprehensive resource and search tool for RAS superfamily oncogenes from various species
Directory of Open Access Journals (Sweden)
Singh Tej P
2011-07-01
Full Text Available Abstract Background The Ras superfamily plays an important role in the control of cell signalling and division. Mutations in the Ras genes convert them into active oncogenes. The Ras oncogenes form a major thrust of global cancer research as they are involved in the development and progression of tumors. This has resulted in the exponential growth of data on Ras superfamily across different public databases and in literature. However, no dedicated public resource is currently available for data mining and analysis on this family. The present database was developed to facilitate straightforward accession, retrieval and analysis of information available on Ras oncogenes from one particular site. Description We have developed the RAS Oncogene Database (RASOnD as a comprehensive knowledgebase that provides integrated and curated information on a single platform for oncogenes of Ras superfamily. RASOnD encompasses exhaustive genomics and proteomics data existing across diverse publicly accessible databases. This resource presently includes overall 199,046 entries from 101 different species. It provides a search tool to generate information about their nucleotide and amino acid sequences, single nucleotide polymorphisms, chromosome positions, orthologies, motifs, structures, related pathways and associated diseases. We have implemented a number of user-friendly search interfaces and sequence analysis tools. At present the user can (i browse the data (ii search any field through a simple or advance search interface and (iii perform a BLAST search and subsequently CLUSTALW multiple sequence alignment by selecting sequences of Ras oncogenes. The Generic gene browser, GBrowse, JMOL for structural visualization and TREEVIEW for phylograms have been integrated for clear perception of retrieved data. External links to related databases have been included in RASOnD. Conclusions This database is a resource and search tool dedicated to Ras oncogenes. It has
Exploring and Expanding the Fatty-Acid-Binding Protein Superfamily in Fasciola Species.
Morphew, Russell M; Wilkinson, Toby J; Mackintosh, Neil; Jahndel, Veronika; Paterson, Steve; McVeigh, Paul; Abbas Abidi, Syed M; Saifullah, Khalid; Raman, Muthusamy; Ravikumar, Gopalakrishnan; LaCourse, James; Maule, Aaron; Brophy, Peter M
2016-09-02
The liver flukes Fasciola hepatica and F. gigantica infect livestock worldwide and threaten food security with climate change and problematic control measures spreading disease. Fascioliasis is also a foodborne disease with up to 17 million humans infected. In the absence of vaccines, treatment depends on triclabendazole (TCBZ), and overuse has led to widespread resistance, compromising future TCBZ control. Reductionist biology from many laboratories has predicted new therapeutic targets. To this end, the fatty-acid-binding protein (FABP) superfamily has proposed multifunctional roles, including functions intersecting vaccine and drug therapy, such as immune modulation and anthelmintic sequestration. Research is hindered by a lack of understanding of the full FABP superfamily complement. Although discovery studies predicted FABPs as promising vaccine candidates, it is unclear if uncharacterized FABPs are more relevant for vaccine formulations. We have coupled genome, transcriptome, and EST data mining with proteomics and phylogenetics to reveal a liver fluke FABP superfamily of seven clades: previously identified clades I-III and newly identified clades IV-VII. All new clade FABPs were analyzed using bioinformatics and cloned from both liver flukes. The extended FABP data set will provide new study tools to research the role of FABPs in parasite biology and as therapy targets.
Kuznetsova, Ekaterina; Nocek, Boguslaw; Brown, Greg; Makarova, Kira S; Flick, Robert; Wolf, Yuri I; Khusnutdinova, Anna; Evdokimova, Elena; Jin, Ke; Tan, Kemin; Hanson, Andrew D; Hasnain, Ghulam; Zallot, Rémi; de Crécy-Lagard, Valérie; Babu, Mohan; Savchenko, Alexei; Joachimiak, Andrzej; Edwards, Aled M; Koonin, Eugene V; Yakunin, Alexander F
2015-07-24
The haloacid dehalogenase (HAD)-like enzymes comprise a large superfamily of phosphohydrolases present in all organisms. The Saccharomyces cerevisiae genome encodes at least 19 soluble HADs, including 10 uncharacterized proteins. Here, we biochemically characterized 13 yeast phosphatases from the HAD superfamily, which includes both specific and promiscuous enzymes active against various phosphorylated metabolites and peptides with several HADs implicated in detoxification of phosphorylated compounds and pseudouridine. The crystal structures of four yeast HADs provided insight into their active sites, whereas the structure of the YKR070W dimer in complex with substrate revealed a composite substrate-binding site. Although the S. cerevisiae and Escherichia coli HADs share low sequence similarities, the comparison of their substrate profiles revealed seven phosphatases with common preferred substrates. The cluster of secondary substrates supporting significant activity of both S. cerevisiae and E. coli HADs includes 28 common metabolites that appear to represent the pool of potential activities for the evolution of novel HAD phosphatases. Evolution of novel substrate specificities of HAD phosphatases shows no strict correlation with sequence divergence. Thus, evolution of the HAD superfamily combines the conservation of the overall substrate pool and the substrate profiles of some enzymes with remarkable biochemical and structural flexibility of other superfamily members. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Characterisation of unresolved complex mixtures of hydrocarbons
Gough, Mark Adrian
1989-01-01
Metadata merged with duplicate record (http://hdl.handle.net/10026.1/666) on 20.12.2016 by CS (TIS). This is a digitised version of a thesis that was deposited in the University Library. If you are the author please contact PEARL Admin () to discuss options. The hydrocarbons of Recent Polluted.., sediments, in-reservoir and laboratory biodegraded crude oils, and certain petroleum products (e. g. lubricating oils) often display "humps" or Unresolved Complex...
TNF and TNF Receptor Superfamily Members in HIV infection: New Cellular Targets for Therapy?
Directory of Open Access Journals (Sweden)
Amit Kumar
2013-01-01
Full Text Available Tumor necrosis factor (TNF and TNF receptors (TNFR superfamily members are engaged in diverse cellular phenomena such as cellular proliferation, morphogenesis, apoptosis, inflammation, and immune regulation. Their role in regulating viral infections has been well documented. Viruses have evolved with numerous strategies to interfere with TNF-mediated signaling indicating the importance of TNF and TNFR superfamily in viral pathogenesis. Recent research reports suggest that TNF and TNFRs play an important role in the pathogenesis of HIV. TNFR signaling modulates HIV replication and HIV proteins interfere with TNF/TNFR pathways. Since immune activation and inflammation are the hallmark of HIV infection, the use of TNF inhibitors can have significant impact on HIV disease progression. In this review, we will describe how HIV infection is modulated by signaling mediated through members of TNF and TNFR superfamily and in turn how these latter could be targeted by HIV proteins. Finally, we will discuss the emerging therapeutics options based on modulation of TNF activity that could ultimately lead to the cure of HIV-infected patients.
Sorba, Robert; Sawicki, Marcin
2018-05-01
We perform spatially resolved, pixel-by-pixel Spectral Energy Distribution (SED) fitting on galaxies up to z ˜ 2.5 in the Hubble eXtreme Deep Field (XDF). Comparing stellar mass estimates from spatially resolved and spatially unresolved photometry we find that unresolved masses can be systematically underestimated by factors of up to 5. The ratio of the unresolved to resolved mass measurement depends on the galaxy's specific star formation rate (sSFR): at low sSFRs the bias is small, but above sSFR ˜ 10-9.5 yr-1 the discrepancy increases rapidly such that galaxies with sSFRs ˜ 10-8 yr-1 have unresolved mass estimates of only one-half to one-fifth of the resolved value. This result indicates that stellar masses estimated from spatially unresolved data sets need to be systematically corrected, in some cases by large amounts, and we provide an analytic prescription for applying this correction. We show that correcting stellar mass measurements for this bias changes the normalization and slope of the star-forming main sequence and reduces its intrinsic width; most dramatically, correcting for the mass bias increases the stellar mass density of the Universe at high redshift and can resolve the long-standing discrepancy between the directly measured cosmic SFR density at z ≳ 1 and that inferred from stellar mass densities (`the missing mass problem').
Targeting of the tumor necrosis factor receptor superfamily for cancer immunotherapy
Bremer, Edwin
2013-01-01
The tumor necrosis factor (TNF) ligand and cognate TNF receptor superfamilies constitute an important regulatory axis that is pivotal for immune homeostasis and correct execution of immune responses. TNF ligands and receptors are involved in diverse biological processes ranging from the selective
Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups.
Munyampundu, Jean-Pierre; Xu, You-Ping; Cai, Xin-Zhong
2016-01-01
Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs.
Neutron cross sections in the unresolved resonance region
International Nuclear Information System (INIS)
Janeva, N.; Lukyanov, A.; Koyumdjieva, N.; Volev, K.
2005-01-01
In this work a development of the characteristic function model, created to reveal the resonance cross section structure in the unresolved resonance region is presented. The main advantage of this model is the calculation of resonance averaged self-shielding factors analytically. To determine average values of the cross sections and their functionals the function of joint statistical distribution of the R-matrix real and imaginary parts should be used. The characteristic function of such distribution is determined and the resonance ladder for the unresolved region is optimized to calculate the group averaged functionals in the same way as it is in the resolved resonance region. The main advantage of this model is the calculation of resonance averaged self-shielding factors analytically. The neutron width energy dependence leads to some deformation in the shape of resonances. This deformation is most apparent near the inelastic scattering threshold. For the case when the inelastic channel momentum is zero we present the formula for level shape bellow and over the inelastic threshold and the calculated resonance deformation in dependence of the position of the resonance in respect to the threshold. (authors)
Energy Technology Data Exchange (ETDEWEB)
Rakus,J.; Fedorov, A.; Fedorov, E.; Glasner, M.; Vick, J.; Babbitt, P.; Almo, S.; Gerlt, J.
2007-01-01
The d-mannonate dehydratase (ManD) function was assigned to a group of orthologous proteins in the mechanistically diverse enolase superfamily by screening a library of acid sugars. Structures of the wild type ManD from Novosphingobium aromaticivorans were determined at pH 7.5 in the presence of Mg2+ and also in the presence of Mg2+ and the 2-keto-3-keto-d-gluconate dehydration product; the structure of the catalytically active K271E mutant was determined at pH 5.5 in the presence of the d-mannonate substrate. As previously observed in the structures of other members of the enolase superfamily, ManD contains two domains, an N-terminal a+{beta} capping domain and a ({beta}/a)7{beta}-barrel domain. The barrel domain contains the ligands for the essential Mg2+, Asp 210, Glu 236, and Glu 262, at the ends of the third, fourth, and fifth {beta}-strands of the barrel domain, respectively. However, the barrel domain lacks both the Lys acid/base catalyst at the end of the second {beta}-strand and the His-Asp dyad acid/base catalyst at the ends of the seventh and sixth {beta}-strands, respectively, that are found in many members of the superfamily. Instead, a hydrogen-bonded dyad of Tyr 159 in a loop following the second {beta}-strand and Arg 147 at the end of the second {beta}-strand are positioned to initiate the reaction by abstraction of the 2-proton. Both Tyr 159 and His 212, at the end of the third {beta}-strand, are positioned to facilitate both syn-dehydration and ketonization of the resulting enol intermediate to yield the 2-keto-3-keto-d-gluconate product with the observed retention of configuration. The identities and locations of these acid/base catalysts as well as of cationic amino acid residues that stabilize the enolate anion intermediate define a new structural strategy for catalysis (subgroup) in the mechanistically diverse enolase superfamily. With these differences, we provide additional evidence that the ligands for the essential Mg2+ are the only
Burchell, B.; Nebert, D. W.; Nelson, D. R.; Bock, K. W.; Iyanagi, T.; Jansen, P. L.; Lancet, D.; Mulder, G. J.; Chowdhury, J. R.; Siest, G.
1991-01-01
A nomenclature system for the UDP glucuronosyltransferase superfamily is proposed, based on divergent evolution of the genes. A total of 26 distinct cDNAs in five mammalian species have been sequenced to date. Comparison of the deduced amino acid sequences leads to the definition of two families and
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes.
Hu, H; Haas, S A; Chelly, J; Van Esch, H; Raynaud, M; de Brouwer, A P M; Weinert, S; Froyen, G; Frints, S G M; Laumonnier, F; Zemojtel, T; Love, M I; Richard, H; Emde, A-K; Bienek, M; Jensen, C; Hambrock, M; Fischer, U; Langnick, C; Feldkamp, M; Wissink-Lindhout, W; Lebrun, N; Castelnau, L; Rucci, J; Montjean, R; Dorseuil, O; Billuart, P; Stuhlmann, T; Shaw, M; Corbett, M A; Gardner, A; Willis-Owen, S; Tan, C; Friend, K L; Belet, S; van Roozendaal, K E P; Jimenez-Pocquet, M; Moizard, M-P; Ronce, N; Sun, R; O'Keeffe, S; Chenna, R; van Bömmel, A; Göke, J; Hackett, A; Field, M; Christie, L; Boyle, J; Haan, E; Nelson, J; Turner, G; Baynam, G; Gillessen-Kaesbach, G; Müller, U; Steinberger, D; Budny, B; Badura-Stronka, M; Latos-Bieleńska, A; Ousager, L B; Wieacker, P; Rodríguez Criado, G; Bondeson, M-L; Annerén, G; Dufke, A; Cohen, M; Van Maldergem, L; Vincent-Delorme, C; Echenne, B; Simon-Bouy, B; Kleefstra, T; Willemsen, M; Fryns, J-P; Devriendt, K; Ullmann, R; Vingron, M; Wrogemann, K; Wienker, T F; Tzschach, A; van Bokhoven, H; Gecz, J; Jentsch, T J; Chen, W; Ropers, H-H; Kalscheuer, V M
2016-01-01
X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4(-/-) mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.
Brain Death in Pediatric Patients in Japan: Diagnosis and Unresolved Issues.
Araki, Takashi; Yokota, Hiroyuki; Fuse, Akira
2016-01-01
Brain death (BD) is a physiological state defined as complete and irreversible loss of brain function. Organ transplantation from a patient with BD is controversial in Japan because there are two classifications of BD: legal BD in which the organs can be donated and general BD in which the organs cannot be donated. The significance of BD in the terminal phase remains in the realm of scientific debate. As indicated by the increasing number of organ transplants from brain-dead donors, certain clinical diagnosis for determining BD in adults is becoming established. However, regardless of whether or not organ transplantation is involved, there are many unresolved issues regarding BD in children. Here, we will discuss the historical background of BD determination in children, pediatric emergencies and BD, and unresolved issues related to pediatric BD.
Representation of the neutron cross sections in the unresolved resonance region
International Nuclear Information System (INIS)
de Saussure, G.; Perez, R.B.
1975-01-01
Some limitations of the statistical approach to the representation of cross sections in the unresolved region are discussed and it is suggested that the actual Doppler-broadened cross sections should be used instead. 5 figures
DEFF Research Database (Denmark)
Bianchi, Federica; Fereczkowski, Michal; Zaar, Johannes
2015-01-01
Physiological studies have shown that noise-induced sensorineural hearing loss (SNHL) enhances the amplitude of envelope coding in auditory-nerve fibers. As pitch coding of unresolved complex tones is assumed to rely on temporal envelope coding mechanisms, this study investigated...... for the RP condition. Overall, these findings suggest that both reduced cochlear compression and auditory filter broadening alter the envelope representation of unresolved complex tones, leading to changes in pitch-discrimination performance....... pitchdiscrimination performance in listeners with SNHL. Pitch-discrimination thresholds were obtained in 14 normal-hearing (NH) and 10 hearingimpaired (HI) listeners for sine-phase (SP) and random-phase (RP) unresolved complex tones. The HI listeners performed, on average, similarly as the NH listeners in the SP...
Evolution and Diversity of the Ras Superfamily of Small GTPases in Prokaryotes
Wuichet, Kristin; Søgaard-Andersen, Lotte
2015-01-01
The Ras superfamily of small GTPases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. Originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain GTPases also control complex functions such as cell polarity, motility, predation, development and antibiotic resistance in bacteria. Here, we used a computational genomics approach to understand the abundance, diversity, and evolution of small GTPases in prokaryotes. We collected 520 small GTPase sequences present in 17% of 1,611 prokaryotic genomes analyzed that cover diverse lineages. We identified two discrete families of small GTPases in prokaryotes that show evidence of three distinct catalytic mechanisms. The MglA family includes MglA homologs, which are typically associated with the MglB GTPase activating protein, whereas members of the Rup (Ras superfamily GTPase of unknown function in prokaryotes) family are not predicted to interact with MglB homologs. System classification and genome context analyses support the involvement of small GTPases in diverse prokaryotic signal transduction pathways including two component systems, laying the foundation for future experimental characterization of these proteins. Phylogenetic analysis of prokaryotic and eukaryotic GTPases supports that the last universal common ancestor contained ancestral MglA and Rup family members. We propose that the MglA family was lost from the ancestral eukaryote and that the Ras superfamily members in extant eukaryotes are the result of vertical and horizontal gene transfer events of ancestral Rup GTPases. PMID:25480683
Guaranteed Unresolved Point Source Emission and the Gamma-ray Background
International Nuclear Information System (INIS)
Pavlidou, Vasiliki; Siegal-Gaskins, Jennifer M.; Brown, Carolyn; Fields, Brian D.; Olinto, Angela V.
2007-01-01
The large majority of EGRET point sources remain without an identified low-energy counterpart, and a large fraction of these sources are most likely extragalactic. Whatever the nature of the extragalactic EGRET unidentified sources, faint unresolved objects of the same class must have a contribution to the diffuse extragalactic gamma-ray background (EGRB). Understanding this component of the EGRB, along with other guaranteed contributions from known sources (blazars and normal galaxies), is essential if we are to use this emission to constrain exotic high-energy physics. Here, we follow an empirical approach to estimate whether the contribution of unresolved unidentified sources to the EGRB is likely to be important. Additionally, we discuss how upcoming GLAST observations of EGRET unidentified sources, their fainter counterparts, and the Galactic and extragalactic diffuse backgrounds, will shed light on the nature of the EGRET unidentified sources even without any positional association of such sources with low-energy counterparts
Directory of Open Access Journals (Sweden)
Xiaoming Song
2016-08-01
Full Text Available The AP2/ERF superfamily, one of the most important transcription factor families, plays crucial roles in response to biotic and abiotic stresses. So far, a comprehensive evolutionary inference of its origination and expansion has not been available. Here, we identified 515 AP2/ERF genes in B. napus, a neo-tetraploid forming ~7500 years ago, and found that 82.14% of them were duplicated in the tetraploidization. A prominent subgenome bias was revealed in gene expression, tissue-specific, and gene conversion. Moreover, a large-scale analysis across plants and alga suggested that this superfamily could have been originated from AP2 family, expanding to form other families (ERF, and RAV. This process was accompanied by duplicating and/or alternative deleting AP2 domain, intragenic domain sequence conversion, and/or by acquiring other domains, resulting in copy number variations, alternatively contributing to functional innovation. We found that significant positive selection occurred at certain critical nodes during the evolution of land plants, possibly responding to changing environment. In conclusion, the present research revealed origination, functional innovation, and evolutionary trajectory of the AP2/ERF superfamily, contributing to understanding their roles in plant stress tolerance.
Directory of Open Access Journals (Sweden)
Raghunath Satpathy
2015-01-01
Full Text Available Context: Paracoccidioides brasiliensis, a dimorphic fungus is the causative agent of paracoccidioidomycosis, a disease globally affecting millions of people. The haloacid dehalogenase (HAD superfamily hydrolases enzyme in the fungi, in particular, is known to be responsible in the pathogenesis by adhering to the tissue. Hence, identification of novel drug targets is essential. Aims: In-silico based identification of co-expressed genes along with HAD superfamily hydrolase in P. brasiliensis during the morphogenesis from mycelium to yeast to identify possible genes as drug targets. Materials and Methods: In total, four datasets were retrieved from the NCBI-gene expression omnibus (GEO database, each containing 4340 genes, followed by gene filtration expression of the data set. Further co-expression (CE study was performed individually and then a combination these genes were visualized in the Cytoscape 2. 8.3. Statistical Analysis Used: Mean and standard deviation value of the HAD superfamily hydrolase gene was obtained from the expression data and this value was subsequently used for the CE calculation purpose by selecting specific correlation power and filtering threshold. Results: The 23 genes that were thus obtained are common with respect to the HAD superfamily hydrolase gene. A significant network was selected from the Cytoscape network visualization that contains total 7 genes out of which 5 genes, which do not have significant protein hits, obtained from gene annotation of the expressed sequence tags by BLAST X. For all the protein PSI-BLAST was performed against human genome to find the homology. Conclusions: The gene co-expression network was obtained with respect to HAD superfamily dehalogenase gene in P. Brasiliensis.
Comparative analysis of cation/proton antiporter superfamily in plants.
Ye, Chu-Yu; Yang, Xiaohan; Xia, Xinli; Yin, Weilun
2013-06-01
The cation/proton antiporter superfamily is associated with the transport of monovalent cations across membranes. This superfamily was annotated in the Arabidopsis genome and some members were functionally characterized. In the present study, a systematic analysis of the cation/proton antiporter genes in diverse plant species was reported. We identified 240 cation/proton antiporters in alga, moss, and angiosperm. A phylogenetic tree was constructed showing these 240 members are separated into three families, i.e., Na(+)/H(+) exchangers, K(+) efflux antiporters, and cation/H(+) exchangers. Our analysis revealed that tandem and/or segmental duplications contribute to the expansion of cation/H(+) exchangers in the examined angiosperm species. Sliding window analysis of the nonsynonymous/synonymous substitution ratios showed some differences in the evolutionary fate of cation/proton antiporter paralogs. Furthermore, we identified over-represented motifs among these 240 proteins and found most motifs are family specific, demonstrating diverse evolution of the cation/proton antiporters among three families. In addition, we investigated the co-expressed genes of the cation/proton antiporters in Arabidopsis thaliana. The results showed some biological processes are enriched in the co-expressed genes, suggesting the cation/proton antiporters may be involved in these biological processes. Taken together, this study furthers our knowledge on cation/proton antiporters in plants. Copyright © 2013 Elsevier B.V. All rights reserved.
Comparative analysis of cystatin superfamily in platyhelminths.
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Aijiang Guo
Full Text Available The cystatin superfamily is comprised of cysteine proteinase inhibitors and encompasses at least 3 subfamilies: stefins, cystatins and kininogens. In this study, the platyhelminth cystatin superfamily was identified and grouped into stefin and cystatin subfamilies. The conserved domain of stefins (G, QxVxG was observed in all members of platyhelminth stefins. The three characteristics of cystatins, the cystatin-like domain (G, QxVxG, PW, a signal peptide, and one or two conserved disulfide bonds, were observed in platyhelminths, with the exception of cestodes, which lacked the conserved disulfide bond. However, it is noteworthy that cestode cystatins had two tandem repeated domains, although the second tandem repeated domain did not contain a cystatin-like domain, which has not been previously reported. Tertiary structure analysis of Taenia solium cystatin, one of the cestode cystatins, demonstrated that the N-terminus of T. solium cystatin formed a five turn α-helix, a five stranded β-pleated sheet and a hydrophobic edge, similar to the structure of chicken cystatin. Although no conserved disulfide bond was found in T. solium cystatin, the models of T. solium cystatin and chicken cystatin corresponded at the site of the first disulfide bridge of the chicken cystatin. However, the two models were not similar regarding the location of the second disulfide bridge of chicken cystatin. These results showed that T. solium cystatin and chicken cystatin had similarities and differences, suggesting that the biochemistry of T. solium cystatin could be similar to chicken cystatin in its inhibitory function and that it may have further functional roles. The same results were obtained for other cestode cystatins. Phylogenetic analysis showed that cestode cystatins constituted an independent clade and implied that cestode cystatins should be considered to have formed a new clade during evolution.
The ATPase of the phi29 DNA packaging motor is a member of the hexameric AAA+ superfamily.
Schwartz, Chad; De Donatis, Gian Marco; Fang, Huaming; Guo, Peixuan
2013-08-15
The AAA+ superfamily of proteins is a class of motor ATPases performing a wide range of functions that typically exist as hexamers. The ATPase of phi29 DNA packaging motor has long been a subject of debate in terms of stoichiometry and mechanism of action. Here, we confirmed the stoichiometry of phi29 motor ATPase to be a hexamer and provide data suggesting that the phi29 motor ATPase is a member of the classical hexameric AAA+ superfamily. Native PAGE, EMSA, capillary electrophoresis, ATP titration, and binomial distribution assay show that the ATPase is a hexamer. Mutations in the known Walker motifs of the ATPase validated our previous assumptions that the protein exists as another member of this AAA+ superfamily. Our data also supports the finding that the phi29 DNA packaging motor uses a revolution mechanism without rotation or coiling (Schwartz et al., this issue). Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.
Unresolved gamma rays from high-spin states
International Nuclear Information System (INIS)
Stephens, F.S.
1985-08-01
The γ-rays which are emitted from the highest spin states in nuclei cannot be resolved using present techniques. Nevertheless, methods are being developed to study nuclear structures in this spin range. For example, coincidence data has been used in the study of superdeformations and moments of inertia. While the general properties of these correlation plots are in accord with present expectations, there are several puzzling features of the data which require more study. One unresolved aspect concerns γ-ray energy spreads in a given decay pathway. In addition, higher-order correlation methods are in various stages of inception. 15 refs., 16 figs
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Garry Robert F
2008-02-01
Full Text Available Abstract Background Members of the Baculoviridae encode two types of proteins that mediate virus:cell membrane fusion and penetration into the host cell. Alignments of primary amino acid sequences indicate that baculovirus fusion proteins of group I nucleopolyhedroviruses (NPV form the GP64 superfamily. The structure of these viral penetrenes has not been determined. The GP64 superfamily includes the glycoprotein (GP encoded by members of the Thogotovirus genus of the Orthomyxoviridae. The entry proteins of other baculoviruses, group II NPV and granuloviruses, are class I penetrenes. Results Class III penetrenes encoded by members of the Rhabdoviridae and Herpesviridae have an internal fusion domain comprised of beta sheets, other beta sheet domains, an extended alpha helical domain, a membrane proximal stem domain and a carboxyl terminal anchor. Similar sequences and structural/functional motifs that characterize class III penetrenes are located collinearly in GP64 of group I baculoviruses and related glycoproteins encoded by thogotoviruses. Structural models based on a prototypic class III penetrene, vesicular stomatitis virus glycoprotein (VSV G, were established for Thogoto virus (THOV GP and Autographa california multiple NPV (AcMNPV GP64 demonstrating feasible cysteine linkages. Glycosylation sites in THOV GP and AcMNPV GP64 appear in similar model locations to the two glycosylation sites of VSV G. Conclusion These results suggest that proteins in the GP64 superfamily are class III penetrenes.
Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily
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Marc Lenoir
2015-10-01
Full Text Available The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH and Tec homology (TH domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.
Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.
Lenoir, Marc; Kufareva, Irina; Abagyan, Ruben; Overduin, Michael
2015-10-23
The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.
UNR. A code for processing unresolved resonance data for MCNP
International Nuclear Information System (INIS)
Hogenbirk, A.
1994-09-01
In neutron transport problems the correct treatment of self-shielding is important for those nuclei present in large concentrations. Monte Carlo calculations using continuous-energy cross section data, such as calculations with the code MCNP, offer the advantage that neutron transport is calculated in a very accurate way. Self-shielding in the resolved resonance region is taken into account exactly in MCNP. However, self-shielding in the unresolved resonance region can not be taken into account by MCNP, although the effect of it may be important in many applications. In this report a description is given of the computer code UNR. With this code problem-dependent cross section libraries can be produced for MCNP. In these libraries self-shielded cross section data in the unresolved resonance range are given, which are produced by NJOY-module UNRESR. It is noted, that the treatment for resonance self-shielding presented in this report is approximate. However, the current version of MCNP does not allow the use of probability tables, which would be a general solution. (orig.)
A decade of e-cigarettes: Limited research & unresolved safety concerns.
Kaisar, Mohammad Abul; Prasad, Shikha; Liles, Tylor; Cucullo, Luca
2016-07-15
It is well known that tobacco consumption is a leading cause of preventable deaths worldwide and has been linked to major diseases ranging from cancer to chronic obstructive pulmonary disease, atherosclerosis, stroke and a host of neurological/neurodegenerative disorders. In the past decade a number of alternative vaping products have hit the market, rapidly gaining consumers especially among the younger population. Electronic nicotine delivery systems or e-cigarettes have become the sought-after product due to the belief that they are much safer than traditional cigarettes. However, inadequate research and lack of regulatory guidelines for both the manufacturing process and the content of the vaping solution of the e-cigarette has become a major concern. Highly debated and unresolved questions such as whether e-cigarettes may help smokers quit and whether e-cigarettes will promote the use of nicotine among non-smokers add to the confusion of the safety of e-cigarettes. In this review article, we summarize the current understanding (and lack thereof) of the potential health impacts of e-cigarettes. We will also highlight the most recent studies (in vivo/in vitro) which seem to conflict with the broad safety claims put forward by the manufacturers. Finally, we provide potential solutions to overcome the research gap of the short and long-term health impact of e-cigarettes. Published by Elsevier Ireland Ltd.
A decade of e-cigarettes: Limited research & unresolved safety concerns
International Nuclear Information System (INIS)
Kaisar, Mohammad Abul; Prasad, Shikha; Liles, Tylor; Cucullo, Luca
2016-01-01
It is well known that tobacco consumption is a leading cause of preventable deaths worldwide and has been linked to major diseases ranging from cancer to chronic obstructive pulmonary disease, atherosclerosis, stroke and a host of neurological/neurodegenerative disorders. In the past decade a number of alternative vaping products have hit the market, rapidly gaining consumers especially among the younger population. Electronic nicotine delivery systems or e-cigarettes have become the sought-after product due to the belief that they are much safer than traditional cigarettes. However, inadequate research and lack of regulatory guidelines for both the manufacturing process and the content of the vaping solution of the e-cigarette has become a major concern. Highly debated and unresolved questions such as whether e-cigarettes may help smokers quit and whether e-cigarettes will promote the use of nicotine among non-smokers add to the confusion of the safety of e-cigarettes. In this review article, we summarize the current understanding (and lack thereof) of the potential health impacts of e-cigarettes. We will also highlight the most recent studies (in vivo/in vitro) which seem to conflict with the broad safety claims put forward by the manufacturers. Finally, we provide potential solutions to overcome the research gap of the short and long-term health impact of e-cigarettes.
A Decade of e-Cigarettes: Limited Research & Unresolved Safety Concerns
Kaisar, Mohammad Abul; Prasad, Shikha; Liles, Tylor; Cucullo, Luca
2016-01-01
It is well known that tobacco consumption is a leading cause of preventable deaths worldwide and has been linked to major diseases ranging from cancer to chronic obstructive pulmonary disease, atherosclerosis, stroke and a host of neurological/neurodegenerative disorders. In the past decade a number of alternative vaping products have hit the market, rapidly gaining consumers especially among the younger population. Electronic nicotine delivery systems or e-cigarettes have become the sought-after product due to the belief that they are much safer than traditional cigarettes. However, inadequate research and lack of regulatory guidelines for both the manufacturing process and the content of the vaping solution of the e-cigarette has become a major concern. Highly debated and unresolved questions such as whether e-cigarettes may help smokers quit and whether e-cigarettes will promote the use of nicotine among non-smokers add to the confusion of the safety of e-cigarettes. In this review article, we summarize the current understanding (and lack thereof) of the potential health impacts of e-cigarettes. We will also highlight the most recent studies (in vivo/in vitro) which seem to conflict with the broad safety claims put forward by the manufacturers. Finally, we provide potential solutions to overcome the research gap of the short and long-term health impact of e-cigarettes. PMID:27477296
Directory of Open Access Journals (Sweden)
Antoinesha L. Hollman
2016-03-01
Full Text Available Exposure to environmental hazards has been associated with diseases in humans. The identification of single nucleotide polymorphisms (SNPs in human populations exposed to different environmental hazards, is vital for detecting the genetic risks of some important human diseases. Several studies in this field have been conducted on glutathione S-transferases (GSTs, a phase II detoxification superfamily, to investigate its role in the occurrence of diseases. Human GSTs consist of cytosolic and microsomal superfamilies that are further divided into subfamilies. Based on scientific search engines and a review of the literature, we have found a large amount of published articles on human GST super- and subfamilies that have greatly assisted in our efforts to examine their role in health and disease. Because of its polymorphic variations in relation to environmental hazards such as air pollutants, cigarette smoke, pesticides, heavy metals, carcinogens, pharmaceutical drugs, and xenobiotics, GST is considered as a significant biomarker. This review examines the studies on gene-environment interactions related to various diseases with respect to single nucleotide polymorphisms (SNPs found in the GST superfamily. Overall, it can be concluded that interactions between GST genes and environmental factors play an important role in human diseases.
Directory of Open Access Journals (Sweden)
Yating Dong
Full Text Available Aldehyde dehydrogenases (ALDHs are a superfamily of enzymes which play important role in the scavenging of active aldehydes molecules. In present work, a comprehensive whole-genomic study of ALDH gene superfamily was carried out for an allotetraploid cultivated cotton species, G. hirsutum, as well as in parallel relative to their diploid progenitors, G. arboreum and G. raimondii. Totally, 30 and 58 ALDH gene sequences belong to 10 families were identified from diploid and allotetraploid cotton species, respectively. The gene structures among the members from same families were highly conserved. Whole-genome duplication and segmental duplication might be the major driver for the expansion of ALDH gene superfamily in G. hirsutum. In addition, the expression patterns of GhALDH genes were diverse across tissues. Most GhALDH genes were induced or repressed by salt stress in upland cotton. Our observation shed lights on the molecular evolutionary properties of ALDH genes in diploid cottons and their alloallotetraploid derivatives. It may be useful to mine key genes for improvement of cotton response to salt stress.
Preterm birth, an unresolved issue.
Belizán, Jose M; Hofmeyr, Justus; Buekens, Pierre; Salaria, Natasha
2013-11-15
Premature birth is the world's leading cause of neonatal mortality with worldwide estimates indicating 11.1% of all live births were preterm in 2010. Preterm birth rates are increasing in most countries with continual differences in survival rates amongst rich and poor countries. Preterm birth is currently an important unresolved global issue with research efforts focusing on uterine quiescence and activation, the 'omics' approaches and implementation science in order to reduce the incidence and increase survival rates of preterm babies. The journal Reproductive Health has published a supplement entitled Born Too Soon which addresses factors in the preconception and pregnancy period which may increase the risk of preterm birth and also outlines potential interventions which may reduce preterm birth rates and improve survival of preterm babies by as much as 84% annually. This is critical in order to achieve the Millennium Development Goal (MDG 4) for child survival by 2015 and beyond.
Sexual Harassment: A problem unresolved!
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N Vanishree
2013-01-01
Full Text Available Sexual harassment is a highly prevalent form of gender-based discrimination and sexual exploitation in the workplace and academic environment. In the dental field, there are a few studies regarding sexual harassment among the patients, professors and claims of their students. There is a silence of consent surrounding sexual harassment. It is clearly an issue about which the practicing dentists need to be informed in order to provide knowledgeable assessment and treatment for all patients. Dentists also have a role in advocacy, expert consultation or testimony, research and prevention through education and training. It is a fact that sexual harassment is very commonly encountered by almost everyone especially women. It is the most unresolved and under recognized problem of today especially when professionals are concerned. Preventing sexual harassment requires a considerable investment of time and personnel. This paper reviews the topic of sexual harassment as a problem from its legal aspects and recommendations for further steps to resolve this issue in dentistry.
Robinson, Serina L; Badalamenti, Jonathan P; Dodge, Anthony G; Tassoulas, Lambros J; Wackett, Lawrence P
2018-03-12
Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here, we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla. The BH enzymes reacted exclusively with biuret in the range of 2-11 µmol min -1 mg -1 protein. We then constructed a global protein superfamily network to map structure-function relationships in the BH subfamily and used this to mine > 7000 genomes. High-confidence BH sequences were detected in Actinobacteria, Alpha- and Beta-proteobacteria, and some fungi, archaea and green algae, but not animals or land plants. Unexpectedly, no cyanuric acid hydrolase homologs were detected in > 90% of genomes with BH homologs, suggesting BHs may have arisen independently of s-triazine ring metabolism. This work links genotype to phenotype by enabling accurate genome-mining to predict microbial utilization of biuret. Importantly, it advances understanding of the microbial capacity for biuret biodegradation in agricultural systems. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.
Degradation of aged plants by corrosion: 'Long cell action' in unresolved corrosion issues
International Nuclear Information System (INIS)
Saji, Genn
2009-01-01
In a series of previously published papers the author has identified that 'long cell action' corrosion plays a pivotal role in practically all unresolved corrosion issues for all types of nuclear power plants (e.g. PWR/VVER, BWR/RBMK and CANDU). Some of these unresolved issues are IGSCC, PWSCC, AOA and FAC (erosion-corrosion). In conventional corrosion science it is well established that 'long cell action' can seriously accelerate or suppress the local cell corrosion activities. Although long cell action is another fundamental mechanism of corrosion, especially in a 'soil corrosion' arena, potential involvement of this corrosion process has never been studied in nuclear and fossil power plants as far as the author has been able to establish. The author believes that the omission of this basic corrosion mechanism is the root cause of practically all un-resolved corrosion issues. In this paper, the author further elaborated on his assessment to other key corrosion issues, e.g. steam generator and turbine corrosion issues, while briefly summarizing previous discussions for completeness purposes, as well as introducing additional experimental and theoretical evidence of this basic corrosion mechanism. Due to the importance of this potential mechanism the author is calling for institutional review activities and further verification experiments in the form of a joint international project.
International Nuclear Information System (INIS)
Thatcher, D.
1989-05-01
This report presents a summary of the activities related to Unresolved Safety Issue (USI)A-17, ''Systems Interactions in Nuclear Power Plants,'' and also includes the NRC staff's conclusions based on those activities. The staff's technical findings provide the framework for the final resolution of this unresolved safety issue. The final resolution will be published later as NUREG-1229. 52 refs., 4 tabs
Answering unresolved questions about the relationship between cognitive ability and prejudice
Brandt, M.J.; Crawford, Jarret T
2016-01-01
Previous research finds that lower cognitive ability predicts greater prejudice. We test two unresolved questions about this association using a heterogeneous set of target groups and data from a representative sample of the United States (N = 5,914). First, we test “who are the targets of
Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.
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Daniel L Parton
2016-06-01
Full Text Available The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on an omics scale are not yet widespread, primarily because software infrastructure to enable simulations at this scale has not kept pace. It should now be possible to study protein dynamics across entire (superfamilies, exploiting both available structural biology data and conformational similarities across homologous proteins. Here, we present a new tool for enabling high-throughput simulation in the genomics era. Ensembler takes any set of sequences-from a single sequence to an entire superfamily-and shepherds them through various stages of modeling and refinement to produce simulation-ready structures. This includes comparative modeling to all relevant PDB structures (which may span multiple conformational states of interest, reconstruction of missing loops, addition of missing atoms, culling of nearly identical structures, assignment of appropriate protonation states, solvation in explicit solvent, and refinement and filtering with molecular simulation to ensure stable simulation. The output of this pipeline is an ensemble of structures ready for subsequent molecular simulations using computer clusters, supercomputers, or distributed computing projects like Folding@home. Ensembler thus automates much of the time-consuming process of preparing protein models suitable for simulation, while allowing scalability up to entire superfamilies. A particular advantage of this approach can be found in the construction of kinetic models of conformational dynamics-such as Markov state models (MSMs-which benefit from a diverse array of initial configurations that span the accessible conformational states to aid sampling. We demonstrate the power of this approach by constructing models for all catalytic domains in the human
TGF-β superfamily signaling in testis formation and early male germline development.
Young, Julia C; Wakitani, Shoichi; Loveland, Kate L
2015-09-01
The TGF-β ligand superfamily contains at least 40 members, many of which are produced and act within the mammalian testis to facilitate formation of sperm. Their progressive expression at key stages and in specific cell types determines the fertility of adult males, influencing testis development and controlling germline differentiation. BMPs are essential for the interactive instructions between multiple cell types in the early embryo that drive initial specification of gamete precursors. In the nascent foetal testis, several ligands including Nodal, TGF-βs, Activins and BMPs, serve as key masculinizing switches by regulating male germline pluripotency, somatic and germline proliferation, and testicular vascularization and architecture. In postnatal life, local production of these factors determine adult testis size by regulating Sertoli cell multiplication and differentiation, in addition to specifying germline differentiation and multiplication. Because TGF-β superfamily signaling is integral to testis formation, it affects processes that underlie testicular pathologies, including testicular cancer, and its potential to contribute to subfertility is beginning to be understood. Copyright © 2015 Elsevier Ltd. All rights reserved.
Stability for Function Trade-Offs in the Enolase Superfamily 'Catalytic Module'
Energy Technology Data Exchange (ETDEWEB)
Nagatani, R.A.; Gonzalez, A.; Shoichet, B.K.; Brinen, L.S.; Babbitt, P.C.; /UC, San Francisco /SLAC, SSRL
2007-07-12
Enzyme catalysis reflects a dynamic interplay between charged and polar active site residues that facilitate function, stabilize transition states, and maintain overall protein stability. Previous studies show that substituting neutral for charged residues in the active site often significantly stabilizes a protein, suggesting a stability trade-off for functionality. In the enolase superfamily, a set of conserved active site residues (the ''catalytic module'') has repeatedly been used in nature in the evolution of many different enzymes for the performance of unique overall reactions involving a chemically diverse set of substrates. This catalytic module provides a robust solution for catalysis that delivers the common underlying partial reaction that supports all of the different overall chemical reactions of the superfamily. As this module has been so broadly conserved in the evolution of new functions, we sought to investigate the extent to which it follows the stability-function trade-off. Alanine substitutions were made for individual residues, groups of residues, and the entire catalytic module of o-succinylbenzoate synthase (OSBS), a member of the enolase superfamily from Escherichia coli. Of six individual residue substitutions, four (K131A, D161A, E190A, and D213A) substantially increased protein stability (by 0.46-4.23 kcal/mol), broadly consistent with prediction of a stability-activity trade-off. The residue most conserved across the superfamily, E190, is by far the most destabilizing. When the individual substitutions were combined into groups (as they are structurally and functionally organized), nonadditive stability effects emerged, supporting previous observations that residues within the module interact as two functional groups within a larger catalytic system. Thus, whereas the multiple-mutant enzymes D161A/E190A/D213A and K131A/K133A/D161A/E190A/D213A/K235A (termed 3KDED) are stabilized relative to the wild-type enzyme (by 1
SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.
Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Stafford, William Noble; Leslie, Christina
2007-05-22
Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, called string kernels, for use with support vector machine (SVM) classifiers. However, while some of these approaches exhibit state-of-the-art performance at the binary protein classification problem, i.e. discriminating between a particular protein class and all other classes, few of these studies have addressed the real problem of multi-class superfamily or fold recognition. Moreover, there are only limited software tools and systems for SVM-based protein classification available to the bioinformatics community. We present a new multi-class SVM-based protein fold and superfamily recognition system and web server called SVM-Fold, which can be found at http://svm-fold.c2b2.columbia.edu. Our system uses an efficient implementation of a state-of-the-art string kernel for sequence profiles, called the profile kernel, where the underlying feature representation is a histogram of inexact matching k-mer frequencies. We also employ a novel machine learning approach to solve the difficult multi-class problem of classifying a sequence of amino acids into one of many known protein structural classes. Binary one-vs-the-rest SVM classifiers that are trained to recognize individual structural classes yield prediction scores that are not comparable, so that standard "one-vs-all" classification fails to perform well. Moreover, SVMs for classes at different levels of the protein structural hierarchy may make useful predictions, but one-vs-all does not try to combine these multiple predictions. To deal with these problems, our method learns relative weights between one-vs-the-rest classifiers and encodes information about the protein structural hierarchy for multi-class prediction. In large-scale benchmark results based on the SCOP database, our code weighting approach
URR-PACK: Calculating Self-Shielding in the Unresolved Resonance Energy Range
International Nuclear Information System (INIS)
Cullen, Dermott E.; Trkov, Andrej
2016-07-01
This report describes HOW to calculate self-shielding in the unresolved resonance region (URR), in terms of the computer codes we provide to allow a user to do these calculations himself. Here we only describe HOW to calculate; a longer companion report describes in detail WHY it is necessary to include URR self-shielding.
TUZ, Resonance Integrals in Unresolved Region, Various Temperature, From Porter-Thomas Distribution
International Nuclear Information System (INIS)
Kuncir, G.F.
1969-01-01
1 - Nature of physical problem solved: TUZ computes resonance integrals for a wide variety of temperatures, compositions, and geometries for the unresolved resonances. 2 - Method of solution: The resonances are considered to be defined by an average over the Porter-Thomas distribution of neutron widths
Evolution of Enzymatic Activities in the Enolase Superfamily: L-Rhamnonate Dehydratase
Energy Technology Data Exchange (ETDEWEB)
Rakus,J.; Fedorov, A.; Fedorov, E.; Glaner, M.; Hubbard, B.; Delli, J.; Babbitt, P.; Almo, S.; Gerlt, J.
2008-01-01
The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: l-rhamnonate (6-deoxy-l-mannonate) has the 'best' kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg2+; the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy-l-rhamnonate (obtained by reduction of the product with NaBH4). Like other members of the enolase superfamily, RhamD contains an N-terminal a + {beta} capping domain and a C-terminal ({beta}/a)7{beta}-barrel (modified TIM-barrel) catalytic domain with the active site located at the interface between the two domains. In contrast to other members, the specificity-determining '20s loop' in the capping domain is extended in length and the '50s loop' is truncated. The ligands for the Mg2+ are Asp 226, Glu 252 and Glu 280 located at the ends of the third, fourth and fifth {beta}-strands, respectively. The active site of RhamD contains a His 329-Asp 302 dyad at the ends of the seventh and sixth {beta}-strands, respectively, with His 329 positioned to function as the general base responsible for abstraction of the C2 proton of l-rhamnonate to form a Mg2+-stabilized enediolate intermediate. However, the active site does not contain other acid/base catalysts that have been implicated in the reactions catalyzed by other members of the MR subgroup of the enolase superfamily. Based on the structure of the liganded complex, His 329 also is expected to function as the general acid that both facilitates departure of the 3-OH group in a syn-dehydration reaction and
International Nuclear Information System (INIS)
Yashiro, Wataru; Harasse, Sebastien; Kawabata, Katsuyuki; Kuwabara, Hiroaki; Yamazaki, Takashi; Momose, Atsushi
2011-01-01
X-ray Talbot interferometry has been widely used as a technique for x-ray phase imaging and tomography. We propose a method using this interferometry for mapping distribution of parameters characterizing anisotropic microstructures, which are typically of the order of μm in size and cannot be resolved by the imaging system, in a sample. The method uses reduction in fringe visibility, which is caused by such unresolvable microstructures, in moire images obtained using an interferometer. We applied the method to a chloroprene rubber sponge sample, which exhibited uniaxial anisotropy of reduced visibility. We measured the dependencies of reduced visibility on both the Talbot order and the orientation of the sample and obtained maps of three parameters and their anisotropies that characterize the unresolvable anisotropic microstructures in the sample. The maps indicated that the anisotropy of the sample's visibility contrast mainly originated from the anisotropy of the microstructure elements' average size. Our method directly provides structural information on unresolvable microstructures in real space, which is only accessible through the ultra-small-angle x-ray scattering measurements in reciprocal space, and is expected to be broadly applied to material, biological, and medical sciences.
Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents.
Gogolevsky, Konstantin P; Kramerov, Dmitri A
2006-05-24
A new short interspersed element (SINE) was isolated from the genome of desert kangaroo rat (Dipodomys deserti) using single-primer PCR. This SINE consists of two monomers: the left monomer (IDL) resembles rodent ID element and other tRNAAla(CGC)-derived SINEs, whereas the right one (Geo) shows no similarity with known SINE sequences. PCR and hybridization analyses demonstrated that IDL-Geo SINE is restricted to the rodent superfamily Geomyoidea (families Geomyidea and Heteromyidea). Isolation and analysis of IDL-Geo from California pocket mouse (Chaetodipus californicus) and Botta's pocket gopher (Thomomys bottae) revealed some species-specific features of this SINE family. The structure and evolution of known dimeric SINEs are discussed.
Tian, Feng-Xia; Zang, Jian-Lei; Wang, Tan; Xie, Yu-Li; Zhang, Jin; Hu, Jian-Jun
2015-01-01
Aldehyde dehydrogenases (ALDHs) constitute a superfamily of NAD(P)+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.
Directory of Open Access Journals (Sweden)
Feng-Xia Tian
Full Text Available Aldehyde dehydrogenases (ALDHs constitute a superfamily of NAD(P+-dependent enzymes that catalyze the irreversible oxidation of a wide range of reactive aldehydes to their corresponding nontoxic carboxylic acids. ALDHs have been studied in many organisms from bacteria to mammals; however, no systematic analyses incorporating genome organization, gene structure, expression profiles, and cis-acting elements have been conducted in the model tree species Populus trichocarpa thus far. In this study, a comprehensive analysis of the Populus ALDH gene superfamily was performed. A total of 26 Populus ALDH genes were found to be distributed across 12 chromosomes. Genomic organization analysis indicated that purifying selection may have played a pivotal role in the retention and maintenance of PtALDH gene families. The exon-intron organizations of PtALDHs were highly conserved within the same family, suggesting that the members of the same family also may have conserved functionalities. Microarray data and qRT-PCR analysis indicated that most PtALDHs had distinct tissue-specific expression patterns. The specificity of cis-acting elements in the promoter regions of the PtALDHs and the divergence of expression patterns between nine paralogous PtALDH gene pairs suggested that gene duplications may have freed the duplicate genes from the functional constraints. The expression levels of some ALDHs were up- or down-regulated by various abiotic stresses, implying that the products of these genes may be involved in the adaptation of Populus to abiotic stresses. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus ALDH gene superfamily and provide insights into the function and evolution of ALDH gene families in vascular plants.
Aggarwal, Bharat B; Gupta, Subash C; Kim, Ji Hye
2012-01-19
Although activity that induced tumor regression was observed and termed tumor necrosis factor (TNF) as early as the 1960s, the true identity of TNF was not clear until 1984, when Aggarwal and coworkers reported, for the first time, the isolation of 2 cytotoxic factors: one, derived from macrophages (molecular mass 17 kDa), was named TNF, and the second, derived from lymphocytes (20 kDa), was named lymphotoxin. Because the 2 cytotoxic factors exhibited 50% amino acid sequence homology and bound to the same receptor, they came to be called TNF-α and TNF-β. Identification of the protein sequences led to cloning of their cDNA. Based on sequence homology to TNF-α, now a total of 19 members of the TNF superfamily have been identified, along with 29 interacting receptors, and several molecules that interact with the cytoplasmic domain of these receptors. The roles of the TNF superfamily in inflammation, apoptosis, proliferation, invasion, angiogenesis, metastasis, and morphogenesis have been documented. Their roles in immunologic, cardiovascular, neurologic, pulmonary, and metabolic diseases are becoming apparent. TNF superfamily members are active targets for drug development, as indicated by the recent approval and expanding market of TNF blockers used to treat rheumatoid arthritis, psoriasis, Crohns disease, and osteoporosis, with a total market of more than US $20 billion. As we learn more about this family, more therapeutics will probably emerge. In this review, we summarize the initial discovery of TNF-α, and the insights gained regarding the roles of this molecule and its related family members in normal physiology and disease.
Meeting report - TGF-β superfamily: signaling in development and disease.
Zhang, Ying E; Newfeld, Stuart J
2013-11-01
The latest advances on the transforming growth factor β (TGF-β) and bone morphogenetic protein (BMP) signaling pathways were reported at the July 2013 FASEB Summer Research Conference 'The TGF-β Superfamily: Development and Disease'. The meeting was held in Steamboat Springs, Colorado, USA at 6700 feet above sea level in the Rocky Mountains. This was the seventh biannual meeting in the series. In attendance were investigators from a broad range of disciplines with a common interest in the mechanics of TGF-β and BMP signaling pathways, their normal developmental and homeostatic functions, and the diseases associated with pathway misregulation.
Pineda, Sandy S; Sollod, Brianna L; Wilson, David; Darling, Aaron; Sunagar, Kartik; Undheim, Eivind A B; Kely, Laurence; Antunes, Agostinho; Fry, Bryan G; King, Glenn F
2014-03-05
Spiders have evolved pharmacologically complex venoms that serve to rapidly subdue prey and deter predators. The major toxic factors in most spider venoms are small, disulfide-rich peptides. While there is abundant evidence that snake venoms evolved by recruitment of genes encoding normal body proteins followed by extensive gene duplication accompanied by explosive structural and functional diversification, the evolutionary trajectory of spider-venom peptides is less clear. Here we present evidence of a spider-toxin superfamily encoding a high degree of sequence and functional diversity that has evolved via accelerated duplication and diversification of a single ancestral gene. The peptides within this toxin superfamily are translated as prepropeptides that are posttranslationally processed to yield the mature toxin. The N-terminal signal sequence, as well as the protease recognition site at the junction of the propeptide and mature toxin are conserved, whereas the remainder of the propeptide and mature toxin sequences are variable. All toxin transcripts within this superfamily exhibit a striking cysteine codon bias. We show that different pharmacological classes of toxins within this peptide superfamily evolved under different evolutionary selection pressures. Overall, this study reinforces the hypothesis that spiders use a combinatorial peptide library strategy to evolve a complex cocktail of peptide toxins that target neuronal receptors and ion channels in prey and predators. We show that the ω-hexatoxins that target insect voltage-gated calcium channels evolved under the influence of positive Darwinian selection in an episodic fashion, whereas the κ-hexatoxins that target insect calcium-activated potassium channels appear to be under negative selection. A majority of the diversifying sites in the ω-hexatoxins are concentrated on the molecular surface of the toxins, thereby facilitating neofunctionalisation leading to new toxin pharmacology.
Simulated cosmic microwave background maps at 0.5 deg resolution: Unresolved features
Kogut, A.; Hinshaw, G.; Bennett, C. L.
1995-01-01
High-contrast peaks in the cosmic microwave background (CMB) anisotropy can appear as unresolved sources to observers. We fit simluated CMB maps generated with a cold dark matter model to a set of unresolved features at instrumental resolution 0.5 deg-1.5 deg to derive the integral number density per steradian n (greater than absolute value of T) of features brighter than threshold temperature absolute value of T and compare the results to recent experiments. A typical medium-scale experiment observing 0.001 sr at 0.5 deg resolution would expect to observe one feature brighter than 85 micro-K after convolution with the beam profile, with less than 5% probability to observe a source brighter than 150 micro-K. Increasing the power-law index of primordial density perturbations n from 1 to 1.5 raises these temperature limits absolute value of T by a factor of 2. The MSAM features are in agreement with standard cold dark matter models and are not necessarily evidence for processes beyond the standard model.
Structure of TTHA1623, a novel metallo-β-lactamase superfamily protein from Thermus thermophilus HB8
International Nuclear Information System (INIS)
Yamamura, Akihiro; Okada, Akitoshi; Kameda, Yasuhiro; Ohtsuka, Jun; Nakagawa, Noriko; Ebihara, Akio; Nagata, Koji; Tanokura, Masaru
2009-01-01
The crystal structures of TTHA1623 from T. thermophilus HB8 in an iron-bound and a zinc-bound form have been determined to 2.8 and 2.2 Å resolution, respectively. TTHA1623 is a metallo-β-lactamase superfamily protein from the extremely thermophilic bacterium Thermus thermophilus HB8. Homologues of TTHA1623 exist in a wide range of bacteria and archaea and one eukaryote, Giardia lamblia, but their function remains unknown. To analyze the structural properties of TTHA1623, the crystal structures of its iron-bound and zinc-bound forms have been determined to 2.8 and 2.2 Å resolution, respectively. TTHA1623 possesses an αββα-fold similar to that of other metallo-β-lactamase superfamily proteins with glyoxalase II-type metal coordination. However, TTHA1623 exhibits a putative substrate-binding pocket with a unique shape
Isolation of a novel LPS-induced component of the ML superfamily in Ciona intestinalis.
Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo
2015-11-01
ML superfamily represents a group of proteins playing important roles in lipid metabolism and innate immune response. In this study, we report the identification of the first component of the ML superfamily in the invertebrate Ciona intestinalis by means of a subtractive hybridization strategy. Sequence homology and phylogenetic analysis showed that this protein forms a specific clade with vertebrate components of the Niemann-Pick type C2 protein and, for this reason, it has been named Ci-NPC2. The putative Ci-NPC2 is a 150 amino acids long protein with a short signal peptide, seven cysteine residues, three putative lipid binding site and a three-dimensional model showing a characteristic β-strand structure. Gene expression analysis demonstrated that the Ci-NPC2 protein is positively upregulated after LPS inoculum with a peak of expression 1 h after challenge. Finally, in-situ hybridization demonstrated that the Ci-NPC2 protein is preferentially expressed in hemocytes inside the vessel lumen. Copyright © 2015 Elsevier Ltd. All rights reserved.
McCoy, Jason G; Ren, Zhenning; Stanevich, Vitali; Lee, Jumin; Mitra, Sharmistha; Levin, Elena J; Poget, Sebastien; Quick, Matthias; Im, Wonpil; Zhou, Ming
2016-06-07
The phosphoenolpyruvate:carbohydrate phosphotransferase systems are found in bacteria, where they play central roles in sugar uptake and regulation of cellular uptake processes. Little is known about how the membrane-embedded components (EIICs) selectively mediate the passage of carbohydrates across the membrane. Here we report the functional characterization and 2.55-Å resolution structure of a maltose transporter, bcMalT, belonging to the glucose superfamily of EIIC transporters. bcMalT crystallized in an outward-facing occluded conformation, in contrast to the structure of another glucose superfamily EIIC, bcChbC, which crystallized in an inward-facing occluded conformation. The structures differ in the position of a structurally conserved substrate-binding domain that is suggested to play a central role in sugar transport. In addition, molecular dynamics simulations suggest a potential pathway for substrate entry from the periplasm into the bcMalT substrate-binding site. These results provide a mechanistic framework for understanding substrate recognition and translocation for the glucose superfamily EIIC transporters. Copyright © 2016 Elsevier Ltd. All rights reserved.
Parameterizing unresolved obstacles with source terms in wave modeling: A real-world application
Mentaschi, Lorenzo; Kakoulaki, Georgia; Vousdoukas, Michalis; Voukouvalas, Evangelos; Feyen, Luc; Besio, Giovanni
2018-06-01
Parameterizing the dissipative effects of small, unresolved coastal features, is fundamental to improve the skills of wave models. The established technique to deal with this problem consists in reducing the amount of energy advected within the propagation scheme, and is currently available only for regular grids. To find a more general approach, Mentaschi et al., 2015b formulated a technique based on source terms, and validated it on synthetic case studies. This technique separates the parameterization of the unresolved features from the energy advection, and can therefore be applied to any numerical scheme and to any type of mesh. Here we developed an open-source library for the estimation of the transparency coefficients needed by this approach, from bathymetric data and for any type of mesh. The spectral wave model WAVEWATCH III was used to show that in a real-world domain, such as the Caribbean Sea, the proposed approach has skills comparable and sometimes better than the established propagation-based technique.
National Research Council Canada - National Science Library
2001-01-01
.... In September 1999, we reported that the preliminary results of the ongoing Pearl Harbor pilot were mixed and recommended that the Departments of Defense and the Navy address unresolved issues related...
DEFF Research Database (Denmark)
Geisler, C; Rubin, B; Caspar-Bauguil, S
1992-01-01
Several molecules belonging to the Ig superfamily are expressed together with noncovalently associated subunits. This applies for membrane-bound IgM and IgD, some of the FcR, and the Ti dimers of the TCR. The interactions between members of the Ig superfamily and their associated subunits are sti...
Machielsen, M.P.; Uria, A.R.; Kengen, S.W.M.; Oost, van der J.
2006-01-01
The gene encoding a novel alcohol dehydrogenase that belongs to the aldo-keto reductase superfamily has been identified in the hyperthermophilic archaeon Pyrococcus furiosus. The gene, referred to as adhD, was functionally expressed in Escherichia coli and subsequently purified to homogeneity. The
Energy Technology Data Exchange (ETDEWEB)
Sakai, A.; Fedorov, A; Fedorov, E; Schnoes, A; Glasner, M; Burley, S; Babbitt, P; Almo, S; Gerlt, J
2009-01-01
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the a-proton of a carboxylate substrate that is coordinated to an essential Mg2+. The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the e-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologous MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, gi 70731221; anti, Mycobacterium smegmatis, gi 118470554) document that the conserved Lys at the end of the second e-strand in the (e/a)7e-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of 'pseudoconvergent' evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction.
Sakai, Ayano; Fedorov, Alexander A.; Fedorov, Elena V.; Schnoes, Alexandra M.; Glasner, Margaret E.; Brown, Shoshana; Rutter, Marc E.; Bain, Kevin; Chang, Shawn; Gheyi, Tarun; Sauder, J. Michael; Burley, Stephen K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.
2009-01-01
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature’s strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the α-proton of a carboxylate substrate that is coordinated to an essential Mg2+. The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the β-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologues MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, GI:70731221; anti, Mycobacterium smegmatis, GI:118470554) document that the conserved Lys at the end of the second β-strand in the (β/α)7β-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of “pseudoconvergent” evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction. PMID:19220063
Directory of Open Access Journals (Sweden)
Silvia Dal Santo
Full Text Available BACKGROUND: Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP comprises four distinct families: expansin A (EXPA, expansin B (EXPB, expansin-like A (EXLA and expansin-like B (EXLB. There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far. METHODOLOGY/PRINCIPAL FINDINGS: We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon-intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa, compared to those from Arabidopsis thaliana and rice (Oryza sativa. We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering. CONCLUSION: Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the
Shagin, Dmitry A; Barsova, Ekaterina V; Yanushevich, Yurii G; Fradkov, Arkady F; Lukyanov, Konstantin A; Labas, Yulii A; Semenova, Tatiana N; Ugalde, Juan A; Meyers, Ann; Nunez, Jose M; Widder, Edith A; Lukyanov, Sergey A; Matz, Mikhail V
2004-05-01
Homologs of the green fluorescent protein (GFP), including the recently described GFP-like domains of certain extracellular matrix proteins in Bilaterian organisms, are remarkably similar at the protein structure level, yet they often perform totally unrelated functions, thereby warranting recognition as a superfamily. Here we describe diverse GFP-like proteins from previously undersampled and completely new sources, including hydromedusae and planktonic Copepoda. In hydromedusae, yellow and nonfluorescent purple proteins were found in addition to greens. Notably, the new yellow protein seems to follow exactly the same structural solution to achieving the yellow color of fluorescence as YFP, an engineered yellow-emitting mutant variant of GFP. The addition of these new sequences made it possible to resolve deep-level phylogenetic relationships within the superfamily. Fluorescence (most likely green) must have already existed in the common ancestor of Cnidaria and Bilateria, and therefore GFP-like proteins may be responsible for fluorescence and/or coloration in virtually any animal. At least 15 color diversification events can be inferred following the maximum parsimony principle in Cnidaria. Origination of red fluorescence and nonfluorescent purple-blue colors on several independent occasions provides a remarkable example of convergent evolution of complex features at the molecular level.
Building a Phylogenetic Tree of the Human and Ape Superfamily Using DNA-DNA Hybridization Data
Maier, Caroline Alexander
2004-01-01
The study describes the process of DNA-DNA hybridization and the history of its use by Sibley and Alquist in simple, straightforward, and interesting language that students easily understand to create their own phylogenetic tree of the hominoid superfamily. They calibrate the DNA clock and use it to estimate the divergence dates of the various…
A CATALOG OF NEAR-IR SOURCES FOUND TO BE UNRESOLVED WITH MILLIARCSECOND RESOLUTION
Energy Technology Data Exchange (ETDEWEB)
Richichi, A. [National Astronomical Research Institute of Thailand, 191 Siriphanich Bldg., Huay Kaew Rd., Suthep, Muang, Chiang Mai 50200 (Thailand); Fors, O. [Departament Astronomia i Meteorologia and Institut de Ciencies del Cosmos (ICC), Universitat de Barcelona (UB/IEEC), Marti i Franques 1, E-08028 Barcelona (Spain); Cusano, F. [INAF-Osservatorio Astronomico di Bologna, Via Ranzani 1, I-40127 Bologna (Italy); Moerchen, M., E-mail: andrea@narit.or.th [European Southern Observatory, Casilla 19001, Santiago 19 (Chile)
2012-12-15
Calibration is one of the long-standing problems in optical interferometric measurements, particularly with long baselines which demand stars with angular sizes on the milliarcsecond scale and no detectable companions. While systems of calibrators have been generally established for the near-infrared in the bright source regime (K {approx}< 3 mag), modern large interferometers are sensitive to significantly fainter magnitudes. We aim to provide a list of sources found to be unresolved from direct observations with high angular resolution and dynamic range, which can be used to choose interferometric calibrators. To this purpose, we have used a large number of lunar occultations recorded with the ISAAC instrument at the Very Large Telescope to select sources found to be unresolved and without close companions. An algorithm has been used to determine the limiting angular resolution achieved for each source, taking into account a noise model built from occulted and unocculted portions of the light curves. We have obtained upper limits on the angular sizes of 556 sources, with magnitudes ranging from K{sub s} Almost-Equal-To 4 to 10, with a median of 7.2 mag. The upper limits on possible undetected companions (within Almost-Equal-To 0.''5) range from K{sub s} Almost-Equal-To 8 to 13, with a median of 11.5 mag. One-third of the sources have angular sizes {<=}1 mas, and two-thirds have sizes {<=}2 mas. This list of unresolved sources matches well the capabilities of current large interferometric facilities. We also provide available cross-identifications, magnitudes, spectral types, and other auxiliary information. A fraction of the sources are found to be potentially variable. The list covers parts of the Galactic Bulge and in particular the vicinity of the Galactic Center, where extinction is very significant and traditional lists of calibrators are often insufficient.
Impact of MCNP unresolved resonance probability-table treatment on uranium and plutonium benchmarks
International Nuclear Information System (INIS)
Mosteller, R.D.; Little, R.C.
1998-01-01
Versions of MCNP up through and including 4B have not accurately modeled neutron self-shielding effects in the unresolved resonance energy region. Recently, a probability-table treatment has been incorporated into a developmental version of MCNP. This paper presents MCNP results for a variety of uranium and plutonium critical benchmarks, calculated with and without the probability-table treatment
Absorption and emission profiles of unresolved arrays near local thermodynamic equilibrium
Energy Technology Data Exchange (ETDEWEB)
Busquet, M.; Klapisch, M. E-mail: klapisch@this.nrl.navy.mil; Bar-Shalom, A
2003-11-01
The absorption and emission arrays in the unresolved transition array (UTA) and super transition array (STA) models are usually assumed to have the same Gaussian spectral shape. It is shown, starting from a Boltzmann population distribution, that the assumption of profile identity for both absorption and emission is inconsistent with Kirchhoff's law. A correcting formula is established. It is extended to the cases where one or two effective population temperatures are involved. Examples are shown where the effect is noticeable.
Absorption and emission profiles of unresolved arrays near local thermodynamic equilibrium
International Nuclear Information System (INIS)
Busquet, M.; Klapisch, M.; Bar-Shalom, A.
2003-01-01
The absorption and emission arrays in the unresolved transition array (UTA) and super transition array (STA) models are usually assumed to have the same Gaussian spectral shape. It is shown, starting from a Boltzmann population distribution, that the assumption of profile identity for both absorption and emission is inconsistent with Kirchhoff's law. A correcting formula is established. It is extended to the cases where one or two effective population temperatures are involved. Examples are shown where the effect is noticeable
Directory of Open Access Journals (Sweden)
Persson Bengt
2010-10-01
Full Text Available Abstract Background The Medium-chain Dehydrogenases/Reductases (MDR form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the pairwise sequence identity is typically around 25%, there are members from all kingdoms of life, the chain-lengths vary as does the oligomericity, and the members are partaking in a multitude of biological processes. There are profile hidden Markov models (HMMs available for detecting MDR superfamily members, but none for determining which MDR family each protein belongs to. The current torrential influx of new sequence data enables elucidation of more and more protein families, and at an increasingly fine granularity. However, gathering good quality training data usually requires manual attention by experts and has therefore been the rate limiting step for expanding the number of available models. Results We have developed an automated algorithm for HMM refinement that produces stable and reliable models for protein families. This algorithm uses relationships found in data to generate confident seed sets. Using this algorithm we have produced HMMs for 86 distinct MDR families and 34 of their subfamilies which can be used in automated annotation of new sequences. We find that MDR forms with 2 Zn2+ ions in general are dehydrogenases, while MDR forms with no Zn2+ in general are reductases. Furthermore, in Bacteria MDRs without Zn2+ are more frequent than those with Zn2+, while the opposite is true for eukaryotic MDRs, indicating that Zn2+ has been recruited into the MDR superfamily after the initial life kingdom separations. We have also developed a web site http://mdr-enzymes.org that provides textual and numeric search against various characterised MDR family properties, as well as sequence scan functions for reliable classification of novel MDR sequences. Conclusions Our method of refinement can be readily applied to
Ersoy, Baran A.; Tarun, Akansha; D’Aquino, Katharine; Hancer, Nancy J.; Ukomadu, Chinweike; White, Morris F.; Michel, Thomas; Manning, Brendan D.; Cohen, David E.
2013-01-01
Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenc...
International Nuclear Information System (INIS)
Le, Binh Van; Lee, Hyun Sook; Cho, Yona; Kang, Sung Gyun; Kim, Dong Young; Kim, Yang-Gyun; Kim, Kyeong Kyu
2007-01-01
A putative member of the haloacid dehalogenase superfamily from T. onnurineus has been expressed, purified and crystallized using 1.6 M magnesium sulfate as a precipitant. The crystals belonged to the triclinic space group P1 and diffracted to 1.8 Å resolution. The haloacid dehalogenase (HAD) protein superfamily is one of the largest enzyme families and shows hydrolytic activity towards diverse substrates. Structural analyses of enzymes belonging to the HAD family are required to elucidate the molecular basis underlying their broad substrate specificity and reaction mechanism. For this purpose, TON-1713, a hypothetical protein from Thermococcus onnurineus that is a member of the HAD superfamily, was expressed in Escherichia coli, purified and crystallized at 295 K using 1.6 M magnesium sulfate as a precipitant. X-ray diffraction data were collected to 1.8 Å resolution using a synchrotron-radiation source. The crystals belong to the triclinic space group P1, with unit-cell parameters a = 52.5, b = 65.8, c = 203.4 Å, α = 71.1, β = 79.9, γ = 74.3°
Testing of cross-section functionals in the unresolved resonance region
International Nuclear Information System (INIS)
Koshcheev, V.N.; Krivtsov, A.S.; Sinitsa, V.V.; Ukraintsev, V.F.
1994-01-01
The results of a comparison of the GRUCON, MMK and NJOY data processing codes in the treatment of evaluated neutron data in the unresolved resonance region are presented. The sets of average resonance parameters of 238 U and 239 Pu isotopes, which have been published by Munos-Cobos et al., and Ribon et al., were used in this exercise. Average cross-sections, self-shielding factors and Doppler broadening self-shielding factors are compared with the original results presented by the above-mentioned authors. Conclusions regarding the reliability of the neutron data processing codes are made. (author). 6 refs, 7 tabs
Oxidative stress and life histories: unresolved issues and current needs.
Speakman, John R; Blount, Jonathan D; Bronikowski, Anne M; Buffenstein, Rochelle; Isaksson, Caroline; Kirkwood, Tom B L; Monaghan, Pat; Ozanne, Susan E; Beaulieu, Michaël; Briga, Michael; Carr, Sarah K; Christensen, Louise L; Cochemé, Helena M; Cram, Dominic L; Dantzer, Ben; Harper, Jim M; Jurk, Diana; King, Annette; Noguera, Jose C; Salin, Karine; Sild, Elin; Simons, Mirre J P; Smith, Shona; Stier, Antoine; Tobler, Michael; Vitikainen, Emma; Peaker, Malcolm; Selman, Colin
2015-12-01
Life-history theory concerns the trade-offs that mold the patterns of investment by animals between reproduction, growth, and survival. It is widely recognized that physiology plays a role in the mediation of life-history trade-offs, but the details remain obscure. As life-history theory concerns aspects of investment in the soma that influence survival, understanding the physiological basis of life histories is related, but not identical, to understanding the process of aging. One idea from the field of aging that has gained considerable traction in the area of life histories is that life-history trade-offs may be mediated by free radical production and oxidative stress. We outline here developments in this field and summarize a number of important unresolved issues that may guide future research efforts. The issues are as follows. First, different tissues and macromolecular targets of oxidative stress respond differently during reproduction. The functional significance of these changes, however, remains uncertain. Consequently there is a need for studies that link oxidative stress measurements to functional outcomes, such as survival. Second, measurements of oxidative stress are often highly invasive or terminal. Terminal studies of oxidative stress in wild animals, where detailed life-history information is available, cannot generally be performed without compromising the aims of the studies that generated the life-history data. There is a need therefore for novel non-invasive measurements of multi-tissue oxidative stress. Third, laboratory studies provide unrivaled opportunities for experimental manipulation but may fail to expose the physiology underpinning life-history effects, because of the benign laboratory environment. Fourth, the idea that oxidative stress might underlie life-history trade-offs does not make specific enough predictions that are amenable to testing. Moreover, there is a paucity of good alternative theoretical models on which contrasting
Kim, Eun Oh; Lee, Ihn Suk; Choi, Yoo A; Lee, Sang Ju; Chang, Yoon Kyung; Yoon, Hye Eun; Jang, Yi Sun; Lee, Jong Min; Kim, Hye Soo; Yang, Chul Woo; Kim, Suk Young; Hwang, Hyeon Seok
2014-01-01
Background and Aim: Patients with chronic kidney disease (CKD) often have subclinical hypothyroidism. However, few reports have investigated changes in the status of subclinical hypothyroidism in CKD patients and its clinical significance in CKD progression. Methods: We included 168 patients with nondialysis-dependent CKD stages 2-4. The normalization of subclinical hypothyroidism during follow-up was assessed, and the association between transitions in subclinical hypothyroid status and the rate of decline of the estimated glomerular filtration rate (eGFR) was investigated. Results: At baseline, 127 patients were euthyroid and 41 (24.4%) patients were diagnosed with subclinical hypothyroidism. Of these 41 patients, 21 (51.2%) spontaneously resolved to euthyroid during follow-up. The rate of eGFR decline of patients with resolved subclinical hypothyroidism was similar to that of euthyroid patients. The patients with unresolved subclinical hypothyroidism showed a steeper renal function decline than patients with euthyroidism or resolved subclinical hypothyroidism (all p hypothyroidism than in those who were euthyroid (p = 0.006). In multivariate linear regression for rate of eGFR decrease, unresolved subclinical hypothyroidism (β = -5.77, p = 0.001), baseline renal function (β = -0.12, p hypothyroidism did not resolve to euthyroidism, and this lack of resolution was independently associated with rapid renal function decline. PMID:24396286
Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion.
Farré, Domènec; Martínez-Vicente, Pablo; Engel, Pablo; Angulo, Ana
2017-05-01
Pathogens have developed a plethora of strategies to undermine host immune defenses in order to guarantee their survival. For large DNA viruses, these immune evasion mechanisms frequently rely on the expression of genes acquired from host genomes. Horizontally transferred genes include members of the immunoglobulin superfamily, whose products constitute the most diverse group of proteins of vertebrate genomes. Their promiscuous immunoglobulin domains, which comprise the building blocks of these molecules, are involved in a large variety of functions mediated by ligand-binding interactions. The flexible structural nature of the immunoglobulin domains makes them appealing targets for viral capture due to their capacity to generate high functional diversity. Here, we present an up-to-date review of immunoglobulin superfamily gene homologs encoded by herpesviruses, poxviruses, and adenoviruses, that include CD200, CD47, Fc receptors, interleukin-1 receptor 2, interleukin-18 binding protein, CD80, carcinoembryonic antigen-related cell adhesion molecules, and signaling lymphocyte activation molecules. We discuss their distinct structural attributes, binding properties, and functions, shaped by evolutionary pressures to disarm specific immune pathways. We include several novel genes identified from extensive genome database surveys. An understanding of the properties and modes of action of these viral proteins may guide the development of novel immune-modulatory therapeutic tools. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Laroche, Marilyn; Dajani, Hilmi R; Prévost, François; Marcoux, André M
2013-01-01
This study investigated speech auditory brainstem responses (speech ABR) with variants of a synthetic vowel in quiet and in background noise. Its objectives were to study the noise robustness of the brainstem response at the fundamental frequency F0 and at the first formant F1, evaluate how the resolved/unresolved harmonics regions in speech contribute to the response at F0, and investigate the origin of the response at F0 to resolved and unresolved harmonics in speech. In total, 18 normal-hearing subjects (11 women, aged 18-33 years) participated in this study. Speech ABRs were recorded using variants of a 300 msec formant-synthesized /a/ vowel in quiet and in white noise. The first experiment employed three variants containing the first three formants F1 to F3, F1 only, and F2 and F3 only with relative formant levels following those reported in the literature. The second experiment employed three variants containing F1 only, F2 only, and F3 only, with the formants equalized to the same level and the signal-to-noise ratio (SNR) maintained at -5 dB. Overall response latency was estimated, and the amplitude and local SNR of the envelope following response at F0 and of the frequency following response at F1 were compared for the different stimulus variants in quiet and in noise. The response at F0 was more robust to noise than that at F1. There were no statistically significant differences in the response at F0 caused by the three stimulus variants in both experiments in quiet. However, the response at F0 with the variant dominated by resolved harmonics was more robust to noise than the response at F0 with the stimulus variants dominated by unresolved harmonics. The latencies of the responses in all cases were very similar in quiet, but the responses at F0 due to resolved and unresolved harmonics combined nonlinearly when both were present in the stimulus. Speech ABR has been suggested as a marker of central auditory processing. The results of this study support
Unresolved pain in children: a relational ethics perspective.
Olmstead, Deborah L; Scott, Shannon D; Austin, Wendy J
2010-11-01
It is considered the right of children to have their pain managed effectively. Yet, despite extensive research findings, policy guidelines and practice standard recommendations for the optimal management of paediatric pain, clinical practices remain inadequate. Empirical evidence definitively shows that unrelieved pain in children has only harmful consequences, with no benefits. Contributing factors identified in this undermanaged pain include the significant role of nurses. Nursing attitudes and beliefs about children's pain experiences, the relationships nurses share with children who are suffering, and knowledge deficits in pain management practices are all shown to impact unresolved pain in children. In this article, a relational ethics perspective is used to explore the need for nurses to engage in authentic relationships with children who are experiencing pain, and to use evidence-based practices to manage that pain in order for this indefensible suffering of children to end.
Accounting for model error due to unresolved scales within ensemble Kalman filtering
Mitchell, Lewis; Carrassi, Alberto
2014-01-01
We propose a method to account for model error due to unresolved scales in the context of the ensemble transform Kalman filter (ETKF). The approach extends to this class of algorithms the deterministic model error formulation recently explored for variational schemes and extended Kalman filter. The model error statistic required in the analysis update is estimated using historical reanalysis increments and a suitable model error evolution law. Two different versions of the method are describe...
DEFF Research Database (Denmark)
Kristensen, Stine Gry; Andersen, Kasper; Clement, Christian Alexandro
2014-01-01
In mammals, members of the transforming growth factor-beta (TGF-β) superfamily are known to have key roles in the regulation of follicular growth and development. The aim of the study was to evaluate the expression of TGF-β superfamily growth factors, their receptors, downstream SMAD signalling m...... growth. Moreover, the presence of multiple TGF-β/BMP antagonists imply that certain growth factors are subjected to local regulation on different levels which address another important level of intraovarian regulation of follicle development in humans.......In mammals, members of the transforming growth factor-beta (TGF-β) superfamily are known to have key roles in the regulation of follicular growth and development. The aim of the study was to evaluate the expression of TGF-β superfamily growth factors, their receptors, downstream SMAD signalling...... molecules and TGF- β/BMP antagonists during early human folliculogenesis.Human preantral follicles were enzymatically isolated from surplus ovarian tissue obtained from women having ovarian cortical tissue frozen for fertility preservation. A total of 348 human preantral follicles, ranging from 40 to 200 µm...
Matching of singly- and doubly-unresolved limits of tree-level QCD squared matrix elements
Energy Technology Data Exchange (ETDEWEB)
Somogyi, Gabor [University of Debrecen and Institute of Nuclear Research of the Hungarian Academy of Sciences, H-4001 Debrecen, PO Box 51 (Hungary); Trocsanyi, Zoltan [University of Debrecen and Institute of Nuclear Research of the Hungarian Academy of Sciences, H-4001 Debrecen, PO Box 51 (Hungary); Duca, Vittorio Del [Istituto Nazionale di Fisica Nucleare, Sez. di Torino, via P. Giuria, 1 - 10125 Torino (Italy)
2005-06-01
We describe how to disentangle the singly- and doubly-unresolved (soft and/or collinear) limits of tree-level QCD squared matrix elements. Using the factorization formulae presented in this paper, we outline a viable general subtraction scheme for computing next-to-next-to-leading order corrections for electron-positron annihilation into jets.
Carmona-Antoñanzas, Greta; Carmichael, Stephen N; Heumann, Jan; Taggart, John B; Gharbi, Karim; Bron, James E; Bekaert, Michaël; Sturm, Armin
2015-01-01
Salmon lice, Lepeophtheirus salmonis (Krøyer, 1837), are fish ectoparasites causing significant economic damage in the mariculture of Atlantic salmon, Salmo salar Linnaeus, 1758. The control of L. salmonis at fish farms relies to a large extent on treatment with anti-parasitic drugs. A problem related to chemical control is the potential for development of resistance, which in L. salmonis is documented for a number of drug classes including organophosphates, pyrethroids and avermectins. The ATP-binding cassette (ABC) gene superfamily is found in all biota and includes a range of drug efflux transporters that can confer drug resistance to cancers and pathogens. Furthermore, some ABC transporters are recognised to be involved in conferral of insecticide resistance. While a number of studies have investigated ABC transporters in L. salmonis, no systematic analysis of the ABC gene family exists for this species. This study presents a genome-wide survey of ABC genes in L. salmonis for which, ABC superfamily members were identified through homology searching of the L. salmonis genome. In addition, ABC proteins were identified in a reference transcriptome of the parasite generated by high-throughput RNA sequencing (RNA-seq) of a multi-stage RNA library. Searches of both genome and transcriptome allowed the identification of a total of 33 genes / transcripts coding for ABC proteins, of which 3 were represented only in the genome and 4 only in the transcriptome. Eighteen sequences were assigned to ABC subfamilies known to contain drug transporters, i.e. subfamilies B (4 sequences), C (11) and G (2). The results suggest that the ABC gene family of L. salmonis possesses fewer members than recorded for other arthropods. The present survey of the L. salmonis ABC gene superfamily will provide the basis for further research into potential roles of ABC transporters in the toxicity of salmon delousing agents and as potential mechanisms of drug resistance.
Extrinsic and intrinsic motivation at 30: Unresolved scientific issues.
Reiss, Steven
2005-01-01
The undermining effect of extrinsic reward on intrinsic motivation remains unproven. The key unresolved issues are construct invalidity (all four definitions are unproved and two are illogical); measurement unreliability (the free-choice measure requires unreliable, subjective judgments to infer intrinsic motivation); inadequate experimental controls (negative affect and novelty, not cognitive evaluation, may explain "undermining" effects); and biased metareviews (studies with possible floor effects excluded, but those with possible ceiling effects included). Perhaps the greatest error with the undermining theory, however, is that it does not adequately recognize the multifaceted nature of intrinsic motivation (Reiss, 2004a). Advice to limit the use of applied behavior analysis based on "hidden" undermining effects is ideologically inspired and is unsupported by credible scientific evidence.
Identification of unresolved safety issues relating to nuclear power plants. Report to Congress
International Nuclear Information System (INIS)
1979-01-01
The report describes the review undertaken over the last year that resulted in identifying 17 issues as Unresolved Safety Issues. In addition, the report provides specific discussions of why certain issues were not included. The report also provides a brief background discussion describing Section 210 of the Energy Reorganization Act and the NRC program for the resolution of generic issues described in NUREG-0410
Evolutionary history and stress regulation of the lectin superfamily in higher plants
Directory of Open Access Journals (Sweden)
Ramachandran Srinivasan
2010-03-01
Full Text Available Abstract Background Lectins are a class of carbohydrate-binding proteins. They play roles in various biological processes. However, little is known about their evolutionary history and their functions in plant stress regulation. The availability of full genome sequences from various plant species makes it possible to perform a whole-genome exploration for further understanding their biological functions. Results Higher plant genomes encode large numbers of lectin proteins. Based on their domain structures and phylogenetic analyses, a new classification system has been proposed. In this system, 12 different families have been classified and four of them consist of recently identified plant lectin members. Further analyses show that some of lectin families exhibit species-specific expansion and rapid birth-and-death evolution. Tandem and segmental duplications have been regarded as the major mechanisms to drive lectin expansion although retrogenes also significantly contributed to the birth of new lectin genes in soybean and rice. Evidence shows that lectin genes have been involved in biotic/abiotic stress regulations and tandem/segmental duplications may be regarded as drivers for plants to adapt various environmental stresses through duplication followed by expression divergence. Each member of this gene superfamily may play specialized roles in a specific stress condition and function as a regulator of various environmental factors such as cold, drought and high salinity as well as biotic stresses. Conclusions Our studies provide a new outline of the plant lectin gene superfamily and advance the understanding of plant lectin genes in lineage-specific expansion and their functions in biotic/abiotic stress-related developmental processes.
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
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Alexandra M Schnoes
2009-12-01
Full Text Available Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families; the two other protein sequence databases (GenBank NR and TrEMBL and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.
Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.
Schnoes, Alexandra M; Brown, Shoshana D; Dodevski, Igor; Babbitt, Patricia C
2009-12-01
Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.
An orphan viral TNF receptor superfamily member identified in lymphocystis disease virus.
Pontejo, Sergio M; Sánchez, Carolina; Martín, Rocío; Mulero, Victoriano; Alcami, Antonio; Alejo, Alí
2013-06-07
Lymphocystis disease virus (LCDV) is a large icosahedral dsDNA-containing virus of the Lymphocystivirus genus within the Iridoviridae family that can cause disease in more than 140 marine and freshwater fish species. While several isolates have been charcaterized and classified into distinct genotypes the complete genomic sequence is currently only available from two species, the LCDV-1, isolated from flounder (Platichtys flesus) in Europe and the LCDV-C, isolated from Japanese cultured flounder (Paralichthys olivaceus) in China. Analysis of the genome of LCDV-C showed it to encode a protein named LDVICp016 with similarities to the Tumour necrosis factor receptor (TNFR) superfamily with immunomodulatory potential. We have expressed and purified the recombinant protein LDVICp016 and screened for potential interaction partners using surface plasmon resonance. Commercially available human and mouse members of the TNF superfamily (TNFSF), along with a representative set of fish-derived TNFSF were tested.We have found the LDVICp016 protein to be secreted and we have identified a second viral TNFR encoded by ORF 095 of the same virus. None of the 42 tested proteins were found to interact with LDVICp016. We show that LDVICp016 is a secreted protein belonging to the TNF receptor family that may be part of a larger gene family in Lymphocystiviruses. While the ligand of this protein remains unknown, possibly due to the species specific nature of this interaction, further investigations into the potential role of this protein in the blockade of immune responses in its fish host are required.
Integration of collinear-type doubly unresolved counterterms in NNLO jet cross sections
Del Duca, Vittorio; Somogyi, Gábor; Trócsányi, Zoltán
2013-06-01
In the context of a subtraction method for jet cross sections at NNLO accuracy in the strong coupling, we perform the integration over the two-particle factorised phase space of the collinear-type contributions to the doubly unresolved counterterms. We present the final result as a convolution in colour space of the Born cross section and of an insertion operator, which is written in terms of master integrals that we expand in the dimensional regularisation parameter.
Integration of collinear-type doubly unresolved counterterms in NNLO jet cross sections
Del Duca, Vittorio; Trocsanyi, Zoltan
2013-01-01
In the context of a subtraction method for jet cross sections at NNLO accuracy in the strong coupling, we perform the integration over the two-particle factorised phase space of the collinear-type contributions to the doubly unresolved counterterms. We present the final result as a convolution in colour space of the Born cross section and of an insertion operator, which is written in terms of master integrals that we expand in the dimensional regularisation parameter.
Directory of Open Access Journals (Sweden)
Jair Alves Ferreira Júnior
Full Text Available ABSTRACT: Nematodes of the superfamily Metastrongyloidea affect the respiratory, cardiovascular, and nervous systems of domestic carnivores and are uncommonly detected in wild animals. This report describes the lesions associated with pulmonary parasitism by nematodes of the superfamily Metastrongyloidea in a wild crab-eating fox ( Cerdocyon thous in the Federal District, Brazil. Grossly, there was pulmonary hyperemia, edema, and emphysema. Microscopically, there was granulomatous arteritis associated with intravascular metastrongylid. The anatomical location, characteristic lesion, and histological features of the parasite suggested that the nematode involved in this case is Angiostrongylus vasorum . This worm is frequently reported parasitizing pulmonary arteries of domestic canids but is uncommonly described in wild canids in Midwestern Brazil.
Chalk Catchment Transit Time: Unresolved Issues
Energy Technology Data Exchange (ETDEWEB)
Darling, W. G.; Gooddy, D. C. [British Geological Survey, Crowmarsh Gifford, Wallingford, Oxfordshire (United Kingdom); Barker, J. A. [School of Civil Engineering and the Environment, University of Southampton, Southampton (United Kingdom); Robinson, M. [Centre for Ecology and Hydrology, Crowmarsh Gifford, Wallingford, Oxfordshire (United Kingdom)
2013-07-15
The mean transit time (MTT) of a catchment is the average residence time of water from rainfall to river outflow at the foot of the catchment. As such, MTT has important water quality as well as resource implications. Many catchments worldwide have been measured for MTT using environmental isotopes, yet the Chalk, an important aquifer in NW Europe, has received little attention in this regard. The catchment of the River Lambourn in southern England has been intermittently studied since the 1960s using isotopic methods. A tritium peak measured in the river during the 1970s indicates an apparent MTT of {approx}15 years, but the thick unsaturated zone (average {approx}50 m) of the catchment suggests that the MTT should be much greater because of the average downward movement through the Chalk of {approx}1 m/a consistently indicated by tritium and other tracers. Recent work in the catchment using SF{sub 6} as a residence time indicator has given groundwater ages in the narrow range 11-18 yrs, apparently supporting the river tritium data but in conflict with the unsaturated zone data even allowing for a moderate proportion of rapid bypass flow. The MTT of the catchment remains unresolved for the time being. (author)
Directory of Open Access Journals (Sweden)
Qingping Xu
Full Text Available NlpC/P60 superfamily papain-like enzymes play important roles in all kingdoms of life. Two members of this superfamily, LRAT-like and YaeF/YiiX-like families, were predicted to contain a catalytic domain that is circularly permuted such that the catalytic cysteine is located near the C-terminus, instead of at the N-terminus. These permuted enzymes are widespread in virus, pathogenic bacteria, and eukaryotes. We determined the crystal structure of a member of the YaeF/YiiX-like family from Bacillus cereus in complex with lysine. The structure, which adopts a ligand-induced, "closed" conformation, confirms the circular permutation of catalytic residues. A comparative analysis of other related protein structures within the NlpC/P60 superfamily is presented. Permutated NlpC/P60 enzymes contain a similar conserved core and arrangement of catalytic residues, including a Cys/His-containing triad and an additional conserved tyrosine. More surprisingly, permuted enzymes have a hydrophobic S1 binding pocket that is distinct from previously characterized enzymes in the family, indicative of novel substrate specificity. Further analysis of a structural homolog, YiiX (PDB 2if6 identified a fatty acid in the conserved hydrophobic pocket, thus providing additional insights into possible function of these novel enzymes.
Energy Technology Data Exchange (ETDEWEB)
Yew,W.; Fedorov, A.; Fedorov, E.; Rakus, J.; Pierce, R.; Almo, S.; Gerlt, J.
2006-01-01
Many members of the mechanistically diverse enolase superfamily have unknown functions. In this report the authors use both genome (operon) context and screening of a library of acid sugars to assign the L-fuconate dehydratase (FucD) function to a member of the mandelate racemase (MR) subgroup of the superfamily encoded by the Xanthomonas campestris pv. campestris str. ATCC 33913 genome (GI: 21233491). Orthologues of FucD are found in both bacteria and eukaryotes, the latter including the rTS beta protein in Homo sapiens that has been implicated in regulating thymidylate synthase activity. As suggested by sequence alignments and confirmed by high-resolution structures in the presence of active site ligands, FucD and MR share the same active site motif of functional groups: three carboxylate ligands for the essential Mg2+ located at the ends of th third, fourth, and fifth-strands in the (/)7-barrel domain (Asp 248, Glu 274, and Glu 301, respectively), a Lys-x-Lys motif at the end of the second-strand (Lys 218 and Lys 220), a His-Asp dyad at the end of the seventh and sixth-strands (His 351 and Asp 324, respectively), and a Glue at the end of the eighth-strand (Glu 382). The mechanism of the FucD reaction involves initial abstraction of the 2-proton by Lys 220, acid catalysis of the vinylogous-elimination of the 3-OH group by His 351, and stereospecific ketonization of the resulting 2-keto-3-deoxy-L-fuconate product. Screening of the library of acid sugars revealed substrate and functional promiscuity: In addition to L-fuconate, FucD also catalyzes the dehydration of L-galactonate, D-arabinonate, D-altronate, L-talonate, and D-ribonate. The dehydrations of L-fuconate, L-galactonate, and D-arabinonate are initiated by abstraction of the 2-protons by Lys 220. The dehydrations of L-talonate and D-ribonate are initiated by abstraction of the 2-protons by His 351; however, protonation of the enediolate intermediates by the conjugate acid of Lys 220 yields L
Energy Technology Data Exchange (ETDEWEB)
Bolzoni, Paolo [Hamburg Univ. (Germany). II. Inst. fuer Theoretische Physik; Somogyi, Gabor [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany); Trocsanyi, Zoltan [Debrecen Univ. (Hungary); Hungarian Academy of Sciences, Debrecen (Hungary). Inst. of Nuclear Research
2010-11-15
We perform the integration of all iterated singly-unresolved subtraction terms over the two-particle factorized phase space. We also sum over the unresolved parton flavours. The final result can be written as a convolution (in colour space) of the Born cross section and an insertion operator. We spell out the insertion operator in terms of 24 basic integrals that are defined explicitly. We compute the coefficients of the Laurent-expansion of these integrals in two different ways, with the method of Mellin-Barnes representations and sector decomposition. Finally, we present the Laurentexpansion of the full insertion operator for the specific examples of electron-positron annihilation into two and three jets. (orig.)
Bolzoni, Paolo; Somogyi, Gábor; Trócsányi, Zoltán
2011-01-01
We perform the integration of all iterated singly-unresolved subtraction terms, as defined in ref. [1], over the two-particle factorized phase space. We also sum over the unresolved parton flavours. The final result can be written as a convolution (in colour space) of the Born cross section and an insertion operator. We spell out the insertion operator in terms of 24 basic integrals that are defined explicitly. We compute the coefficients of the Laurent expansion of these integrals in two different ways, with the method of Mellin-Barnes representations and sector decomposition. Finally, we present the Laurent-expansion of the full insertion operator for the specific examples of electron-positron annihilation into two and three jets.
Two differentially regulated Arabidopsis genes define a new branch of the DFR superfamily
DEFF Research Database (Denmark)
Østergaard, L; Lauvergeat, V; Naested, H
2001-01-01
that, whereas high expression of AtCRL1 in mature seeds declines during subsequent vegetative growth, transcriptional activity from the AtCRL2 promoter increases during vegetative growth. Expression of both genes is restricted to vascular tissue. Based upon their homology to proteins involved in lignin......Two tandem genes were identified on Arabidopsis chromosome II (AtCRL1 and AtCRL2) encoding proteins with homology to members of the dihydroflavonol-4-reductase (DFR) superfamily. The encoded CRL1 and CRL2 proteins share 87% mutual amino acid sequence identity whereas their promoter regions...
DEFF Research Database (Denmark)
Steenholdt, C; Enevold, C; Ainsworth, M A
2012-01-01
Single nucleotide polymorphisms (SNPs) in TNF receptor superfamily (TNFRSF) 1A and 1B, and Fas ligand (FASLG) genes, have been associated with responsiveness to infliximab (IFX) in Crohn's disease.......Single nucleotide polymorphisms (SNPs) in TNF receptor superfamily (TNFRSF) 1A and 1B, and Fas ligand (FASLG) genes, have been associated with responsiveness to infliximab (IFX) in Crohn's disease....
Directory of Open Access Journals (Sweden)
De Souza Robson F
2009-08-01
Full Text Available Abstract The Anabaena sensory rhodopsin transducer (ASRT is a small protein that has been claimed to function as a signaling molecule downstream of the cyanobacterial sensory rhodopsin. However, orthologs of ASRT have been detected in several bacteria that lack rhodopsin, raising questions about the generality of this function. Using sequence profile searches we show that ASRT defines a novel superfamily of β-sandwich fold domains. Through contextual inference based on domain architectures and predicted operons and structural analysis we present strong evidence that these domains bind small molecules, most probably sugars. We propose that the intracellular versions like ASRT probably participate as sensors that regulate a diverse range of sugar metabolism operons or even the light sensory behavior in Anabaena by binding sugars or related metabolites. We also show that one of the extracellular versions define a predicted sugar-binding structure in a novel cell-surface lipoprotein found across actinobacteria, including several pathogens such as Tropheryma, Actinomyces and Thermobifida. The analysis of this superfamily also provides new data to investigate the evolution of carbohydrate binding modes in β-sandwich domains with very different topologies. Reviewers: This article was reviewed by M. Madan Babu and Mark A. Ragan.
Energy Technology Data Exchange (ETDEWEB)
Yu, Shanshan; Li, Han; Gao, Feng; Zhou, Ying, E-mail: zhouying@moon.ibp.ac.cn
2015-08-07
Thioesterase superfamily member 2 (THEM2) is an essential protein for mammalian cell proliferation. It belongs to the hotdog-fold thioesterase superfamily and catalyzes hydrolysis of thioester bonds of acyl-CoA in vitro, while its in vivo function remains unrevealed. In this study, Zebra fish was selected as a model organism to facilitate the investigations on THEM2. First, we solved the crystal structure of recombinant fTHEM2 at the resolution of 1.80 Å, which displayed a similar scaffolding as hTHEM2. Second, functional studies demonstrated that fTHEM2 is capable of hydrolyzing palmitoyl-CoA in vitro. In addition, injection of morpholino against fTHEM2 at one-cell stage resulted in distorted early embryo development, including delayed cell division, retarded development and increased death rate. The above findings validated our hypothesis that fTHEM2 could serve as an ideal surrogate for studying the physiological functions of THEM2. - Highlights: • The crystal structure of recombinant fTHEM2 is presented. • fTHEM2 is capable of hydrolyzing palmitoyl-CoA. • The influence of fTHEM2 on early embryo development is demonstrated.
Liang, Pei; He, Lei; Xu, Yanquan; Chen, Xueqing; Huang, Yan; Ren, Mengyu; Liang, Chi; Li, Xuerong; Xu, Jin; Lu, Gang; Yu, Xinbing
2014-10-01
Cathepsin C is an important exopeptidase of papain superfamily and plays a number of great important roles during the parasitic life cycle. The amino acid sequence of cathepsin C from Clonorchis sinensis (C. sinensis) showed 54, 53, and 49% identities to that of Schistosoma japonicum, Schistosoma mansoni, and Homo sapiens, respectively. Phylogenetic analysis utilizing the sequences of papain superfamily of C. sinensis demonstrated that cathepsin C and cathepsin Bs came from a common ancestry. Cathepsin C of C. sinensis (Cscathepsin C) was identified as an excretory/secretory product by Western blot analysis. The results of transcriptional level and translational level of Cscathepsin C at metacercaria stage were higher than that at adult worms. Immunolocalization analysis indicated that Cscathepsin C was specifically distributed in the suckers (oral sucker and ventral sucker), eggs, vitellarium, intestines, and testis of adult worms. In the metacercaria, it was mainly detected on the cyst wall and excretory bladder. Combining with the results mentioned above, it implies that Cscathepsin C may be an essential proteolytic enzyme for proteins digestion of hosts, nutrition assimilation, and immune invasion of C. sinensis. Furthermore, it may be a potential diagnostic antigen and drug target against C. sinensis infection.
Schnabel, K E; Ahyong, S T; Maas, E W
2011-02-01
The monophyletic status of the squat lobster superfamily Galatheoidea has come under increasing doubt by studies using evidence as diverse as larval and adult somatic morphology, sperm ultrastructure, and molecular data. Here we synthesize phylogenetic data from these diverse strands, with the addition of new molecular and morphological data to examine the phylogeny of the squat lobsters and assess the status of the Galatheoidea. A total of 64 species from 16 of the 17 currently recognised anomuran families are included. Results support previous work pointing towards polyphyly in the superfamily Galatheoidea and Paguroidea, specifically, suggesting independent origins of the Galatheidae+Porcellanidae and the Chirostylidae+Kiwaidae. Morphological characters are selected that support clades resolved in the combined analysis and the taxonomic status of Galatheoidea sensu lato is revised. Results indicate that Chirostylidae are more closely related to an assemblage including Aegloidea, Lomisoidea and Paguroidea than to the remaining Galatheoidea and are referred to the superfamily Chirostyloidea to include the Chirostylidae and Kiwaidae. A considerable amount of research highlighting morphological differences supporting this split is discussed. The Galatheoidea sensu stricto is restricted to the families Galatheidae and Porcellanidae, and diagnoses for both Chirostyloidea and Galatheoidea are provided. Present results highlight the need for a detailed revision of a number of taxa, challenge some currently used morphological synapomorphies, and emphasise the need for integrated studies with wide taxon sampling and multiple data sources to resolve complex phylogenetic questions. Copyright © 2010 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
Masaki Takatsuka
Full Text Available Iron is an essential metal for living organisms but its level must be strictly controlled in cells, because ferrous ion induces toxicity by generating highly active reactive oxygen, hydroxyl radicals, through the Fenton reaction. In addition, ferric ion shows low solubility under physiological conditions. To overcome these obstacles living organisms possess Ferritin superfamily proteins that are distributed in all three domains of life: bacteria, archaea, and eukaryotes. These proteins minimize hydroxyl radical formation by ferroxidase activity that converts Fe(2+ into Fe(3+ and sequesters iron by storing it as a mineral inside a protein cage. In this study, we discovered that mycobacterial DNA-binding protein 1 (MDP1, a histone-like protein, has similar activity to ferritin superfamily proteins. MDP1 prevented the Fenton reaction and protects DNA by the ferroxidase activity. The K(m values of the ferroxidase activity by MDP1 of Mycobacterium bovis bacillus Calmette-Guérin (BCG-3007c, Mycobacterium tuberculosis (Rv2986c, and Mycobacterium leprae (ML1683; ML-LBP were 0.292, 0.252, and 0.129 mM, respectively. Furthermore, one MDP1 molecule directly captured 81.4±19.1 iron atoms, suggesting the role of this protein in iron storage. This study describes for the first time a ferroxidase-iron storage protein outside of the ferritin superfamily proteins and the protective role of this bacterial protein from DNA damage.
Feng, Jin-Shan; Tan, Lei; Gu, Huai-Qiang; Liu, Wu-Ming
2017-12-01
We theoretically analyze the ground-state cooling of an optically levitated nanosphere in the unresolved-sideband regime by introducing a coupled high-quality-factor cavity. On account of the quantum interference stemming from the presence of the coupled cavity, the spectral density of the optical force exerting on the nanosphere gets changed and then the symmetry between the heating and the cooling processes is broken. Through adjusting the detuning of a strong-dissipative cavity mode, one obtains an enhanced net cooling rate for the nanosphere. It is illustrated that the ground-state cooling can be realized in the unresolved sideband regime even if the effective optomechanical coupling is weaker than the frequency of the nanosphere, which can be understood by the picture that the effective interplay of the nanosphere and the auxiliary cavity mode brings the system back to an effective resolved regime. Besides, the coupled cavity refines the dynamical stability of the system.
Perera, Varahenage R.; Lapek, John D.; Newton, Gerald L.; Gonzalez, David J.; Pogliano, Kit
2018-01-01
Bacillithiol is a low molecular weight thiol found in Firmicutes that is analogous to glutathione, which is absent in these bacteria. Bacillithiol transferases catalyze the transfer of bacillithiol to various substrates. The S-transferase-like (STL) superfamily contains over 30,000 putative members, including bacillithiol transferases. Proteins in this family are extremely divergent and are related by structural rather than sequence similarity, leaving it unclear if all share the same biochemical activity. Bacillus subtilis encodes eight predicted STL superfamily members, only one of which has been shown to be a bacillithiol transferase. Here we find that the seven remaining proteins show varying levels of metal dependent bacillithiol transferase activity. We have renamed the eight enzymes BstA-H. Mass spectrometry and gene expression studies revealed that all of the enzymes are produced to varying levels during growth and sporulation, with BstB and BstE being the most abundant and BstF and BstH being the least abundant. Interestingly, several bacillithiol transferases are induced in the mother cell during sporulation. A strain lacking all eight bacillithiol transferases showed normal growth in the presence of stressors that adversely affect growth of bacillithiol-deficient strains, such as paraquat and CdCl2. Thus, the STL bacillithiol transferases represent a new group of proteins that play currently unknown, but potentially significant roles in bacillithiol-dependent reactions. We conclude that these enzymes are highly divergent, perhaps to cope with an equally diverse array of endogenous or exogenous toxic metabolites and oxidants. PMID:29451913
Directory of Open Access Journals (Sweden)
Shi-Min Yuan
2018-04-01
Full Text Available Pulmonary artery hypertension (PAH is very rare in childhood, and it can be divided into heritable, idiopathic drug- and toxin-induced and other disease (connective tissue disease, human immunodeficiency virus infection, portal hypertension, congenital heart disease, or schistosomiasis-associated types. PAH could not be interpreted solely by pathophysiological theories. The impact of the transforming growth factor-β superfamily-related genes on the development of PAH in children remains to be clarified. Pertinent literature on the transforming growth factor-β superfamily-related genes in relation to PAH in children published after the year 2000 was reviewed and analyzed. Bone morphogenetic protein receptor type II gene mutation promotes cell division or prevents cell death, resulting in an overgrowth of cells in small arteries throughout the lungs. About 20% of individuals with a bone morphogenetic protein receptor type II gene mutation develop symptomatic PAH. In heritable PAH, bone morphogenetic protein receptor type II mutations may be absent; while mutations of other genes, such as type I receptor activin receptor-like kinase 1 and the type III receptor endoglin (both associated with hereditary hemorrhagic telangiectasia, caveolin-1 and KCNK3, the gene encoding potassium channel subfamily K, member 3, can be detected, instead. Gene mutations, environmental changes and acquired adjustment, etc. may explain the development of PAH. The researches on PAH rat model and familial PAH members may facilitate the elucidations of the mechanisms and further provide theories for prophylaxis and treatment of PAH. Key Words: bone morphogenetic proteins, mutation, pulmonary hypertension
International Nuclear Information System (INIS)
Koshcheev, V.N.; Manturov, G.N.; Sinitsa, V.V.
1991-01-01
The effects of the neutron strength function uncertainties on the calculated values of the self-shielding factors and energy dependence of the total and capture 238 U cross-sections in the unresolved resonance region are investigated. (author). 26 refs, 5 figs
Report on the Workshop Resolved and Unresolved Stellar PopUlaTIoNs (RASPUTIN)
Bono, G.; Valenti, E.
2014-12-01
The workshop aimed at sharing and discussing observations and diagnostics, together with models and simulations, of the resolved and unresolved stellar populations in galaxies from the Milky Way to the distant Universe. Special attention was paid to recent results concerning galaxy formation and evolution, fostering the exchange of ideas and techniques in dealing with nearby stellar populations. There will be no published proceedings, but presentations are available for download from the workshop web page (www.eso.org/sci/meetings/2014/rasputin2014).
Fetal antigen 1 (FA1), a circulating member of the epidermal growth factor (EGF) superfamily
DEFF Research Database (Denmark)
Jensen, Charlotte Harken; Krogh, T N; Støving, René Klinkby
1997-01-01
We describe an ELISA technique for quantification of fetal antigen 1 (FA1), a glycoprotein belonging to the EGF-superfamily. The ELISA is based on immunospecifically purified polyclonal antibodies and has a dynamic range of 0.7-5.3 ng/ml, intra- and inter-assay C.V.s of less than 3.2% and an aver......We describe an ELISA technique for quantification of fetal antigen 1 (FA1), a glycoprotein belonging to the EGF-superfamily. The ELISA is based on immunospecifically purified polyclonal antibodies and has a dynamic range of 0.7-5.3 ng/ml, intra- and inter-assay C.V.s of less than 3.......2% and an average recovery of 105% in serum and 98% in urine. Comparison of FA1 in amniotic fluid, serum and urine revealed parallel titration curves, identical elution volumes following size chromatography, immunological identity and similar profiles when analysed by MALDI-MS. The reference interval for serum FA1...... was 12.3-46.6 ng/ml and the levels were 10 times higher in patients with renal failure. FA1 showed no diurnal variation, no variation during the menstrual cycle and was not influenced by the acute phase reaction. In humans (n = 10) the renal clearance of FA1 was 11 ml/min and an identical high renal...
van Bruggen, A H; Jochimsen, K N; Steinberger, E M; Segers, P; Gillis, M
1993-01-01
Thermal melting profiles of hybrids between 3H-labeled rRNA of Rhizomonas suberifaciens, the causal agent of corky root of lettuce, and chromosomal DNAs from 27 species of gram-negative bacteria indicated that the genus Rhizomonas belongs to superfamily IV of De Ley. On the basis of the melting temperatures of DNA hybrids with rRNAs from the type strains of R. suberifaciens, Sphingomonas paucimobilis, and Sphingomonas capsulata, Rhizomonas strains constitute a separate branch in superfamily IV, which is closely related to but separate from branches containing Zymomonas mobilis, Sphingomonas spp., and S. capsulata. Sphingomonas yanoikuyae and Rhizomonas sp. strain WI4 are located toward the base of the Rhizomonas rRNA branch. DNA-DNA hybridization indicated that S. yanoikuyae is equidistant from Rhizomonas sp. strain WI4 and S. paucimobilis. Sequences of 270 bp of 16S ribosomal DNAs from eight strains of Rhizomonas spp., eight strains of Sphingomonas spp., and Agrobacterium tumefaciens indicated that S. yanoikuyae and Rhizomonas sp. strains WI4 and CA16 are genetically more closely related to R. suberifaciens than to Sphingomonas spp. Thus, S. yanoikuyae may need to be transferred to the genus Rhizomonas on the basis of the results of further study.
Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics
Hirokawa, N.; Takemura, R.
Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.
Cell Adhesion Molecules of the Immunoglobulin Superfamily in the Nervous System
DEFF Research Database (Denmark)
Walmod, Peter Schledermann; Pedersen, Martin Volmer; Berezin, Vladimir
2007-01-01
Cell adhesion molecules (CAMs) are proteins mediating cell-cell or cell-extracellular matrix (ECM) interactions. CAMs are traditionally divided into four groups, the cadherins, the selectins, the integrins and CAMs belonging to the immunoglobulin superfamily (IgSF). The present chapter describes...... CAMs belonging to IgSF, that exclusively or in part, are expressed in the nervous system. The chapter includes descriptions of myelin protein zero (P0), integrin-associated protein (CD47), neuroplastin, activated leukocyte-cell adhesion molecule (ALCAM), melanoma cell adhesion molecule (MCAM......), myelinassociated glycoprotein (MAG), the neural cell adhesion molecules 1 and 2 (NCAM, NCAM2), Down Syndrome cell adhesion molecule (DSCAM) and Down Syndrome cell adhesion molecule-like-1 (DSCAML1), sidekick 1 and 2 (SDK1, SDK2), signal-regulatory proteins (SIRPs), nectins, nectin-like proteins (necls...
Astrophysical interpretation of the anisotropies in the unresolved gamma-ray background
Ando, Shin'ichiro; Fornasa, Mattia; Fornengo, Nicolao; Regis, Marco; Zechlin, Hannes-S.
2017-06-01
Recently, a new measurement of the auto- and cross-correlation angular power spectrum (APS) of the isotropic gamma-ray background was performed, based on 81 months of data of the Fermi Large-Area Telescope (LAT). Here, we fit, for the first time, the new APS data with a model describing the emission of unresolved blazars. These sources are expected to dominate the anisotropy signal. The model we employ in our analysis reproduces well the blazars resolved by Fermi LAT. When considering the APS obtained by masking the sources listed in the 3FGL catalog, we find that unresolved blazars underproduce the measured APS below ˜1 GeV . Contrary to past results, this suggests the presence of a new contribution to the low-energy APS, with a significance of, at least, 5 σ . The excess can be ascribed to a new class of faint gamma-ray emitters. If we consider the APS obtained by masking the sources in the 2FGL catalog, there is no underproduction of the APS below 1 GeV, but the new source class is still preferred over the blazars-only scenario (with a significance larger than 10 σ ). The properties of the new source class and the level of anisotropies induced in the isotropic gamma-ray background are the same, independent of the APS data used. In particular, the new gamma-ray emitters must have a soft energy spectrum, with a spectral index ranging, approximately, from 2.7 to 3.2. This complicates their interpretation in terms of known sources, since, normally, star-forming and radio galaxies are observed with a harder spectrum. The new source class identified here is also expected to contribute significantly to the intensity of the isotropic gamma-ray background.
Central unresolved issues in thermal energy storage for building heating and cooling
Energy Technology Data Exchange (ETDEWEB)
Swet, C.J.; Baylin, F.
1980-07-01
This document explores the frontier of the rapidly expanding field of thermal energy storage, investigates unresolved issues, outlines research aimed at finding solutions, and suggests avenues meriting future research. Issues related to applications include value-based ranking of storage concepts, temperature constraints, consistency of assumptions, nomenclature and taxonomy, and screening criteria for materials. Issues related to technologies include assessing seasonal storage concepts, diurnal coolness storage, selection of hot-side storage concepts for cooling-only systems, phase-change storage in building materials, freeze protection for solar water heating systems, and justification of phase-change storage for active solar space heating.
Energy Technology Data Exchange (ETDEWEB)
Hincks, Adam D.; Hajian, Amir [Canadian Institute for Theoretical Astrophysics, University of Toronto, Toronto, ON M5S 3H8 (Canada); Addison, Graeme E., E-mail: hincks@cita.utoronto.ca, E-mail: ahajian@cita.utoronto.ca, E-mail: gaddison@phas.ubc.ca [Department of Physics and Astronomy, University of British Columbia, Vancouver, BC V6T 1Z4 (Canada)
2013-05-01
We cross-correlate the 100 μm Improved Reprocessing of the IRAS Survey (IRIS) map and galaxy clusters at 0.1 < z < 0.3 in the maxBCG catalogue taken from the Sloan Digital Sky Survey, measuring an angular cross-power spectrum over multipole moments 150 < l < 3000 at a total significance of over 40σ. The cross-spectrum, which arises from the spatial correlation between unresolved dusty galaxies that make up the cosmic infrared background (CIB) in the IRIS map and the galaxy clusters, is well-fit by a single power law with an index of −1.28±0.12, similar to the clustering of unresolved galaxies from cross-correlating far-infrared and submillimetre maps at longer wavelengths. Using a recent, phenomenological model for the spectral and clustering properties of the IRIS galaxies, we constrain the large-scale bias of the maxBCG clusters to be 2.6±1.4, consistent with existing analyses of the real-space cluster correlation function. The success of our method suggests that future CIB-optical cross-correlations using Planck and Herschel data will significantly improve our understanding of the clustering and redshift distribution of the faint CIB sources.
International Nuclear Information System (INIS)
Akana, J.; Federov, A.; Federov, E.; Novak, W.; Babbitt, P.; Almo, S.; Gerlt, J.
2006-01-01
The 'ribulose phosphate binding' superfamily defined by the Structural Classification of Proteins (SCOP) database is considered the result of divergent evolution from a common (β/α) 8 -barrel ancestor. The superfamily includes D-ribulose 5-phosphate 3-epimerase (RPE), orotidine 5'-monophosphate decarboxylase (OMPDC), and 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC), members of the OMPDC suprafamily, as well as enzymes involved in histidine and tryptophan biosynthesis that utilize phosphorylated metabolites as substrates. We now report studies of the functional and structural relationships of RPE to the members of the superfamily. As suggested by the results of crystallographic studies of the RPEs from rice and Plasmodium falciparum, the RPE from Streptococcus pyogenes is activated by Zn 2+ which binds with a stoichiometry of one ion per polypeptide. Although wild type RPE has a high affinity for Zn 2+ and inactive apoenzyme cannot be prepared, the affinity for Zn 2+ is decreased by alanine substitutions for the two histidine residues that coordinate the Zn 2+ ion (H34A and H67A); these mutant proteins can be prepared in an inactive, metal-free form and activated by exogenous Zn 2+ . The crystal structure of the RPE was solved at 1.8 Angstroms resolution in the presence of D-xylitol 5-phosphate, an inert analogue of the D-xylulose 5-phosphate substrate. This structure suggests that the 2,3-enediolate intermediate in the 1,1-proton transfer reaction is stabilized by bidentate coordination to the Zn 2+ that also is liganded to His 34, Asp 36, His 67, and Asp 176; the carboxylate groups of the Asp residues are positioned also to function as the acid/base catalysts. Although the conformation of the bound analogue resembles those of ligands bound in the active sites of OMPDC and KGPDC, the identities of the active site residues that coordinate the essential Zn 2+ and participate as acid/base catalysts are not conserved. We conclude that only the phosphate
Energy Technology Data Exchange (ETDEWEB)
Akana,J.; Federov, A.; Federov, E.; Novak, W.; Babbitt, P.; Almo, S.; Gerlt, J.
2006-01-01
The 'ribulose phosphate binding' superfamily defined by the Structural Classification of Proteins (SCOP) database is considered the result of divergent evolution from a common ({beta}/{alpha}){sub 8}-barrel ancestor. The superfamily includes D-ribulose 5-phosphate 3-epimerase (RPE), orotidine 5'-monophosphate decarboxylase (OMPDC), and 3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC), members of the OMPDC suprafamily, as well as enzymes involved in histidine and tryptophan biosynthesis that utilize phosphorylated metabolites as substrates. We now report studies of the functional and structural relationships of RPE to the members of the superfamily. As suggested by the results of crystallographic studies of the RPEs from rice and Plasmodium falciparum, the RPE from Streptococcus pyogenes is activated by Zn{sup 2+} which binds with a stoichiometry of one ion per polypeptide. Although wild type RPE has a high affinity for Zn{sup 2+} and inactive apoenzyme cannot be prepared, the affinity for Zn{sup 2+} is decreased by alanine substitutions for the two histidine residues that coordinate the Zn{sup 2+} ion (H34A and H67A); these mutant proteins can be prepared in an inactive, metal-free form and activated by exogenous Zn{sup 2+}. The crystal structure of the RPE was solved at 1.8 Angstroms resolution in the presence of D-xylitol 5-phosphate, an inert analogue of the D-xylulose 5-phosphate substrate. This structure suggests that the 2,3-enediolate intermediate in the 1,1-proton transfer reaction is stabilized by bidentate coordination to the Zn{sup 2+} that also is liganded to His 34, Asp 36, His 67, and Asp 176; the carboxylate groups of the Asp residues are positioned also to function as the acid/base catalysts. Although the conformation of the bound analogue resembles those of ligands bound in the active sites of OMPDC and KGPDC, the identities of the active site residues that coordinate the essential Zn{sup 2+} and participate as acid/base catalysts
Molecular cloning of a peroxisomal Ca2+-dependent member of the mitochondrial carrier superfamily
Weber, Franz E.; Minestrini, Gianluca; Dyer, James H.; Werder, Moritz; Boffelli, Dario; Compassi, Sabina; Wehrli, Ernst; Thomas, Richard M.; Schulthess, Georg; Hauser, Helmut
1997-01-01
A cDNA from a novel Ca2+-dependent member of the mitochondrial solute carrier superfamily was isolated from a rabbit small intestinal cDNA library. The full-length cDNA clone was 3,298 nt long and coded for a protein of 475 amino acids, with four elongation factor-hand motifs located in the N-terminal half of the molecule. The 25-kDa N-terminal polypeptide was expressed in Escherichia coli, and it was demonstrated that it bound Ca2+, undergoing a reversible and specific conformational change as a result. The conformation of the polypeptide was sensitive to Ca2+ which was bound with high affinity (Kd ≈ 0.37 μM), the apparent Hill coefficient for Ca2+-induced changes being about 2.0. The deduced amino acid sequence of the C-terminal half of the molecule revealed 78% homology to Grave disease carrier protein and 67% homology to human ADP/ATP translocase; this sequence homology identified the protein as a new member of the mitochondrial transporter superfamily. Northern blot analysis revealed the presence of a single transcript of about 3,500 bases, and low expression of the transporter could be detected in the kidney but none in the liver. The main site of expression was the colon with smaller amounts found in the small intestine proximal to the ileum. Immunoelectron microscopy localized the transporter in the peroxisome, although a minor fraction was found in the mitochondria. The Ca2+ binding N-terminal half of the transporter faces the cytosol. PMID:9238007
Alva, Vikram; Lupas, Andrei N
2016-08-01
The tubular lipid-binding (TULIP) superfamily has emerged in recent years as a major mediator of lipid sensing and transport in eukaryotes. It currently encompasses three protein families, SMP-like, BPI-like, and Takeout-like, which share a common fold. This fold consists of a long helix wrapped in a highly curved anti-parallel β-sheet, enclosing a central, lipophilic cavity. The SMP-like proteins, which include subunits of the ERMES complex and the extended synaptotagmins (E-Syts), appear to be mainly located at membrane contacts sites (MCSs) between organelles, mediating inter-organelle lipid exchange. The BPI-like proteins, which include the bactericidal/permeability-increasing protein (BPI), the LPS (lipopolysaccharide)-binding protein (LBP), the cholesteryl ester transfer protein (CETP), and the phospholipid transfer protein (PLTP), are either involved in innate immunity against bacteria through their ability to sense lipopolysaccharides, as is the case for BPI and LBP, or in lipid exchange between lipoprotein particles, as is the case for CETP and PLTP. The Takeout-like proteins, which are comprised of insect juvenile hormone-binding proteins and arthropod allergens, transport, where known, lipid hormones to target tissues during insect development. In all cases, the activity of these proteins is underpinned by their ability to bind large, hydrophobic ligands in their central cavity and segregate them away from the aqueous environment. Furthermore, where they are involved in lipid exchange, recent structural studies have highlighted their ability to establish lipophilic, tubular channels, either between organelles in the case of SMP domains or between lipoprotein particles in the case of CETP. Here, we review the current knowledge on the structure, versatile functions, and evolution of the TULIP superfamily. We propose a deep evolutionary split in this superfamily, predating the Last Eukaryotic Common Ancestor, between the SMP-like proteins, which act on
Containment-emergency-sump performance. Technical findings related to Unresolved Safety Issue A-43
International Nuclear Information System (INIS)
1983-04-01
This report summarizes key technical findings related to the Unresolved Safety Issue A-43, Containment Emergency Sump Performance, and provides recommendations for resolution of attendant safety issues. The key safety questions relate to: (a) effects of insulation debris on sump performance; (b) sump hydraulic performance as determined by design features, submergence, and plant induced effects, and (c) recirculation pump performance wherein air and/or particulate ingestion can occur. The technical findings presented in this report provide information relevant to the design and performance evaluation of the containment emergency sump
Lukk, Tiit; Sakai, Ayano; Kalyanaraman, Chakrapani; Brown, Shoshana D.; Imker, Heidi J.; Song, Ling; Fedorov, Alexander A.; Fedorov, Elena V.; Toro, Rafael; Hillerich, Brandan; Seidel, Ronald; Patskovsky, Yury; Vetting, Matthew W.; Nair, Satish K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.
2012-01-01
The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. PMID:22392983
International Nuclear Information System (INIS)
Vold, Erik L.; Scannapieco, Tony J.
2007-01-01
A sub-grid mix model based on a volume-of-fluids (VOF) representation is described for computational simulations of the transient mixing between reactive fluids, in which the atomically mixed components enter into the reactivity. The multi-fluid model allows each fluid species to have independent values for density, energy, pressure and temperature, as well as independent velocities and volume fractions. Fluid volume fractions are further divided into mix components to represent their 'mixedness' for more accurate prediction of reactivity. Time dependent conversion from unmixed volume fractions (denoted cf) to atomically mixed (af) fluids by diffusive processes is represented in resolved scale simulations with the volume fractions (cf, af mix). In unresolved scale simulations, the transition to atomically mixed materials begins with a conversion from unmixed material to a sub-grid volume fraction (pf). This fraction represents the unresolved small scales in the fluids, heterogeneously mixed by turbulent or multi-phase mixing processes, and this fraction then proceeds in a second step to the atomically mixed fraction by diffusion (cf, pf, af mix). Species velocities are evaluated with a species drift flux, ρ i u di = ρ i (u i -u), used to describe the fluid mixing sources in several closure options. A simple example of mixing fluids during 'interfacial deceleration mixing with a small amount of diffusion illustrates the generation of atomically mixed fluids in two cases, for resolved scale simulations and for unresolved scale simulations. Application to reactive mixing, including Inertial Confinement Fusion (ICF), is planned for future work.
Unresolved resonance self shielding calculation: causes and importance of discrepancies
International Nuclear Information System (INIS)
Ribon, P.; Tellier, H.
1986-01-01
To compute the self shielding coefficient, it is necessary to know the point-wise cross-sections. In the unresolved resonance region, the parameters of each level are not known; only the average parameters. Therefore the authors simulate the point-wise cross-section by random sampling of the energy levels and resonance parameters with respect to the Wigner law and the x 2 distributions, and by computing the cross-section in the same way as in the resolved regions. The result of this statistical calculation obviously depends on the initial parameters but also on the method of sampling, on the formalism which is used to compute the cross-section or on the weighting neutron flux. In this paper, the authors survey the main phenomena which can induce discrepancies in self shielding computations. Results are given for typical dilutions which occur in nuclear reactors
Li, Yubin; Harris, Linda; Dooner, Hugo K
2013-09-01
Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor.
Sugrue, Elena; Fraser, Nicholas J.; Hopkins, Davis H.; Carr, Paul D.; Khurana, Jeevan L.; Oakeshott, John G.; Scott, Colin
2015-01-01
The amidohydrolase superfamily has remarkable functional diversity, with considerable structural and functional annotation of known sequences. In microbes, the recent evolution of several members of this family to catalyze the breakdown of environmental xenobiotics is not well understood. An evolutionary transition from binuclear to mononuclear metal ion coordination at the active sites of these enzymes could produce large functional changes such as those observed in nature, but there are few clear examples available to support this hypothesis. To investigate the role of binuclear-mononuclear active-site transitions in the evolution of new function in this superfamily, we have characterized two recently evolved enzymes that catalyze the hydrolysis of the synthetic herbicides molinate (MolA) and phenylurea (PuhB). In this work, the crystal structures, mutagenesis, metal ion analysis, and enzyme kinetics of both MolA and PuhB establish that these enzymes utilize a mononuclear active site. However, bioinformatics and structural comparisons reveal that the closest putative ancestor of these enzymes had a binuclear active site, indicating that a binuclear-mononuclear transition has occurred. These proteins may represent examples of evolution modifying the characteristics of existing catalysts to satisfy new requirements, specifically, metal ion rearrangement leading to large leaps in activity that would not otherwise be possible. PMID:25636851
Unresolved tensions in consumer engagement in CER: a US research perspective.
Workman, Thomas; Maurer, Maureen; Carman, Kristin
2013-03-01
Efforts to engage patients and consumers in comparative effectiveness research (CER) in the USA are still in the early stages, and the outcomes of these partnerships have yet to be fully understood or realized. Our work assisting federal agencies and national organizations who engage patients and consumers in CER reveal three unresolved tensions around the representation of the patient experience in the research process, the culture of research and capacity to partner with patients and consumers, and the conflict between the methodological approaches to CER and the outcomes of interest to patients and caregivers. Several approaches to address these tensions have emerged, yet resolving these tensions will require addressing many system-level challenges and building an evidence base for consumer engagement in CER.
International Nuclear Information System (INIS)
Anaf, J.; Chalhoub, E.S.
1990-01-01
The procedures for calculating contributions of resolved and unresolved resonances and background cross sections, in XLACS code, were revised. Constant weighting function and zero Kelvin temperature were considered. Discrepancies found were corrected and now the validated XLACS code generates results that are correct and in accordance with its originally established procedures. (author)
Meng, Elaine C; Babbitt, Patricia C
2011-06-01
In functionally diverse enzyme superfamilies (SFs), conserved structural and active site features reflect catalytic capabilities 'hard-wired' in each SF architecture. Overlaid on this foundation, evolutionary changes in active site machinery, structural topology and other aspects of structural organization and interactions support the emergence of new reactions, mechanisms, and substrate specificity. This review connects topological with functional variation in each of the haloalkanoic acid dehalogenase (HAD) and vicinal oxygen chelate fold (VOC) SFs and a set of redox-active thioredoxin (Trx)-fold SFs to illustrate a few of the varied themes nature has used to evolve new functions from a limited set of structural scaffolds. Copyright © 2011 Elsevier Ltd. All rights reserved.
Ma, Dongying; Francischetti, Ivo M B; Ribeiro, Jose M C; Andersen, John F
2015-06-01
Secreted protein components of hookworm species include a number of representatives of the cysteine-rich/antigen 5/pathogenesis-related 1 (CAP) protein family known as Ancylostoma-secreted proteins (ASPs). Some of these have been considered as candidate antigens for the development of vaccines against hookworms. The functions of most CAP superfamily members are poorly understood, but one form, the hookworm platelet inhibitor (HPI), has been isolated as a putative antagonist of the platelet integrins αIIbβ3 and α2β1. Here, the crystal structure of HPI is described and its structural features are examined in relation to its possible function. The HPI structure is similar to those of other ASPs and shows incomplete conservation of the sequence motifs CAP1 and CAP2 that are considered to be diagnostic of CAP superfamily members. The asymmetric unit of the HPI crystal contains a dimer with an extensive interaction interface, but chromatographic measurements indicate that it is primarily monomeric in solution. In the dimeric structure, the putative active-site cleft areas from both monomers are united into a single negatively charged depression. A potential Lys-Gly-Asp disintegrin-like motif was identified in the sequence of HPI, but is not positioned at the apex of a tight turn, making it unlikely that it interacts with the integrin. Recombinant HPI produced in Escherichia coli was found not to inhibit the adhesion of human platelets to collagen or fibrinogen, despite having a native structure as shown by X-ray diffraction. This result corroborates previous analyses of recombinant HPI and suggests that it might require post-translational modification or have a different biological function.
Unresolved resonance self shielding calculation: causes and importance of discrepancies
International Nuclear Information System (INIS)
Ribon, P.; Tellier, H.
1986-09-01
To compute the self shielding coefficient, it is necessary to know the point-wise cross-sections. In the unresolved resonance region, we do not know the parameters of each level but only the average parameters. Therefore we simulate the point-wise cross-section by random sampling of the energy levels and resonance parameters with respect to the Wigner law and the X 2 distributions, and by computing the cross-section in the same way as in the resolved regions. The result of this statistical calculation obviously depends on the initial parameters but also on the method of sampling, on the formalism which is used to compute the cross-section or on the weighting neutron flux. In this paper, we will survey the main phenomena which can induce discrepancies in self shielding computations. Results are given for typical dilutions which occur in nuclear reactors. 8 refs
Rakus, John F.; Kalyanaraman, Chakrapani; Fedorov, Alexander A.; Fedorov, Elena V.; Mills-Groninger, Fiona P.; Toro, Rafael; Bonanno, Jeffrey; Bain, Kevin; Sauder, J. Michael; Burley, Stephen K.; Almo, Steven C.; Jacobson, Matthew P.; Gerlt, John A.
2009-01-01
The structure of an uncharacterized member of the enolase superfamily from Oceanobacillus iheyensis (GI: 23100298; IMG locus tag Ob2843; PDB Code 2OQY) was determined by the New York SGX Research Center for Structural Genomics (NYSGXRC). The structure contained two Mg2+ ions located 10.4 Å from one another, with one located in the canonical position in the (β/α)7β-barrel domain (although the ligand at the end of the fifth β-strand is His, unprecedented in structurally characterized members of the superfamily); the second is located in a novel site within the capping domain. In silico docking of a library of mono- and diacid sugars to the active site predicted a diacid sugar as a likely substrate. Activity screening of a physical library of acid sugars identified galactarate as the substrate (kcat = 6.8 s−1, KM = 620 μM; kcat/KM = 1.1 × 104 M−1 s−1), allowing functional assignment of Ob2843 as galactarate dehydratase (GalrD-II) The structure of a complex of the catalytically impaired Y90F mutant with Mg2+ and galactarate allowed identification of a Tyr 164-Arg 162 dyad as the base that initiates the reaction by abstraction of the α-proton and Tyr 90 as the acid that facilitates departure of the β-OH leaving group. The enzyme product is 2-keto-3-deoxy-D-threo-4,5-dihydroxyadipate, the enantiomer of the product obtained in the GalrD reaction catalyzed by a previously characterized bifunctional L-talarate/galactarate dehydratase (TalrD/GalrD). On the basis of the different active site structures and different regiochemistries, we recognize that these functions represent an example of apparent, not actual, convergent evolution of function. The structure of GalrD-II and its active site architecture allow identification of the seventh functionally and structurally characterized subgroup in the enolase superfamily. This study provides an additional example that an integrated sequence/structure-based strategy employing computational approaches is a viable
Barker, H. W.; Stephens, G. L.; Partain, P. T.; Bergman, J. W.; Bonnel, B.; Campana, K.; Clothiaux, E. E.; Clough, S.; Cusack, S.; Delamere, J.; Edwards, J.; Evans, K. F.; Fouquart, Y.; Freidenreich, S.; Galin, V.; Hou, Y.; Kato, S.; Li, J.; Mlawer, E.; Morcrette, J.-J.; O'Hirok, W.; Räisänen, P.; Ramaswamy, V.; Ritter, B.; Rozanov, E.; Schlesinger, M.; Shibata, K.; Sporyshev, P.; Sun, Z.; Wendisch, M.; Wood, N.; Yang, F.
2003-08-01
The primary purpose of this study is to assess the performance of 1D solar radiative transfer codes that are used currently both for research and in weather and climate models. Emphasis is on interpretation and handling of unresolved clouds. Answers are sought to the following questions: (i) How well do 1D solar codes interpret and handle columns of information pertaining to partly cloudy atmospheres? (ii) Regardless of the adequacy of their assumptions about unresolved clouds, do 1D solar codes perform as intended?One clear-sky and two plane-parallel, homogeneous (PPH) overcast cloud cases serve to elucidate 1D model differences due to varying treatments of gaseous transmittances, cloud optical properties, and basic radiative transfer. The remaining four cases involve 3D distributions of cloud water and water vapor as simulated by cloud-resolving models. Results for 25 1D codes, which included two line-by-line (LBL) models (clear and overcast only) and four 3D Monte Carlo (MC) photon transport algorithms, were submitted by 22 groups. Benchmark, domain-averaged irradiance profiles were computed by the MC codes. For the clear and overcast cases, all MC estimates of top-of-atmosphere albedo, atmospheric absorptance, and surface absorptance agree with one of the LBL codes to within ±2%. Most 1D codes underestimate atmospheric absorptance by typically 15-25 W m-2 at overhead sun for the standard tropical atmosphere regardless of clouds.Depending on assumptions about unresolved clouds, the 1D codes were partitioned into four genres: (i) horizontal variability, (ii) exact overlap of PPH clouds, (iii) maximum/random overlap of PPH clouds, and (iv) random overlap of PPH clouds. A single MC code was used to establish conditional benchmarks applicable to each genre, and all MC codes were used to establish the full 3D benchmarks. There is a tendency for 1D codes to cluster near their respective conditional benchmarks, though intragenre variances typically exceed those for
Directory of Open Access Journals (Sweden)
Ying Wang
Full Text Available Mutations in the immunoglobulin superfamily, member 1 gene (IGSF1/Igsf1 cause an X-linked form of central hypothyroidism. The canonical form of IGSF1 is a transmembrane glycoprotein with 12 immunoglobulin (Ig loops. The protein is co-translationally cleaved into two sub-domains. The carboxyl-terminal domain (CTD, which contains the last 7 Ig loops, is trafficked to the plasma membrane. Most pathogenic mutations in IGSF1 map to the portion of the gene encoding the CTD. IGSF1/Igsf1 encodes a variety of transcripts. A little studied, but abundant splice variant encodes a truncated form of the protein, predicted to contain the first 2 Ig loops of the full-length IGSF1. The protein (hereafter referred to as IGSF1 isoform 2 or IGSF1-2 is likely retained in most individuals with IGSF1 mutations. Here, we characterized basic biochemical properties of the protein as a foray into understanding its potential function. IGSF1-2, like the IGSF1-CTD, is a glycoprotein. In both mouse and rat, the protein is N-glycosylated at a single asparagine residue in the first Ig loop. Contrary to earlier predictions, neither the murine nor rat IGSF1-2 is secreted from heterologous or homologous cells. In addition, neither protein associates with the plasma membrane. Rather, IGSF1-2 appears to be retained in the endoplasmic reticulum. Whether the protein plays intracellular functions or is trafficked through the secretory pathway under certain physiologic or pathophysiologic conditions has yet to be determined.
Optical model calculation for the unresolved/resolved resonance region of Fe-56
Energy Technology Data Exchange (ETDEWEB)
Kawano, Toshihiko [Kyushu Univ., Fukuoka (Japan); Froehner, F.H.
1997-03-01
We have studied optical model fits to total neutron cross sections of structural materials using the accurate data base for {sup 56}Fe existing in the resolved and unresolved resonance region. Averages over resolved resonances were calculated with Lorentzian weighting in Reich-Moore (reduced R matrix) approximation. Starting from the best available optical potentials we found that adjustment of the real and imaginary well depths does not work satisfactorily with the conventional weak linear energy dependence of the well depths. If, however, the linear dependences are modified towards low energies, the average total cross sections can be fitted quite well, from the resolved resonance region up to 20 MeV and higher. (author)
Li, Yubin; Harris, Linda; Dooner, Hugo K.
2013-01-01
Mutator (Mu) elements, one of the most diverse superfamilies of DNA transposons, are found in all eukaryotic kingdoms, but are particularly numerous in plants. Most of the present knowledge on the transposition behavior of this superfamily comes from studies of the maize (Zea mays) Mu elements, whose transposition is mediated by the autonomous Mutator-Don Robertson (MuDR) element. Here, we describe the maize element TED (for Transposon Ellen Dempsey), an autonomous cousin that differs significantly from MuDR. Element excision and reinsertion appear to require both proteins encoded by MuDR, but only the single protein encoded by TED. Germinal excisions, rare with MuDR, are common with TED, but arise in one of the mitotic divisions of the gametophyte, rather than at meiosis. Instead, transposition-deficient elements arise at meiosis, suggesting that the double-strand breaks produced by element excision are repaired differently in mitosis and meiosis. Unlike MuDR, TED is a very low-copy transposon whose number and activity do not undergo dramatic changes upon inbreeding or outcrossing. Like MuDR, TED transposes mostly to unlinked sites and can form circular transposition products. Sequences closer to TED than to MuDR were detected only in the grasses, suggesting a rather recent evolutionary split from a common ancestor. PMID:24038653
Eom, Dae Seok; Inoue, Shinya; Patterson, Larissa B; Gordon, Tiffany N; Slingwine, Rebecca; Kondo, Shigeru; Watanabe, Masakatsu; Parichy, David M
2012-01-01
The zebrafish adult pigment pattern has emerged as a useful model for understanding the development and evolution of adult form as well as pattern-forming mechanisms more generally. In this species, a series of horizontal melanophore stripes arises during the larval-to-adult transformation, but the genetic and cellular bases for stripe formation remain largely unknown. Here, we show that the seurat mutant phenotype, consisting of an irregular spotted pattern, arises from lesions in the gene encoding Immunoglobulin superfamily member 11 (Igsf11). We find that Igsf11 is expressed by melanophores and their precursors, and we demonstrate by cell transplantation and genetic rescue that igsf11 functions autonomously to this lineage in promoting adult stripe development. Further analyses of cell behaviors in vitro, in vivo, and in explant cultures ex vivo demonstrate that Igsf11 mediates adhesive interactions and that mutants for igsf11 exhibit defects in both the migration and survival of melanophores and their precursors. These findings identify the first in vivo requirements for igsf11 as well as the first instance of an immunoglobulin superfamily member functioning in pigment cell development and patterning. Our results provide new insights into adult pigment pattern morphogenesis and how cellular interactions mediate pattern formation.
Directory of Open Access Journals (Sweden)
Dae Seok Eom
Full Text Available The zebrafish adult pigment pattern has emerged as a useful model for understanding the development and evolution of adult form as well as pattern-forming mechanisms more generally. In this species, a series of horizontal melanophore stripes arises during the larval-to-adult transformation, but the genetic and cellular bases for stripe formation remain largely unknown. Here, we show that the seurat mutant phenotype, consisting of an irregular spotted pattern, arises from lesions in the gene encoding Immunoglobulin superfamily member 11 (Igsf11. We find that Igsf11 is expressed by melanophores and their precursors, and we demonstrate by cell transplantation and genetic rescue that igsf11 functions autonomously to this lineage in promoting adult stripe development. Further analyses of cell behaviors in vitro, in vivo, and in explant cultures ex vivo demonstrate that Igsf11 mediates adhesive interactions and that mutants for igsf11 exhibit defects in both the migration and survival of melanophores and their precursors. These findings identify the first in vivo requirements for igsf11 as well as the first instance of an immunoglobulin superfamily member functioning in pigment cell development and patterning. Our results provide new insights into adult pigment pattern morphogenesis and how cellular interactions mediate pattern formation.
New method to analyze super-family events observed with emulsion chambers
International Nuclear Information System (INIS)
Amenomori, M.
1997-01-01
The authors have developed a clustering method to analyze family events observed with emulsion chambers at high mountains. The main purpose of this analysis is to estimate the main production height of individual events, angular spread of gamma-rays in each event and so on. These enable them to investigate hadronic interactions at energies over 10 16 eV inaccessible by the present high-energy accelerators. they examined their clustering method using Monte Carlo events, and found that for the family events whose production height is low (within 2-3 km above the observation point in air), their production heights and lateral spreads are well reproduced. They further applied their method to the super-family events (ΣE γ > 1000 TeV) observed with emulsion chambers at Mt. Kanbala (5500 m above sea-level). The results seem to suggest that particle production with large transverse momentum occurs with considerable frequency even in the fragmentation region in the energy region over 10 16 eV
Hwang, Dae-Sik; Lee, Bo-Young; Kim, Hui-Su; Lee, Min Chul; Kyung, Do-Hyun; Om, Ae-Son; Rhee, Jae-Sung; Lee, Jae-Seong
2014-11-18
Nuclear receptors (NRs) are a large superfamily of proteins defined by a DNA-binding domain (DBD) and a ligand-binding domain (LBD). They function as transcriptional regulators to control expression of genes involved in development, homeostasis, and metabolism. The number of NRs differs from species to species, because of gene duplications and/or lineage-specific gene losses during metazoan evolution. Many NRs in arthropods interact with the ecdysteroid hormone and are involved in ecdysone-mediated signaling in arthropods. The nuclear receptor superfamily complement has been reported in several arthropods, including crustaceans, but not in copepods. We identified the entire NR repertoire of the copepod Tigriopus japonicus, which is an important marine model species for ecotoxicology and environmental genomics. Using whole genome and transcriptome sequences, we identified a total of 31 nuclear receptors in the genome of T. japonicus. Nomenclature of the nuclear receptors was determined based on the sequence similarities of the DNA-binding domain (DBD) and ligand-binding domain (LBD). The 7 subfamilies of NRs separate into five major clades (subfamilies NR1, NR2, NR3, NR4, and NR5/6). Although the repertoire of NR members in, T. japonicus was similar to that reported for other arthropods, there was an expansion of the NR1 subfamily in Tigriopus japonicus. The twelve unique nuclear receptors identified in T. japonicus are members of NR1L. This expansion may be a unique lineage-specific feature of crustaceans. Interestingly, E78 and HR83, which are present in other arthropods, were absent from the genomes of T. japonicus and two congeneric copepod species (T. japonicus and Tigriopus californicus), suggesting copepod lineage-specific gene loss. We identified all NR receptors present in the copepod, T. japonicus. Knowledge of the copepod nuclear receptor repertoire will contribute to a better understanding of copepod- and crustacean-specific NR evolution.
Venters, Tonia M.
2011-01-01
We present new theoretical estimates of the contribution of unresolved star-forming galaxies to the extragalactic gamma-ray background (EGB) as measured by EGRET and the Fermi-LAT. We employ several methods for determining the star-forming galaxy contribution the the EGB, including a method positing a correlation between the gamma-ray luminosity of a galaxy and its rate of star formation as calculated from the total infrared luminosity, and a method that makes use of a model of the evolution of the galaxy gas mass with cosmic time. We find that depending on the model, unresolved star-forming galaxies could contribute significantly to the EGB as measured by the Fermi-LAT at energies between approx. 300 MeV and approx. few GeV. However, the overall spectrum of unresolved star-forming galaxies can explain neither the EGRET EGB spectrum at energies between 50 and 200 MeV nor the Fermi-LAT EGB spectrum at energies above approx. few GeV.
Energy Technology Data Exchange (ETDEWEB)
Nguyen,T.; Brown, S.; Fedorov, A.; Fedorov, E.; Babbitt, P.; Almo, S.; Raushel, F.
2008-01-01
The amidohydrolase superfamily is a functionally diverse set of enzymes that catalyzes predominantly hydrolysis reactions involving sugars, nucleic acids, amino acids, and organophosphate esters. One of the most divergent members of this superfamily, uronate isomerase from Escherichia coli, catalyzes the isomerization of d-glucuronate to d-fructuronate and d-galacturonate to d-tagaturonate and is the only uronate isomerase in this organism. A gene encoding a putative uronate isomerase in Bacillus halodurans (Bh0705) was identified based on sequence similarity to uronate isomerases from other organisms. Kinetic evidence indicates that Bh0705 is relatively specific for the isomerization of d-glucuronate to d-fructuronate, confirming this functional assignment. Despite a low sequence identity to all other characterized uronate isomerases, phylogenetic and network-based analysis suggests that a second gene in this organism, Bh0493, is also a uronate isomerase, although it is an outlier in the group, with <20% sequence identity to any other characterized uronate isomerase from another species. The elucidation of the X-ray structure at a resolution of 2.0 Angstroms confirms that Bh0493 is a member of the amidohydrolase superfamily with conserved residues common to other members of the uronate isomerase family. Functional characterization of this protein shows that unlike Bh0705, Bh0493 can utilize both d-glucuronate and d-galacturonate as substrates. In B. halodurans, Bh0705 is found in an operon for the metabolism of d-glucuronate, whereas Bh0493 is in an operon for the metabolism of d-galacturonate. These results provide the first identification of a uronate isomerase that operates in a pathway distinct from that for d-glucuronate. While most organisms that contain this pathway have only one gene for a uronate isomerase, sequence analysis and operon context show that five other organisms also appear to have two genes and one organism appears to have three genes for
DEFF Research Database (Denmark)
Nielsen, Malene Schjønning; Simonsen, Anja Hviid; Siersma, Volkert
2016-01-01
in diagnostically unresolved patients. METHODS: Data on 348 patients were retrospectively evaluated. All participants had a standardized diagnostic workup and follow-up in a memory clinic. RESULTS: Aβ42 levels and Aβ42/p-tau ratios were reduced and levels of t-tau and p-tau as well as the t-tau × p-tau/Aβ42 ratio...
International Nuclear Information System (INIS)
Van'kov, A.A.; Blokhin, A.I.; Manokhin, V.N.; Kravchenko, I.V.
1985-01-01
This paper analyses the reasons for the differences which exist between group-averaged evaluated cross-section data from different evaluated data files for U235, U238 and Pu239 in the unresolved resonance energy region. (author)
Progress Towards an LES Wall Model Including Unresolved Roughness
Craft, Kyle; Redman, Andrew; Aikens, Kurt
2015-11-01
Wall models used in large eddy simulations (LES) are often based on theories for hydraulically smooth walls. While this is reasonable for many applications, there are also many where the impact of surface roughness is important. A previously developed wall model has been used primarily for jet engine aeroacoustics. However, jet simulations have not accurately captured thick initial shear layers found in some experimental data. This may partly be due to nozzle wall roughness used in the experiments to promote turbulent boundary layers. As a result, the wall model is extended to include the effects of unresolved wall roughness through appropriate alterations to the log-law. The methodology is tested for incompressible flat plate boundary layers with different surface roughness. Correct trends are noted for the impact of surface roughness on the velocity profile. However, velocity deficit profiles and the Reynolds stresses do not collapse as well as expected. Possible reasons for the discrepancies as well as future work will be presented. This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575. Computational resources on TACC Stampede were provided under XSEDE allocation ENG150001.
Gas kinematics in FIRE simulated galaxies compared to spatially unresolved H I observations
El-Badry, Kareem; Bradford, Jeremy; Quataert, Eliot; Geha, Marla; Boylan-Kolchin, Michael; Weisz, Daniel R.; Wetzel, Andrew; Hopkins, Philip F.; Chan, T. K.; Fitts, Alex; Kereš, Dušan; Faucher-Giguère, Claude-André
2018-06-01
The shape of a galaxy's spatially unresolved, globally integrated 21-cm emission line depends on its internal gas kinematics: galaxies with rotationally supported gas discs produce double-horned profiles with steep wings, while galaxies with dispersion-supported gas produce Gaussian-like profiles with sloped wings. Using mock observations of simulated galaxies from the FIRE project, we show that one can therefore constrain a galaxy's gas kinematics from its unresolved 21-cm line profile. In particular, we find that the kurtosis of the 21-cm line increases with decreasing V/σ and that this trend is robust across a wide range of masses, signal-to-noise ratios, and inclinations. We then quantify the shapes of 21-cm line profiles from a morphologically unbiased sample of ˜2000 low-redshift, H I-detected galaxies with Mstar = 107-11 M⊙ and compare to the simulated galaxies. At Mstar ≳ 1010 M⊙, both the observed and simulated galaxies produce double-horned profiles with low kurtosis and steep wings, consistent with rotationally supported discs. Both the observed and simulated line profiles become more Gaussian like (higher kurtosis and less-steep wings) at lower masses, indicating increased dispersion support. However, the simulated galaxies transition from rotational to dispersion support more strongly: at Mstar = 108-10 M⊙, most of the simulations produce more Gaussian-like profiles than typical observed galaxies with similar mass, indicating that gas in the low-mass simulated galaxies is, on average, overly dispersion supported. Most of the lower-mass-simulated galaxies also have somewhat lower gas fractions than the median of the observed population. The simulations nevertheless reproduce the observed line-width baryonic Tully-Fisher relation, which is insensitive to rotational versus dispersion support.
Directory of Open Access Journals (Sweden)
Bettinotti Maria
2004-03-01
Full Text Available Abstract Genes in the Leukocyte Antigen 6 (Ly-6 superfamily encode glycosyl-phosphatidylinositol (GPI anchored glycoproteins (gp with conserved domains of 70 to 100 amino acids and 8 to 10 cysteine residues. Murine Ly-6 genes encode important lymphocyte and hematopoietic stem cell antigens. Recently, a new member of the human Ly-6 gene superfamily has been described, CD177. CD177 is polymorphic and has at least two alleles, PRV-1 and NB1. CD177 was first described as PRV-1, a gene that is overexpressed in neutrophils from approximately 95% of patients with polycythemia vera and from about half of patients with essential thrombocythemia. CD177 encodes NB1 gp, a 58–64 kD GPI gp that is expressed by neutrophils and neutrophil precursors. NB1 gp carries Human Neutrophil Antigen (HNA-2a. Investigators working to identify the gene encoding NB1 gp called the CD177 allele they described NB1. NB1 gp is unusual in that neutrophils from some healthy people lack the NB1 gp completely and in most people NB1 gp is expressed by a subpopulation of neutrophils. The function of NB1 gp and the role of CD177 in the pathogenesis and clinical course of polycythemia vera and essential thrombocythemia are not yet known. However, measuring neutrophil CD177 mRNA levels has become an important marker for diagnosing the myeloproliferative disorders polycythemia vera and essential thrombocythemia.
Dong, Zheng; Zhou, Hongyu; Tao, Peng
2018-02-01
PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.
Flexible concrete link slabs used as expansion joints in bridge decks
DEFF Research Database (Denmark)
Lárusson, Lárus Helgi; Fischer, Gregor
2011-01-01
of water through the expansion joint and subsequent corrosion of girders and girder bearings. Investigations on joint-less superstructures using conventional steel reinforcement in so-called concrete link slabs indicate improved performance and economic feasibility. However, this concept requires...... relatively large amounts of steel reinforcement for crack control purposes and consequently provides a relatively large flexural stiffness and negative moment capacity at the joint between the spans. These contradicting requirements and effects in existing replacement concepts for damaged mechanical bridge...... joints are currently unresolved. In the proposed system described in this paper, a ductile cement-based composite section reinforced with Glass Fiber Reinforced Polymers (GFRP) replaces the damaged expansion joint. The combination of this ductile concrete together with corrosion resistant GFRP...
Somogyi, Gabor
2013-01-01
We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of the regularised doubly virtual contribution to the NNLO cross section becomes feasible.
International Nuclear Information System (INIS)
Serkiz, A.W.
1983-05-01
This report summarizes key technical findings relevant to the Unresolved Safety Issue A-1, Water Hammer. These findings were derived from studies of reported water hammer occurrences and underlying causes and provide key insights into means to minimize or eliminate further water hammer occurrences. It should also be noted that this report does not represent a substitute for current rules and regulations
International Nuclear Information System (INIS)
1984-03-01
This report, which includes responses to public comments, summarizes key technical findings relevant to the Unresolved Safety Issue A-1, Water Hammer. These findings were derived from studies of reported water hammer occurrences and underlying causes and provide key insights into means to minimize or eliminate further water hammer occurrences. This report does not represent a substitute for current rules and regulations
Simulation analysis of photometric data for attitude estimation of unresolved space objects
Du, Xiaoping; Gou, Ruixin; Liu, Hao; Hu, Heng; Wang, Yang
2017-10-01
The attitude information acquisition of unresolved space objects, such as micro-nano satellites and GEO objects under the way of ground-based optical observations, is a challenge to space surveillance. In this paper, a useful method is proposed to estimate the SO attitude state according to the simulation analysis of photometric data in different attitude states. The object shape model was established and the parameters of the BRDF model were determined, then the space object photometric model was established. Furthermore, the photometric data of space objects in different states are analyzed by simulation and the regular characteristics of the photometric curves are summarized. The simulation results show that the photometric characteristics are useful for attitude inversion in a unique way. Thus, a new idea is provided for space object identification in this paper.
Chromospheric counterparts of solar transition region unresolved fine structure loops
Pereira, Tiago M. D.; Rouppe van der Voort, Luc; Hansteen, Viggo H.; De Pontieu, Bart
2018-04-01
Low-lying loops have been discovered at the solar limb in transition region temperatures by the Interface Region Imaging Spectrograph (IRIS). They do not appear to reach coronal temperatures, and it has been suggested that they are the long-predicted unresolved fine structures (UFS). These loops are dynamic and believed to be visible during both heating and cooling phases. Making use of coordinated observations between IRIS and the Swedish 1-m Solar Telescope, we study how these loops impact the solar chromosphere. We show for the first time that there is indeed a chromospheric signal of these loops, seen mostly in the form of strong Doppler shifts and a conspicuous lack of chromospheric heating. In addition, we find that several instances have a inverse Y-shaped jet just above the loop, suggesting that magnetic reconnection is driving these events. Our observations add several puzzling details to the current knowledge of these newly discovered structures; this new information must be considered in theoretical models. Two movies associated to Fig. 1 are available at http://https://www.aanda.org
Directory of Open Access Journals (Sweden)
Shu-Ting Pan
2016-06-01
Full Text Available The human cytochrome P450 (CYP superfamily consisting of 57 functional genes is the most important group of Phase I drug metabolizing enzymes that oxidize a large number of xenobiotics and endogenous compounds, including therapeutic drugs and environmental toxicants. The CYP superfamily has been shown to expand itself through gene duplication, and some of them become pseudogenes due to gene mutations. Orthologs and paralogs are homologous genes resulting from speciation or duplication, respectively. To explore the evolutionary and functional relationships of human CYPs, we conducted this bioinformatic study to identify their corresponding paralogs, homologs, and orthologs. The functional implications and implications in drug discovery and evolutionary biology were then discussed. GeneCards and Ensembl were used to identify the paralogs of human CYPs. We have used a panel of online databases to identify the orthologs of human CYP genes: NCBI, Ensembl Compara, GeneCards, OMA (“Orthologous MAtrix” Browser, PATHER, TreeFam, EggNOG, and Roundup. The results show that each human CYP has various numbers of paralogs and orthologs using GeneCards and Ensembl. For example, the paralogs of CYP2A6 include CYP2A7, 2A13, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 2F1, 2J2, 2R1, 2S1, 2U1, and 2W1; CYP11A1 has 6 paralogs including CYP11B1, 11B2, 24A1, 27A1, 27B1, and 27C1; CYP51A1 has only three paralogs: CYP26A1, 26B1, and 26C1; while CYP20A1 has no paralog. The majority of human CYPs are well conserved from plants, amphibians, fishes, or mammals to humans due to their important functions in physiology and xenobiotic disposition. The data from different approaches are also cross-validated and validated when experimental data are available. These findings facilitate our understanding of the evolutionary relationships and functional implications of the human CYP superfamily in drug discovery.
Somogyi, Gábor
2013-04-01
We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of fully differential rates for electron-positron annihilation into two and three jets at NNLO accuracy becomes feasible.
Somogyi, Gabor
2013-01-01
We finish the definition of a subtraction scheme for computing NNLO corrections to QCD jet cross sections. In particular, we perform the integration of the soft-type contributions to the doubly unresolved counterterms via the method of Mellin-Barnes representations. With these final ingredients in place, the definition of the scheme is complete and the computation of fully differential rates for electron-positron annihilation into two and three jets at NNLO accuracy becomes feasible.
Characterization of the Tetraspan Junctional Complex (4JC) superfamily.
Chou, Amy; Lee, Andre; Hendargo, Kevin J; Reddy, Vamsee S; Shlykov, Maksim A; Kuppusamykrishnan, Harikrishnan; Medrano-Soto, Arturo; Saier, Milton H
2017-03-01
Connexins or innexins form gap junctions, while claudins and occludins form tight junctions. In this study, statistical data, derived using novel software, indicate that these four junctional protein families and eleven other families of channel and channel auxiliary proteins are related by common descent and comprise the Tetraspan (4 TMS) Junctional Complex (4JC) Superfamily. These proteins all share similar 4 transmembrane α-helical (TMS) topologies. Evidence is presented that they arose via an intragenic duplication event, whereby a 2 TMS-encoding genetic element duplicated tandemly to give 4 TMS proteins. In cases where high resolution structural data were available, the conclusion of homology was supported by conducting structural comparisons. Phylogenetic trees reveal the probable relationships of these 15 families to each other. Long homologues containing fusions to other recognizable domains as well as internally duplicated or fused domains are reported. Large "fusion" proteins containing 4JC domains proved to fall predominantly into family-specific patterns as follows: (1) the 4JC domain was N-terminal; (2) the 4JC domain was C-terminal; (3) the 4JC domain was duplicated or occasionally triplicated and (4) mixed fusion types were present. Our observations provide insight into the evolutionary origins and subfunctions of these proteins as well as guides concerning their structural and functional relationships. Copyright © 2016 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
M. Laroche
2011-03-01
Full Text Available Speech auditory brainstem responses (speech ABR reflect activity that is phase-locked to the harmonics of the fundamental frequency (F0 up to at least the first formant (F1. Recent evidence suggests that responses at F0 in the presence of noise are more robust than responses at F1, and are also dissociated in some learning-impaired children. Peripheral auditory processing can be broadly divided into resolved and unresolved harmonic regions. This study investigates the contribution of these two regions to the speech ABR, and their susceptibility to noise. We recorded, in quiet and in background white noise, evoked responses in twelve normal hearing adults in response to three variants of a synthetic vowel: i Allformants, which contains all first three formants, ii F1Only, which is dominated by resolved harmonics, and iii F2&F3Only, which is dominated by unresolved harmonics. There were no statistically significant differences in the response at F0 due to the three variants of the stimulus in quiet, nor did the noise affect this response with the Allformants and F1Only variants. On the other hand, the response at F0 with the F2&F3Only variant was significantly weaker in noise than with the two other variants (p<0.001. With the response at F1, there was no difference with the Allformants and F1Only variants in quiet, but was expectedly weaker with the F2&F3Only variant (p<0.01. The addition of noise significantly weakened the response at F1 with the F1Only variant (p<0.05, but this weakening only tended towards significance with the Allformants variant (p=0.07. The results of this study indicate that resolved and unresolved harmonics are processed in different but interacting pathways that converge in the upper brainstem. The results also support earlier work on the differential susceptibility of responses at F0 and F1 to added noise.
Multiple Receptor Subtypes for the CGRP Super-Family
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R. Quirion
2001-01-01
Full Text Available Molecular evidence for the existence of multiple receptors for CGRP has been rather difficult to obtain. Over 10 years after suggesting the existence of at least two classes (CGRP1 and CGRP2 of CGRP receptors on the basis of pharmacological data[1], molecular data on the CGRP2 receptor subtype are still lacking as well as potent and selective antagonists. The situation is somewhat different for the functional CGRP1 subtype which is likely composed of diverse subunits CRLR, RAMP1 and possibly RCP[2]. Moreover, BIBN 4096BS was recently reported as the first nonpeptide highly potent CGRP1 receptor antagonist[3]. However, in situ hybridization and receptor autoradiographic data have clearly shown the existence of major mismatches (e.g., cerebellum between the discrete localization of CRLR, RAMP1, and specific CGRP binding sites supporting the existence of CGRP receptor subtypes. Functional studies have also provided evidence in that regard (for a recent review: [4]. Accordingly, additional studies aiming at cloning additional CGRP receptors are certainly warranted. Similarly, recent evidence from various laboratories including ours suggests the existence of more than one class (CRLR and RAMP2 of adrenomedullin receptors at least in the rat brain. In contrast, most evidence suggests the existence of a single class of amylin receptors. In brief, it appears that multiple receptors or receptor complexes do exist for CGRP and related peptides but their composition is apparently unique among the GPCR super-family and additional data are needed to fully establish the molecular organization of each subtype. Supported by CIHR of Canada.
Abraham, Anup; Chandler, Douglas E
2017-10-01
Proteins of the CAP superfamily play numerous roles in reproduction, innate immune responses, cancer biology, and venom toxicology. Here we document the breadth of the CAP (Cysteine-RIch Secretory Protein (CRISP), Antigen 5, and Pathogenesis-Related) protein superfamily and trace the major events in its evolution using amino acid sequence homology and the positions of exon/intron borders within their genes. Seldom acknowledged in the literature, we find that many of the CAP subfamilies present in mammals, where they were originally characterized, have distinct homologues in the invertebrate phyla. Early eukaryotic CAP genes contained only one exon inherited from prokaryotic predecessors and as evolution progressed an increasing number of introns were inserted, reaching 2-5 in the invertebrate world and 5-15 in the vertebrate world. Focusing on the CRISP subfamily, we propose that these proteins evolved in three major steps: (1) origination of the CAP/PR/SCP domain in bacteria, (2) addition of a small Hinge domain to produce the two-domain SCP-like proteins found in roundworms and anthropoids, and (3) addition of an Ion Channel Regulatory domain, borrowed from invertebrate peptide toxins, to produce full length, three-domain CRISP proteins, first seen in insects and later to diversify into multiple subtypes in the vertebrate world.
Unresolved Safety Issue A-46 - seismic qualification of equipment in operating plants
International Nuclear Information System (INIS)
Anderson, N.
1985-01-01
Seismic Qualification of Equipment in Operating Plants was designated as an Unresolved Safety Issue (USI) in December, 1980. The USI A-46 program was developed in early 1981 to investigate the adequacy of mechanical and electrical equipment in operating plants to withstand a safe shutdown earthquake. The approach taken was to develop viable, cost effective alternatives to current seismic qualification licensing requirements which could be applied to operating nuclear power plants. The tasks investigated include: (1) identification of seismic sensitive systems and equipment; (2) assessment of adequacy of existing seismic qualification methods; (3) development and assessment of in-situ test procedures to assist in qualification of equipment; (4) seismic qualification of equipment using seismic experience data; and (5) development of methods to generate generic floor response spectra. Progress to date and plans for completion of resolution are reported
Zhang, Weixin; Kou, Yanbo; Xu, Jintao; Cao, Yanli; Zhao, Guolei; Shao, Jing; Wang, Hai; Wang, Zhixing; Bao, Xiaoming; Chen, Guanjun; Liu, Weifeng
2013-01-01
Proper perception of the extracellular insoluble cellulose is key to initiating the rapid synthesis of cellulases by cellulolytic Trichoderma reesei. Uptake of soluble oligosaccharides derived from cellulose hydrolysis represents a potential point of control in the induced cascade. In this study, we identified a major facilitator superfamily sugar transporter Stp1 capable of transporting cellobiose by reconstructing a cellobiose assimilation system in Saccharomyces cerevisiae. The absence of Stp1 in T. reesei resulted in differential cellulolytic response to Avicel versus cellobiose. Transcriptional profiling revealed a different expression profile in the Δstp1 strain from that of wild-type strain in response to Avicel and demonstrated that Stp1 somehow repressed induction of the bulk of major cellulase and hemicellulose genes. Two other putative major facilitator superfamily sugar transporters were, however, up-regulated in the profiling. Deletion of one of them identified Crt1 that was required for growth and enzymatic activity on cellulose or lactose, but was not required for growth or hemicellulase activity on xylan. The essential role of Crt1 in cellulase induction did not seem to rely on its transporting activity because the overall uptake of cellobiose or sophorose by T. reesei was not compromised in the absence of Crt1. Phylogenetic analysis revealed that orthologs of Crt1 exist in the genomes of many filamentous ascomycete fungi capable of degrading cellulose. These data thus shed new light on the mechanism by which T. reesei senses and transmits the cellulose signal and offers potential strategies for strain improvement. PMID:24085297
Energy Technology Data Exchange (ETDEWEB)
Mushegian, Arcady R., E-mail: mushegian2@gmail.com [Division of Molecular and Cellular Biosciences, National Science Foundation, 4201 Wilson Boulevard, Arlington, VA 22230 (United States); Elena, Santiago F., E-mail: sfelena@ibmcp.upv.es [Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, 46022 València (Spain); The Santa Fe Institute, Santa Fe, NM 87501 (United States)
2015-02-15
Homologs of Tobacco mosaic virus 30K cell-to-cell movement protein are encoded by diverse plant viruses. Mechanisms of action and evolutionary origins of these proteins remain obscure. We expand the picture of conservation and evolution of the 30K proteins, producing sequence alignment of the 30K superfamily with the broadest phylogenetic coverage thus far and illuminating structural features of the core all-beta fold of these proteins. Integrated copies of pararetrovirus 30K movement genes are prevalent in euphyllophytes, with at least one copy intact in nearly every examined species, and mRNAs detected for most of them. Sequence analysis suggests repeated integrations, pseudogenizations, and positive selection in those provirus genes. An unannotated 30K-superfamily gene in Arabidopsis thaliana genome is likely expressed as a fusion with the At1g37113 transcript. This molecular background of endopararetrovirus gene products in plants may change our view of virus infection and pathogenesis, and perhaps of cellular homeostasis in the hosts. - Highlights: • Sequence region shared by plant virus “30K” movement proteins has an all-beta fold. • Most euphyllophyte genomes contain integrated copies of pararetroviruses. • These integrated virus genomes often include intact movement protein genes. • Molecular evidence suggests that these “30K” genes may be selected for function.
Banroques, Josette; Doère, Monique; Dreyfus, Marc; Linder, Patrick; Tanner, N Kyle
2010-03-05
Motif III in the putative helicases of superfamily 2 is highly conserved in both its sequence and its structural context. It typically consists of the sequence alcohol-alanine-alcohol (S/T-A-S/T). Historically, it was thought to link ATPase activity with a "helicase" strand displacement activity that disrupts RNA or DNA duplexes. DEAD-box proteins constitute the largest family of superfamily 2; they are RNA-dependent ATPases and ATP-dependent RNA binding proteins that, in some cases, are able to disrupt short RNA duplexes. We made mutations of motif III (S-A-T) in the yeast DEAD-box protein Ded1 and analyzed in vivo phenotypes and in vitro properties. Moreover, we made a tertiary model of Ded1 based on the solved structure of Vasa. We used Ded1 because it has relatively high ATPase and RNA binding activities; it is able to displace moderately stable duplexes at a large excess of substrate. We find that the alanine and the threonine in the second and third positions of motif III are more important than the serine, but that mutations of all three residues have strong phenotypes. We purified the wild-type and various mutants expressed in Escherichia coli. We found that motif III mutations affect the RNA-dependent hydrolysis of ATP (k(cat)), but not the affinity for ATP (K(m)). Moreover, mutations alter and reduce the affinity for single-stranded RNA and subsequently reduce the ability to disrupt duplexes. We obtained intragenic suppressors of the S-A-C mutant that compensate for the mutation by enhancing the affinity for ATP and RNA. We conclude that motif III and the binding energy of gamma-PO(4) of ATP are used to coordinate motifs I, II, and VI and the two RecA-like domains to create a high-affinity single-stranded RNA binding site. It also may help activate the beta,gamma-phosphoanhydride bond of ATP. (c) 2009 Elsevier Ltd. All rights reserved.
A case of woman abuse: gender ideologies, power paradoxes, and unresolved conflict.
Rosen, K H; Bird, K
1996-09-01
This paper describes some of the complex individual and relationship processes that occurred in an intimate relationship where love and violence coexisted. It presents a longitudinal, qualitative study of a premarital relationship in which the man had been repeatedly violent towards his female partner. It describes how gender role ideologies, the distribution of power between partners, and unresolved conflict are related to each other and to the emergence of violence and maintenance of couple bonds. A grounded theory approach was used to collect and analyze data for this single case and qualitative study in which both partners were interviewed several times each over the course of 1.5 years. Overall, it was found that intimate relationships that become contexts for expressions of love and violence are indeed complex, and the flexibility to consider the complexities that are involved provide a context for developing creative solutions.
BRICHOS - a superfamily of multidomain proteins with diverse functions
Directory of Open Access Journals (Sweden)
Johansson Jan
2009-09-01
Full Text Available Abstract Background The BRICHOS domain has been found in 8 protein families with a wide range of functions and a variety of disease associations, such as respiratory distress syndrome, dementia and cancer. The domain itself is thought to have a chaperone function, and indeed three of the families are associated with amyloid formation, but its structure and many of its functional properties are still unknown. Findings The proteins in the BRICHOS superfamily have four regions with distinct properties. We have analysed the BRICHOS proteins focusing on sequence conservation, amino acid residue properties, native disorder and secondary structure predictions. Residue conservation shows large variations between the regions, and the spread of residue conservation between different families can vary greatly within the regions. The secondary structure predictions for the BRICHOS proteins show remarkable coherence even where sequence conservation is low, and there seems to be little native disorder. Conclusions The greatly variant rates of conservation indicates different functional constraints among the regions and among the families. We present three previously unknown BRICHOS families; group A, which may be ancestral to the ITM2 families; group B, which is a close relative to the gastrokine families, and group C, which appears to be a truly novel, disjoint BRICHOS family. The C-terminal region of group C has nearly identical sequences in all species ranging from fish to man and is seemingly unique to this family, indicating critical functional or structural properties.
Energy Technology Data Exchange (ETDEWEB)
Riegert, Alexander S. [Department; Thoden, James B. [Department; Schoenhofen, Ian C. [National; Watson, David C. [National; Young, N. Martin [National; Tipton, Peter A. [Department; Holden, Hazel M. [Department
2017-11-03
Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-α-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 Å or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. On the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.
Directory of Open Access Journals (Sweden)
Aleksander F Sikorski
2007-01-01
Full Text Available The review is focused on the domain structure and function of protein 4.1, one of the proteins belonging to the membrane skeleton. The protein 4.1 of the red blood cells (4.1R is a multifunctional protein that localizes to the membrane skeleton and stabilizes erythrocyte shape and membrane mechanical properties, such as deformability and stability, via lateral interactions with spectrin, actin, glycophorin C and protein p55. Protein 4.1 binding is modulated through the action of kinases and/or calmodulin-Ca2+. Non-erythroid cells express the 4.1R homologues: 4.1G (general type, 4.1B (brain type, and 4.1N (neuron type, and the whole group belongs to the protein 4.1 superfamily, which is characterized by the presence of a highly conserved FERM domain at the N-terminus of the molecule. Proteins 4.1R, 4.1G, 4.1N and 4.1B are encoded by different genes. Most of the 4.1 superfamily proteins also contain an actin-binding domain. To date, more than 40 members have been identified. They can be divided into five groups: protein 4.1 molecules, ERM proteins, talin-related molecules, protein tyrosine phosphatase (PTPH proteins and NBL4 proteins. We have focused our attention on the main, well known representatives of 4.1 superfamily and tried to choose the proteins which are close to 4.1R or which have distinct functions. 4.1 family proteins are not just linkers between the plasma membrane and membrane skeleton; they also play an important role in various processes. Some, such as focal adhesion kinase (FAK, non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells, play the role in cell adhesion. The other members control or take part in tumor suppression, regulation of cell cycle progression, inhibition of cell proliferation, downstream signaling of the glutamate receptors, and establishment of cell polarity; some are also involved in cell proliferation, cell motility, and/or cell-to-cell communication.
Comment 4 - policy for sustainable development: Some unresolved issues
International Nuclear Information System (INIS)
Ruttan, V.W.
1992-01-01
We are now in the midst of the third wave of social concern since World War II about the implications of natural resource availability and environmental change for the sustainability of improvements in human well-being. The first wave of concern in the late 1940s and early 1950s focused primarily on the quantitative relationship between resource availability and economic growth. The response to this first wave of concern was technical change in raw material production. The second wave of concern, in the late 1960s and early 1970s, focused on the rising demand for assimilation by the environment of residuals derived from growth in commodity production and consumption - primarily at the local and regional level. Since the mid 1980s, these two early concerns have been supplemented by a third. This more recent concern centers around the implications for environmental quality, food production, and human health of a series of environmental changes such as global warming, ozone depletion, acid rain, and others that are occurring on a transnational scale. Before actions to resolve these more recent challenges to sustainable economic growth are taken, a number of unresolved issues must be confronted to allow a commitment to this resolution to be translated into an internally coherent reform agenda. In this note, he discuss three of these issues
Antisocial behaviour and psychopathy: Uncovering the externalizing link in the P3 modulation.
Pasion, Rita; Fernandes, Carina; Pereira, Mariana R; Barbosa, Fernando
2017-03-22
In 2009, Gao and Raine's meta-analysis analysed P3 modulation over the antisocial spectrum. However, some questions remained open regarding the P3 modulation patterns across impulsive and violent manifestations of antisocial behaviour, phenotypic components of psychopathy, and P3 components. A systematic review of 36 studies was conducted (N=3514) to extend previous results and to address these unresolved questions. A clear link between decreased P3 amplitude and antisocial behaviour was found. In psychopathy, dimensional approaches become more informative than taxonomic models. Distinct etiological pathways of psychopathy were evidenced in cognitive tasks: impulsive-antisocial psychopathic traits mainly predicted blunted P3 amplitude, while interpersonal-affective psychopathic traits explained enhanced P3 amplitude. Supporting the low fear hypothesis, the interpersonal-affective traits were associated with reduced P3 amplitude in emotional-affective learning tasks. From the accumulated knowledge we propose a framework of P3 amplitude modulation that uncovers the externalizing link between psychopathy and antisocial behaviour. However, the main hypotheses are exploratory and call for more data before stablishing robust conclusions. Copyright © 2017 Elsevier Ltd. All rights reserved.
Tavera-Martínez, Laura; Marchant, Margarita
2017-10-20
Research regarding deep-sea benthic foraminifera in the Colombian Caribbean requires further development given the complete lack of information related to the different groups that constitute associations and the ecological functions they fulfill. For this purpose, a taxonomic description of Superfamily Komokioidea was composed from macrofauna samples from between 1,215 m and 3,179 m depth, obtained during the research cruise ANH-COL 4 and COL 5 carried out in 2014. Results showed foraminifera belonging to the three families: Komokiidae, Baculellidae, and Normaninidae, inclu-ding five genera (Lana, Komokia, Ipoa, Normaninam, and Catena) and five species (Lana neglecta, Komokia multiramosa, Normanina conferta, Ipoa fragila, and Catena piriformis). This study presents knowledge regarding deep-sea Colombian Caribbean benthic foraminifera, which to date have not been recorded from this region. Their depth distribution when compared with other studies from the Atlantic and Pacific, allows the expansion of taxonomic inventories and the characterization of biodiversity within poorly explored regions.
Energy Technology Data Exchange (ETDEWEB)
Rosenthal, Cindy [Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudinger Weg 5, D-55099 Mainz (Germany); Mueller, Uwe [Berliner Elektronenspeicherring-Gesellschaft für Synchrotronstrahlung mbH, Albert-Einstein-Strasse 15, D-12489 Berlin (Germany); Panjikar, Santosh [European Molecular Biology Laboratory Hamburg, Outstation Deutsches Elektronen-Synchrotron, Notkestrasse 85, D-22603 Hamburg (Germany); Sun, Lianli [Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudinger Weg 5, D-55099 Mainz (Germany); Department of TCM and Natural Drug Research, College of Pharmaceutical Sciences, 513 Zijingang Campus, Zhejiang University, 310058 Hangzhou (China); Ruppert, Martin [Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudinger Weg 5, D-55099 Mainz (Germany); Zhao, Yu [Department of TCM and Natural Drug Research, College of Pharmaceutical Sciences, 513 Zijingang Campus, Zhejiang University, 310058 Hangzhou (China); Stöckigt, Joachim [Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudinger Weg 5, D-55099 Mainz (Germany); Department of TCM and Natural Drug Research, College of Pharmaceutical Sciences, 513 Zijingang Campus, Zhejiang University, 310058 Hangzhou (China)
2006-12-01
Perakine reductase, a novel member of the aldo-keto reductase enzyme superfamily of higher plants, is involved in the biosynthesis of monoterpenoid indole alkaloids in the Indian medicinal plant Rauvolfia serpentina. The enzyme has been crystallized in C-centered orthorhombic space group and diffracts to 2.0 Å resolution. Perakine reductase (PR) is a novel member of the aldo-keto reductase enzyme superfamily from higher plants. PR from the plant Rauvolfia serpentina is involved in the biosynthesis of monoterpenoid indole alkaloids by performing NADPH-dependent reduction of perakine, yielding raucaffrinoline. However, PR can also reduce cinnamic aldehyde and some of its derivatives. After heterologous expression of a triple mutant of PR in Escherichia coli, crystals of the purified and methylated enzyme were obtained by the hanging-drop vapour-diffusion technique at 293 K with 100 mM sodium citrate pH 5.6 and 27% PEG 4000 as precipitant. Crystals belong to space group C222{sub 1} and diffract to 2.0 Å, with unit-cell parameters a = 58.9, b = 93.0, c = 143.4 Å.
International Nuclear Information System (INIS)
Rosenthal, Cindy; Mueller, Uwe; Panjikar, Santosh; Sun, Lianli; Ruppert, Martin; Zhao, Yu; Stöckigt, Joachim
2006-01-01
Perakine reductase, a novel member of the aldo-keto reductase enzyme superfamily of higher plants, is involved in the biosynthesis of monoterpenoid indole alkaloids in the Indian medicinal plant Rauvolfia serpentina. The enzyme has been crystallized in C-centered orthorhombic space group and diffracts to 2.0 Å resolution. Perakine reductase (PR) is a novel member of the aldo-keto reductase enzyme superfamily from higher plants. PR from the plant Rauvolfia serpentina is involved in the biosynthesis of monoterpenoid indole alkaloids by performing NADPH-dependent reduction of perakine, yielding raucaffrinoline. However, PR can also reduce cinnamic aldehyde and some of its derivatives. After heterologous expression of a triple mutant of PR in Escherichia coli, crystals of the purified and methylated enzyme were obtained by the hanging-drop vapour-diffusion technique at 293 K with 100 mM sodium citrate pH 5.6 and 27% PEG 4000 as precipitant. Crystals belong to space group C222 1 and diffract to 2.0 Å, with unit-cell parameters a = 58.9, b = 93.0, c = 143.4 Å
Results of arthroscopic treatment in unresolved Osgood-Schlatter disease in athletes.
Circi, Esra; Beyzadeoglu, Tahsin
2017-02-01
In this study we aimed to determine outcomes following arthroscopic ossicle excision in athletes with unresolved Osgood-Schlatter disease (OSD). Arthroscopy was performed on 11 patients (11 knees) with OSD between September 2008 and November 2014. Surgical treatment inclusion criteria were determined as: failure of conservative treatment; isolated pain over the tibial tubercle and distal patellar tendon; pain limiting sporting performance at a competitive level. All patients had a documented history of OSD; the mean duration of persistent pain over the tibial tubercle was 15.5 months. The mean age was 23 years. The mean follow-up period was 66.1 months. The mean latency in returning to sports related training activities after the surgery was 6.7 weeks. The mean Kujala patello-femoral score improved from 82.9 points pre-operatively, to 98.5 points at the final follow-up (p operative period, increasing to a score of 96.9 points at final follow-up (p operative period, increasing to 8.5 post-operatively (p advantage of faster recovery and avoiding damage to the patellar tendon.
Slonim, L N; Pinkner, J S; Brändén, C I; Hultgren, S J
1992-01-01
The assembly of adhesive pili in Gram-negative bacteria is modulated by specialized periplasmic chaperone systems. PapD is the prototype member of the superfamily of periplasmic pilus chaperones. Previously, the alignment of chaperone sequences superimposed on the three dimensional structure of PapD revealed the presence of invariant, conserved and variable amino acids. Representative residues that protruded into the PapD cleft were targeted for site directed mutagenesis to investigate the pi...
Directory of Open Access Journals (Sweden)
Donaldson Paul J
2001-08-01
Full Text Available Abstract Background Although MP20 is the second most highly expressed membrane protein in the lens its function remains an enigma. Putative functions for MP20 have recently been inferred from its assignment to the tetraspanin superfamily of integral membrane proteins. Members of this family have been shown to be involved in cellular proliferation, differentiation, migration, and adhesion. In this study, we show that MP20 associates with galectin-3, a known adhesion modulator. Results MP20 and galectin-3 co-localized in selected areas of the lens fiber cell plasma membrane. Individually, these proteins purified with apparent molecular masses of 60 kDa and 22 kDa, respectively. A 104 kDa complex was formed in vitro upon mixing the purified proteins. A 102 kDa complex of MP20 and galectin-3 could also be isolated from detergent-solubilized native fiber cell membranes. Binding between MP20 and galectin-3 was disrupted by lactose suggesting the lectin site was involved in the interaction. Conclusions MP20 adds to a growing list of ligands of galectin-3 and appears to be the first representative of the tetraspanin superfamily identified to possess this specificity.
Quantum dots in nanomedicine: recent trends, advances and unresolved issues
International Nuclear Information System (INIS)
Volkov, Yuri
2015-01-01
The review addresses the current state of progress in the use of ultra-small nanoparticles from the category of quantum dots (QDs), which presently embraces a widening range of nanomaterials of different nature, including “classical” semiconductor groups III-V and II-VI nanocrystals, along with more recently emerged carbon, silicon, gold and other types of nanoparticles falling into this class of nanomaterials due to their similar physical characteristics such as small size and associated quantum confinement effects. A diverse range of QDs applications in nanomedicine has been extensively summarised previously in numerous publications. Therefore, this review is not intended to provide an all-embracing survey of the well documented QDs uses, but is rather focused on the most recent emerging developments, concepts and outstanding unresolved problematic and sometimes controversial issues. Over 125 publications are overviewed and discussed here in the context of major nanomedicine domains, i.e. medical imaging, diagnostics, therapeutic applications and combination of them in multifunctional theranostic systems. - Highlights: • New types of nanomaterials have been recently added to the category of QDs with a potential in nanomedicine. • Within the main nanomedicine domains, best progress has been achieved with QDs for diagnostic tools. • Further studies are required for the theranostic QDs-based leads to reach clinical translation.
Quantum dots in nanomedicine: recent trends, advances and unresolved issues
Energy Technology Data Exchange (ETDEWEB)
Volkov, Yuri, E-mail: yvolkov@tcd.ie
2015-12-18
The review addresses the current state of progress in the use of ultra-small nanoparticles from the category of quantum dots (QDs), which presently embraces a widening range of nanomaterials of different nature, including “classical” semiconductor groups III-V and II-VI nanocrystals, along with more recently emerged carbon, silicon, gold and other types of nanoparticles falling into this class of nanomaterials due to their similar physical characteristics such as small size and associated quantum confinement effects. A diverse range of QDs applications in nanomedicine has been extensively summarised previously in numerous publications. Therefore, this review is not intended to provide an all-embracing survey of the well documented QDs uses, but is rather focused on the most recent emerging developments, concepts and outstanding unresolved problematic and sometimes controversial issues. Over 125 publications are overviewed and discussed here in the context of major nanomedicine domains, i.e. medical imaging, diagnostics, therapeutic applications and combination of them in multifunctional theranostic systems. - Highlights: • New types of nanomaterials have been recently added to the category of QDs with a potential in nanomedicine. • Within the main nanomedicine domains, best progress has been achieved with QDs for diagnostic tools. • Further studies are required for the theranostic QDs-based leads to reach clinical translation.
Multiple Personalities: Childhood Unresolved Conflicts and Trauma In Clark’s All Around The Town
Directory of Open Access Journals (Sweden)
Fatma Hetami
2011-06-01
Full Text Available This paper is aimed at describing how multiple personalities as the unresolved childhood conflict and trauma are revealed in Clark’s All Around the Town. The novel is analyzed by using psychological approach. It is based on the assumption that any work of literature always deals with human life in terms of his personality structure and psychological condition. The results indicate that as a character, Laurie Kenyon is around and developing. It can be seen from her various traits. In one, she is smart and sweet. But on the other hand, she is anxious and gets afraid easily. As an individual, Laurie’s Id is weak. Her Super-ego, which appears as forms of traumatic experience and unresolved childhood conflict, are embedded strongly in Laurie’s personality. Therefore, she tries to create her ego in the form of multiple personalities to help her out of her problems. Abstrak: Tulisan ini merupakan hasil penelitian yang bertujuan untuk mendeskripsikan bagaimana kepribadian ganda sebagai akibat trauma dan konflik masa kecil yang tidak teratasi muncul pada novel All Around the Town Karya Marry Higgins Clark. Novel ini dianalisis dengan menggunakan pendekatan psikologi sastra. Hal tersebut didasarkan pada asumsi bahwa semua karya sastra selalu berhubungan dengan kehidupan manusia khususnya kepribadian dan kondisi psikologis. Hasil analisis menunjukkan bahwa sebagai tokoh, Laurie Kenyon memiliki karakter bulat dan dinamis. Hal ini bisa dilihat dari sifat-sifat yang dimilikinya serta bagaimana kepribadian Laurie berubah dari awal sampai akhir cerita. Di satu sisi Laurie merupakan gadis yang cerdas dan manis. Namun di lain sisi, ia juga pencemas dan penakut. Sebagai individu, Laurie memiliki id yang lemah. Super ego berupa pengalaman trauma dan konflik yang tidak teratasi semasa kecil terlalu kuat tertanam dalam diri Laurie, sehingga ia berusaha menciptak an ego dalam bentuk kepribadian ganda untuk membantunya lepas dari masalah yang dihadapinya. Kata
Identification of the GTPase superfamily in Mycoplasma synoviae and Mycoplasma hyopneumoniae
Directory of Open Access Journals (Sweden)
Clayton Luiz Borges
2007-01-01
Full Text Available Mycoplasmas are the smallest known prokaryotes with self-replication ability. They are obligate parasites, taking up many molecules of their hosts and acting as pathogens in men, animals, birds and plants. Mycoplasma hyopneumoniae is the infective agent of swine mycoplasmosis and Mycoplasma synoviae is responsible for subclinical upper respiratory infections that may result in airsacculitis and synovitis in chickens and turkeys. These highly infectious organisms present a worldwide distribution and are responsible for major economic problems. Proteins of the GTPase superfamily occur in all domains of life, regulating functions such as protein synthesis, cell cycle and differentiation. Despite their functional diversity, all GTPases are believed to have evolved from a single common ancestor. In this work we have identified mycoplasma GTPases by searching the complete genome databases of Mycoplasma synoviae and Mycoplasma hyopneumoniae, J (non-pathogenic and 7448 (pathogenic strains. Fifteen ORFs encoding predicted GTPases were found in M. synoviae and in the two strains of M. hyopneumoniae. Searches for conserved G domains in GTPases were performed and the sequences were classified into families. The GTPase phylogenetic analysis showed that the subfamilies were well resolved into clades. The presence of GTPases in the three strains suggests the importance of GTPases in 'minimalist' genomes.
The Role of Immunoglobulin Superfamily Cell Adhesion Molecules in Cancer Metastasis
Directory of Open Access Journals (Sweden)
Chee Wai Wong
2012-01-01
Full Text Available Metastasis is a major clinical problem and results in a poor prognosis for most cancers. The metastatic pathway describes the process by which cancer cells give rise to a metastatic lesion in a new tissue or organ. It consists of interconnecting steps all of which must be successfully completed to result in a metastasis. Cell-cell adhesion is a key aspect of many of these steps. Adhesion molecules belonging to the immunoglobulin superfamily (Ig-SF commonly play a central role in cell-cell adhesion, and a number of these molecules have been associated with cancer progression and a metastatic phenotype. Surprisingly, the contribution of Ig-SF members to metastasis has not received the attention afforded other cell adhesion molecules (CAMs such as the integrins. Here we examine the steps in the metastatic pathway focusing on how the Ig-SF members, melanoma cell adhesion molecule (MCAM, L1CAM, neural CAM (NCAM, leukocyte CAM (ALCAM, intercellular CAM-1 (ICAM-1 and platelet endothelial CAM-1 (PECAM-1 could play a role. Although much remains to be understood, this review aims to raise the profile of Ig-SF members in metastasis formation and prompt further research that could lead to useful clinical outcomes.
Gajewski, Stefan; Comeaux, Evan Q.; Jafari, Nauzanene; Bharatham, Nagakumar; Bashford, Donald; White, Stephen W.; van Waardenburg, Robert C.A.M.
2011-01-01
Tyrosyl DNA phosphodiesterase I (Tdp1) is a member of the phospholipase D superfamily and hydrolyzes 3′phospho-DNA adducts via two conserved catalytic histidines, one acting as the lead nucleophile and the second as a general acid/base. Substitution of the second histidine specifically to arginine contributes to the neurodegenerative disease SCAN1. We investigated the catalytic role of this histidine in the yeast protein (His432) using a combination of X-ray crystallography, biochemistry, yeast genetics and theoretical chemistry. The structures of wild type Tdp1 and His432Arg both show a phosphorylated form of the nucleophilic histidine that is not observed in the structure of His432Asn. The phosphohistidine is stabilized in the His432Arg structure by the guanidinium group that also restricts access of a nucleophilic water molecule to the Tdp1-DNA intermediate. Biochemical analyses confirm that His432Arg forms an observable and unique Tdp1-DNA adduct during catalysis. Substitution of His432 by Lys does not affect catalytic activity or yeast phenotype, but substitution with Asn, Gln, Leu, Ala, Ser and Thr all result in severely compromised enzymes and Top1-camptothecin dependent lethality. Surprisingly, His432Asn did not show a stable covalent Tdp1-DNA intermediate which suggests another catalytic defect. Theoretical calculations revealed that the defect resides in the nucleophilic histidine and that the pKa of this histidine is crucially dependent upon the second histidine and the incoming phosphate of the substrate. This represents a unique example of substrate-activated catalysis that applies to the entire phospholipase D superfamily. PMID:22155078
Unmasking the hidden NGTS-3Ab: a hot Jupiter in an unresolved binary system
Günther, Maximilian N.; Queloz, Didier; Gillen, Edward; Delrez, Laetitia; Bouchy, François; McCormac, James; Smalley, Barry; Almleaky, Yaseen; Armstrong, David J.; Bayliss, Daniel; Burdanov, Artem; Burleigh, Matthew; Cabrera, Juan; Casewell, Sarah L.; Cooke, Benjamin F.; Csizmadia, Szilárd; Ducrot, Elsa; Eigmüller, Philipp; Erikson, Anders; Gänsicke, Boris T.; Gibson, Neale P.; Gillon, Michaël; Goad, Michael R.; Jehin, Emmanuël; Jenkins, James S.; Louden, Tom; Moyano, Maximiliano; Murray, Catriona; Pollacco, Don; Poppenhaeger, Katja; Rauer, Heike; Raynard, Liam; Smith, Alexis M. S.; Sohy, Sandrine; Thompson, Samantha J.; Udry, Stéphane; Watson, Christopher A.; West, Richard G.; Wheatley, Peter J.
2018-05-01
We present the discovery of NGTS-3Ab, a hot Jupiter found transiting the primary star of an unresolved binary system. We develop a joint analysis of multi-colour photometry, centroids, radial velocity (RV) cross-correlation function (CCF) profiles and their bisector inverse slopes (BIS) to disentangle this three-body system. Data from the Next Generation Transit Survey (NGTS), SPECULOOS and HARPS are analysed and modelled with our new BLENDFITTER software. We find that the binary consists of NGTS-3A (G6V-dwarf) and NGTS-3B (K1V-dwarf) at 5") and are prone to contamination by blended objects. With TESS on the horizon, it is pivotal for the candidate vetting to incorporate all available follow-up information from multi-colour photometry and RV CCF profiles.
Peng, Fred Y; Weselake, Randall J
2013-05-01
The plant-specific B3 superfamily of transcription factors has diverse functions in plant growth and development. Using a genome-wide domain analysis, we identified 92, 187, 58, 90, 81, 55, and 77 B3 transcription factor genes in the sequenced genome of Arabidopsis, Brassica rapa, castor bean (Ricinus communis), cocoa (Theobroma cacao), soybean (Glycine max), maize (Zea mays), and rice (Oryza sativa), respectively. The B3 superfamily has substantially expanded during the evolution in eudicots particularly in Brassicaceae, as compared to monocots in the analysis. We observed domain duplication in some of these B3 proteins, forming more complex domain architectures than currently understood. We found that the length of B3 domains exhibits a large variation, which may affect their exact number of α-helices and β-sheets in the core structure of B3 domains, and possibly have functional implications. Analysis of the public microarray data indicated that most of the B3 gene pairs encoding Arabidopsis-rice orthologs are preferentially expressed in different tissues, suggesting their different roles in these two species. Using ESTs in crops, we identified many B3 genes preferentially expressed in reproductive tissues. In a sequence-based quantitative trait loci analysis in rice and maize, we have found many B3 genes associated with traits such as grain yield, seed weight and number, and protein content. Our results provide a framework for future studies into the function of B3 genes in different phases of plant development, especially the ones related to traits in major crops.
DEFF Research Database (Denmark)
Shaheen, Aqsa; Ismat, Fouzia; Iqbal, Mazhar
2015-01-01
Multidrug resistance mediated by efflux pumps is a well-known phenomenon in infectious bacteria. Although much work has been carried out to characterize multidrug efflux pumps in Gram-negative and Gram-positive bacteria, such information is still lacking for many deadly pathogens. The aim...... of this study was to gain insight into the substrate specificity of previously uncharacterized transporters of Salmonella Typhi to identify their role in the development of multidrug resistance. S. Typhi genes encoding putative members of the major facilitator superfamily were cloned and expressed in the drug......-hypersensitive Escherichia coli strain KAM42, and tested for transport of 25 antibacterial compounds, including representative antibiotics of various classes, antiseptics, dyes and detergents. Of the 15 tested putative transporters, STY0901, STY2458 and STY4874 exhibited a drug-resistance phenotype. Among these, STY4874...
Regulatory analysis for resolution of USI [Unresolved Safety Issue] A-47
International Nuclear Information System (INIS)
Szukiewicz, A.J.
1989-07-01
This report presents a summary of the regulatory analysis conducted by the US Nuclear Regulatory Commission staff to evaluate the value/impact of alternatives for the resolution of Unresolved Safety Issue A-47, ''Safety Implications of Control Systems.'' The NRC staff's resolution presented herein is based on these analyses and on the technical findings and conclusions presented in NUREG-1217, the companion document to this report. The staff has concluded that certain actions should be taken to improve safety in light-water reactor plants. The staff recommended that certain plants improve their control systems to preclude reactor vessel/steam generator overfill events and to prevent steam generator dryout, modify their technical specifications to verify operability of such systems, and modify selected emergency procedures to ensure safe shutdown of the plant following a small-break loss-of-coolant accident. This report was issued as a draft for public comment on May 27, 1988. As a result of the public comments received, this report was revised. The NRC staff's responses to and resolution of the public comments are included as Appendix C to the final report, NUREG-1217
Introduction to theory and analysis of resolved (and unresolved) neutron resonances via SAMMY
Energy Technology Data Exchange (ETDEWEB)
Larson, N.M.
1998-07-01
Neutron cross-section data are important for two distinct purposes: first, they provide insight into the nature of matter, thus assisting in the understanding of fundamental physics; second, they are needed for practical applications (e.g., for calculating when and how a reactor will become critical, or how much shielding is needed for storage of nuclear materials, and for medical applications). Neutron cross section data in the resolved-resonance region are generally obtained by time-of-flight experiments, which must be carefully analyzed if they are to be properly understood and utilized. In this paper, important features of the analysis process are discussed, with emphasis on the particular technique used in the analysis code SAMMY. Other features of the code are also described; these include such topics as calculation of group cross sections (including covariance matrices), generation and fitting of integral quantities, and extensions into the unresolved-resonance region and higher-energy regions.
Unresolved spectral structures emitted from heavy atom plasmas produced by short pulse laser
International Nuclear Information System (INIS)
Fraenkel, M.; Zigler, A.
1999-01-01
Spectra of rare earth elements emitted from ultra short pulse laser produced plasma were recorded using simultaneously high and low resolution, spectrometers. A study of the broad band emission of the Δn = 1 transitions in highly ionized Ba and Sm plasma showed that this band is completely unresolved. The spectra were analyzed using the LTE based on super-transition array (STA) model. The theory reconstructs the entire Ba spectrum using a single temperature and density, whereas for Sm the discrepancies between the theory and experiment are not reconcilable. The agreement in the Ba case is attributed to the fact that BaF 2 target is transparent to the laser's prepulse effects, producing a homogeneous dense plasma, whereas for Sm the dilute plasma created by the prepulse is far from LTE. The obtained results posses a significant implication to the applicability of the STA model, in particular for calculations of opacities and conversion of laser light to X-rays. (orig.)
Unresolved spectral structures emitted from heavy atom plasmas produced by short pulse laser
Energy Technology Data Exchange (ETDEWEB)
Fraenkel, M.; Zigler, A. [Hebrew Univ., Jerusalem (Israel). Racah Inst. of Physics; Bar-Shalom, A.; Oreg, J. [Israel Atomic Energy Commission, Beersheba (Israel). Nuclear Research Center-Negev; Faenov, A.Ya.; Pikuz, T.A. [Multicharged Ions Spectra Data Center of VNIIFTRI, Russian Committee of Standards Moscow region (Russian Federation)
1999-09-01
Spectra of rare earth elements emitted from ultra short pulse laser produced plasma were recorded using simultaneously high and low resolution, spectrometers. A study of the broad band emission of the {delta}n = 1 transitions in highly ionized Ba and Sm plasma showed that this band is completely unresolved. The spectra were analyzed using the LTE based on super-transition array (STA) model. The theory reconstructs the entire Ba spectrum using a single temperature and density, whereas for Sm the discrepancies between the theory and experiment are not reconcilable. The agreement in the Ba case is attributed to the fact that BaF{sub 2} target is transparent to the laser's prepulse effects, producing a homogeneous dense plasma, whereas for Sm the dilute plasma created by the prepulse is far from LTE. The obtained results posses a significant implication to the applicability of the STA model, in particular for calculations of opacities and conversion of laser light to X-rays. (orig.)
Directory of Open Access Journals (Sweden)
Sulan Luo
Full Text Available Conotoxins (CTxs selectively target a range of ion channels and receptors, making them widely used tools for probing nervous system function. Conotoxins have been previously grouped into superfamilies according to signal sequence and into families based on their cysteine framework and biological target. Here we describe the cloning and characterization of a new conotoxin, from Conus vexillum, named αB-conotoxin VxXXIVA. The peptide does not belong to any previously described conotoxin superfamily and its arrangement of Cys residues is unique among conopeptides. Moreover, in contrast to previously characterized conopeptide toxins, which are expressed initially as prepropeptide precursors with a signal sequence, a ''pro'' region, and the toxin-encoding region, the precursor sequence of αB-VxXXIVA lacks a ''pro'' region. The predicted 40-residue mature peptide, which contains four Cys, was synthesized in each of the three possible disulfide arrangements. Investigation of the mechanism of action of αB-VxXXIVA revealed that the peptide is a nicotinic acetylcholine receptor (nAChR antagonist with greatest potency against the α9α10 subtype. (1H nuclear magnetic resonance (NMR spectra indicated that all three αB-VxXXIVA isomers were poorly structured in aqueous solution. This was consistent with circular dichroism (CD results which showed that the peptides were unstructured in buffer, but adopted partially helical conformations in aqueous trifluoroethanol (TFE solution. The α9α10 nAChR is an important target for the development of analgesics and cancer chemotherapeutics, and αB-VxXXIVA represents a novel ligand with which to probe the structure and function of this protein.
International Nuclear Information System (INIS)
Agusa, Tetsuro; Iwata, Hisato; Fujihara, Junko; Kunito, Takashi; Takeshita, Haruo; Tu Binh Minh; Pham Thi Kim Trang; Pham Hung Viet; Tanabe, Shinsuke
2010-01-01
To elucidate the role of genetic factors in arsenic metabolism, we investigated associations of genetic polymorphisms in the members of glutathione S-transferase (GST) superfamily with the arsenic concentrations in hair and urine, and urinary arsenic profile in residents in the Red River Delta, Vietnam. Genotyping was conducted for GST ω1 (GSTO1) Ala140Asp, Glu155del, Glu208Lys, Thr217Asn, and Ala236Val, GST ω2 (GSTO2) Asn142Asp, GST π1 (GSTP1) Ile105Val, GST μ1 (GSTM1) wild/null, and GST θ1 (GSTT1) wild/null. There were no mutation alleles for GSTO1 Glu208Lys, Thr217Asn, and Ala236Val in this population. GSTO1 Glu155del hetero type showed higher urinary concentration of As V than the wild homo type. Higher percentage of DMA V in urine of GSTM1 wild type was observed compared with that of the null type. Strong correlations between GSTP1 Ile105Val and arsenic exposure level and profile were observed in this study. Especially, heterozygote of GSTP1 Ile105Val had a higher metabolic capacity from inorganic arsenic to monomethyl arsenic, while the opposite trend was observed for ability of metabolism from As V to As III . Furthermore, other factors including sex, age, body mass index, arsenic level in drinking water, and genotypes of As (+ 3 oxidation state) methyltransferase (AS3MT) were also significantly co-associated with arsenic level and profile in the Vietnamese. To our knowledge, this is the first study indicating the associations of genetic factors of GST superfamily with arsenic metabolism in a Vietnamese population.
Yakovleva, Lyudmila; Shuman, Stewart
2012-01-01
Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and...
A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily.
Sang, Pau Biak; Srinath, Thiruneelakantan; Patil, Aravind Goud; Woo, Eui-Jeon; Varshney, Umesh
2015-09-30
Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
International Nuclear Information System (INIS)
Sinitsa, V.V.
1984-11-01
The author gives a scheme for the calculation of the self-shielding factors in the unresolved resonance region using the GRUCON applied program package. This package is especially created to be used in the conversion of evaluated neutron cross-section data, as available in existing data libraries, into multigroup microscopic constants. A detailed description of the formulae and algorithms used in the programs is given. Some typical examples of calculation are considered and the results are compared with those of other authors. The calculation accuracy is better than 2%
Tsai, V W W; Lin, S; Brown, D A; Salis, A; Breit, S N
2016-02-01
Anorexia-cachexia associated with cancer and other diseases is a common and often fatal condition representing a large area of unmet medical need. It occurs most commonly in advanced cancer and is probably a consequence of molecules released by tumour cells, or tumour-associated interstitial or immune cells. These may then act directly on muscle to cause atrophy and/or may cause anorexia, which then leads to loss of both fat and lean mass. Although the aetiological triggers for this syndrome are not well characterized, recent data suggest that MIC-1/GDF15, a transforming growth factor-beta superfamily cytokine produced in large amounts by cancer cells and as a part of other disease processes, may be an important trigger. This cytokine acts on feeding centres in the hypothalamus and brainstem to cause anorexia leading to loss of lean and fat mass and eventually cachexia. In animal studies, the circulating concentrations of MIC-1/GDF15 required to cause this syndrome are similar to those seen in patients with advanced cancer, and at least some epidemiological studies support an association between MIC-1/GDF15 serum levels and measures of nutrition. This article will discuss its mechanisms of central appetite regulation, and the available data linking this action to anorexia-cachexia syndromes that suggest it is a potential target for therapy of cancer anorexia-cachexia and conversely may also be useful for the treatment of severe obesity.
DEFF Research Database (Denmark)
Miró-Julià, Cristina; Roselló, Sandra; Martínez, Vanesa G
2011-01-01
The scavenger receptor cysteine-rich superfamily (SRCR-SF) members are transmembrane and/or secreted receptors exhibiting one or several repeats of a cysteine-rich protein module of ∼100 aa, named scavenger receptor cysteine-rich (SRCR). Two types of SRCR domains (A or B) have been reported, which...... differ in the number of coding exons and intradomain cysteines. Although no unifying function has been reported for SRCR-SF members, recognition of pathogen-associated molecular patterns (PAMPs) was recently shown for some of them. In this article, we report the structural and functional characterization...
An analytic approach to probability tables for the unresolved resonance region
Brown, David; Kawano, Toshihiko
2017-09-01
The Unresolved Resonance Region (URR) connects the fast neutron region with the Resolved Resonance Region (RRR). The URR is problematic since resonances are not resolvable experimentally yet the fluctuations in the neutron cross sections play a discernible and technologically important role: the URR in a typical nucleus is in the 100 keV - 2 MeV window where the typical fission spectrum peaks. The URR also represents the transition between R-matrix theory used to described isolated resonances and Hauser-Feshbach theory which accurately describes the average cross sections. In practice, only average or systematic features of the resonances in the URR are known and are tabulated in evaluations in a nuclear data library such as ENDF/B-VII.1. Codes such as AMPX and NJOY can compute the probability distribution of the cross section in the URR under some assumptions using Monte Carlo realizations of sets of resonances. These probability distributions are stored in the so-called PURR tables. In our work, we begin to develop a scheme for computing the covariance of the cross section probability distribution analytically. Our approach offers the possibility of defining the limits of applicability of Hauser-Feshbach theory and suggests a way to calculate PURR tables directly from systematics for nuclei whose RRR is unknown, provided one makes appropriate assumptions about the shape of the cross section probability distribution.
Gazzaniga, David; Brenton, Ashley; Meshkin, Brian
2017-02-24
Precision medicine is a promising technology in patient care that combines genetic analysis with clinical data, such as health, behavioral, functional, environment, and lifestyle information. Here we present the case of a 54-year old woman who, following an accident, had uncontrolled chronic pain and was subsequently labeled a drug seeker. A 54-year-old white woman who was experiencing severe calf pain was referred for treatment. Her pain was insufficiently controlled immediately following knee arthroplasty with multiple opioid medications, as well as non-opioids. Precision medicine testing was ordered for her so that we could assess her pain sensitivity objectively to determine if the pill seeker designation was correct and to determine the best medications for her. Based on the Proove profiles, we determined that she had moderately low pain sensitivity, which means that clinically she may underreport pain and may have decreased medication needs. This result suggested that her continued reporting of unresolved pain was probably due to a condition unresolved by her right knee arthroplasty. In addition, she was found to be at low risk of opioid addiction, based on the Proove Opioid Risk Profile. Taken together, along with the high levels of pain she described, we determined that her pain was not properly controlled and that the designation of pill seeker was incorrect. The next step was to determine which medications and which doses would result in the most favorable outcomes for our patient. To determine this, we used the results of the Proove Opioid Response, Proove Drug Metabolism, and Proove Non-Opioid Profiles to guide her treatment. We reduced her pain medications to a single opioid, Vicodin (acetaminophen and hydrocodone), which also eliminated the adverse side effects she experienced. Precision medicine offers an important health care decision tool which can reduce emotional and physical costs to patients and may reduce the economic health care burden of
International Nuclear Information System (INIS)
Davis, A. B.
2007-01-01
A simple and effective framework is presented for modeling transport processes unfolding at computationally and/or observationally unresolved scales in scattering, absorbing and emitting media. The new approach acts directly on the spatial (i.e., propagation) part of the kernel in the integral formulation of the generic linear transport equation framed for stochastic media with a wide variety of spatial correlations, going far beyond the Markov-Poisson class used in the classic Pomraning-Levermore model. This statistical look at the extinction of un-collided particle beams takes us away from the standard exponential law of transmission. New transmission laws arise that are generally not exponential, often not even for asymptotically large jumps. This means that, from this perspective on random spatial variability, there is no 'effective medium' per se nor homogenization technique that can be used to describe the effects of unresolved fluctuations of the collision coefficient. However, one can still rewrite the transport equation, at least in its integral form, in a manner that looks like its counterpart for uniform media, but with a modified propagation kernel. Implementation in a Monte Carlo scheme is trivially simple and numerical results are presented that illustrate the bulk effect of the new parameterization for plane-parallel geometry. We survey time-domain diagnostics of solar radiative transfer in the Earth's cloudy atmosphere obtained recently from high-resolution ground-based spectroscopy, and it is shown that they are explained comprehensively by the new model. Finally, we discuss possible applications of this modeling framework in nuclear engineering. (authors)
Energy Technology Data Exchange (ETDEWEB)
Dinh, Thanh-Hung, E-mail: dinh@cc.utsunomiya-u.ac.jp; Suzuki, Yuhei; Arai, Goki; Higashiguchi, Takeshi, E-mail: higashi@cc.utsunomiya-u.ac.jp [Department of Electrical and Electronic Engineering, Faculty of Engineering and Center for Optical Research and Education (CORE), Utsunomiya University, Yoto 7-1-2, Utsunomiya, Tochigi 321-8585 (Japan); Li, Bowen [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Dunne, Padraig; O' Sullivan, Gerry [School of Physics, University College Dublin, Belfield, Dublin 4 (Ireland); Fujioka, Shinsuke [Institute of Laser Engineering, Osaka University, 2-6 Yamada-oka, Suita, Osaka 565-0871 (Japan); Hasegawa, Noboru; Kawachi, Tetsuya; Nishikino, Masaharu [Quantum Beam Science Center, Japan Atomic Energy Agency, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215 (Japan)
2015-09-21
We have characterized the spectral structure and the temporal history of the laser-produced high-Z multi-charged ion plasmas for the efficient water window soft x-ray sources. Strong unresolved transition array emission was observed due to 4d–4f and 4f–5g transitions from Au, Pb, and Bi plasmas in the 280–700 eV photon energy region. The temporal behavior of the emission was essentially similar of that of the laser pulse with a slight delay between different transitions. These results provide feedback for accurate modeling of the atomic processes with the radiative hydrodynamic simulations.
Mies, Anna; Platzbecker, Uwe
2017-07-01
Patients with lower-risk myelodysplastic syndromes (MDS) are mainly affected by chronic anemia and fatigue. Treatment strategies aim to improve anemia and quality of life, as well as iron overload due to red blood cell transfusion support. To promote proliferation and differentiation of erythropoiesis, erythropoiesis-stimulating agents (ESAs) such as erythropoietin (EPO) and mimetics are applied as first-line therapy in a large fraction of lower-risk MDS patients. In general, ESAs yield favorable responses in about half of the patients, although responses are often short-lived. In fact, many ESA-refractory patients harbor defects in late-stage erythropoiesis downstream of EPO action. Novel transforming growth factor (TGF)-β superfamily inhibitors sotatercept and luspatercept represent a promising approach to alleviate anemia by stimulating erythroid differentiation. Copyright © 2017 Elsevier Inc. All rights reserved.
Directory of Open Access Journals (Sweden)
N. V. Ryazantseva
2011-01-01
Full Text Available Abstract. A study was performed aiming to investigate interactions between TNFα receptor (TNF1 superfamily and heat shock protein Hsp90, using a Jurkat tumor cell line. The tumor cells cultured in presence of Hsp90 inhibitor (17-AAG showed increased numbers of cells, presenting surface TNFR1 and FasR, which facilitate triggering of programmed cell death. It was also revealed that Hsp90 blockage under the in vitro conditions causes a decrease in FasL, while not affecting TNFα and sTNFR1 production by the tumor cells. (Med. Immunol., 2011, vol. 13, N 2-3, pp 247-252
Cross-modal links among vision, audition, and touch in complex environments.
Ferris, Thomas K; Sarter, Nadine B
2008-02-01
This study sought to determine whether performance effects of cross-modal spatial links that were observed in earlier laboratory studies scale to more complex environments and need to be considered in multimodal interface design. It also revisits the unresolved issue of cross-modal cuing asymmetries. Previous laboratory studies employing simple cues, tasks, and/or targets have demonstrated that the efficiency of processing visual, auditory, and tactile stimuli is affected by the modality, lateralization, and timing of surrounding cues. Very few studies have investigated these cross-modal constraints in the context of more complex environments to determine whether they scale and how complexity affects the nature of cross-modal cuing asymmetries. Amicroworld simulation of battlefield operations with a complex task set and meaningful visual, auditory, and tactile stimuli was used to investigate cuing effects for all cross-modal pairings. Significant asymmetric performance effects of cross-modal spatial links were observed. Auditory cues shortened response latencies for collocated visual targets but visual cues did not do the same for collocated auditory targets. Responses to contralateral (rather than ipsilateral) targets were faster for tactually cued auditory targets and each visual-tactile cue-target combination, suggesting an inhibition-of-return effect. The spatial relationships between multimodal cues and targets significantly affect target response times in complex environments. The performance effects of cross-modal links and the observed cross-modal cuing asymmetries need to be examined in more detail and considered in future interface design. The findings from this study have implications for the design of multimodal and adaptive interfaces and for supporting attention management in complex, data-rich domains.
Relative Stabilities of Conserved and Non-Conserved Structures in the OB-Fold Superfamily
Directory of Open Access Journals (Sweden)
Andrei T. Alexandrescu
2009-05-01
Full Text Available The OB-fold is a diverse structure superfamily based on a β-barrel motif that is often supplemented with additional non-conserved secondary structures. Previous deletion mutagenesis and NMR hydrogen exchange studies of three OB-fold proteins showed that the structural stabilities of sites within the conserved β-barrels were larger than sites in non-conserved segments. In this work we examined a database of 80 representative domain structures currently classified as OB-folds, to establish the basis of this effect. Residue-specific values were obtained for the number of Cα-Cα distance contacts, sequence hydrophobicities, crystallographic B-factors, and theoretical B-factors calculated from a Gaussian Network Model. All four parameters point to a larger average flexibility for the non-conserved structures compared to the conserved β-barrels. The theoretical B-factors and contact densities show the highest sensitivity.Our results suggest a model of protein structure evolution in which novel structural features develop at the periphery of conserved motifs. Core residues are more resistant to structural changes during evolution since their substitution would disrupt a larger number of interactions. Similar factors are likely to account for the differences in stability to unfolding between conserved and non-conserved structures.
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Harshavardhanan Vijayakumar
2016-07-01
Full Text Available Plants, as sessile organisms, can suffer serious growth and developmental consequences under cold stress conditions. Glutathione transferases (GSTs, EC 2.5.1.18 are ubiquitous and multifunctional conjugating proteins, which play a major role in stress responses by preventing oxidative damage by reactive oxygen species (ROS. Currently, understanding of their function(s during different biochemical and signaling pathways under cold stress condition remain unclear. In this study, using combined computational strategy, we identified 65 Brassica oleracea glutathione transferases (BoGST and characterized them based on evolutionary analysis into 11 classes. Inter-species and intra-species duplication was evident between BoGSTs and Arabidopsis GSTs. Based on localization analyses, we propose possible pathways in which GST genes are involved during cold stress. Further, expression analysis of the predicted putative functions for GST genes were investigated in two cold contrasting genotypes (cold tolerance and susceptible under cold condition, most of these genes were highly expressed at 6 h and 1 h in the cold tolerant (CT and cold susceptible (CS lines, respectively. Overall, BoGSTU19, BoGSTU24, BoGSTF10 are candidate genes highly expressed in B. oleracea. Further investigation of GST superfamily in B. oleracea will aid in understanding complex mechanism underlying cold tolerance in plants.
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Zhihua Hua
Full Text Available The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of F-Box (FBX genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811 FBX loci from 18 plant species, ranging from the alga Chlamydomonas reinhardtii to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of FBX loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for Carica papaya to as many as 1350 predicted for Arabidopsis lyrata. This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of FBX genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous FBX loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of FBX genes in each species. Taken together, it appears that the FBX superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid
Liu, Mu; Liu, Jun; Wang, Wei Min
2012-10-01
A novel major facilitator superfamily (MFS) transporter gene, Thmfs1, was isolated from Trichoderma harzianum (T. harzianum). A Thmfs1 over-expressing mutant displayed enhanced antifungal activity and fungicide tolerance, while the Thmfs1 disruption mutant showed the opposite trend. Trichodermin production in Thmfs1 disruption group (185 mg l(-1)) was decreased by less than 17 % compared to the parental strain, suggesting that Thmfs1 is not mainly responsible for trichodermin secretion. Real-time PCR showed that Thmfs1 transcript level could be induced by a certain range of trichodermin concentrations, while expression of Tri5, encoding a trichodiene synthase, was strongly inhibited under these conditions. To our knowledge, Thmfs1 is the first MFS transporter gene identified in T. harzianum.
Durairaj, Rajesh; Pageat, Patrick; Bienboire-Frosini, Cécile
2018-01-01
The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches. We also report that the evolutionary tree of the SCGB superfamily comprises seven unique palm-like clusters, showing the evolutionary pattern and divergence time tree of Fel d 1 with 28 ABP paralogs. Three ABP subunits (A27, BG27, and BG26) share phylogenetic relationships with Fel d 1 chains. The Fel d 1 and ABP subunits show similarities in terms of sequence conservation, identical motifs and binding site clefts. Topologically equivalent positions were visualized through superimposition of ABP A27:BG27 (AB) and ABP A27:BG26 (AG) dimers on a heterodimeric Fel d 1 model. In docking, Fel d 1-ABP dimers exhibit the maximum surface binding ability of AG compared with that of AB dimers and the several polar interactions between ABP dimers with steroids. Hence, cat Fel d 1 is an ABP-like molecule in which monomeric chains 1 and 2 are the equivalent of the ABPA and ABPBG monomers, respectively. These findings suggest that the biological and molecular function of Fel d 1 is similar to that of ABP in chemical communication, possibly via pheromone and/or steroid binding.
Pageat, Patrick; Bienboire-Frosini, Cécile
2018-01-01
The mammalian secretoglobin (SCGB) superfamily contains functionally diverse members, among which the major cat allergen Fel d 1 and mouse salivary androgen-binding protein (ABP) display similar subunits. We searched for molecular similarities between Fel d 1 and ABP to examine the possibility that they play similar roles. We aimed to i) cluster the evolutionary relationships of the SCGB superfamily; ii) identify divergence patterns, structural overlap, and protein-protein docking between Fel d 1 and ABP dimers; and iii) explore the residual interaction between ABP dimers and steroid binding in chemical communication using computational approaches. We also report that the evolutionary tree of the SCGB superfamily comprises seven unique palm-like clusters, showing the evolutionary pattern and divergence time tree of Fel d 1 with 28 ABP paralogs. Three ABP subunits (A27, BG27, and BG26) share phylogenetic relationships with Fel d 1 chains. The Fel d 1 and ABP subunits show similarities in terms of sequence conservation, identical motifs and binding site clefts. Topologically equivalent positions were visualized through superimposition of ABP A27:BG27 (AB) and ABP A27:BG26 (AG) dimers on a heterodimeric Fel d 1 model. In docking, Fel d 1-ABP dimers exhibit the maximum surface binding ability of AG compared with that of AB dimers and the several polar interactions between ABP dimers with steroids. Hence, cat Fel d 1 is an ABP-like molecule in which monomeric chains 1 and 2 are the equivalent of the ABPA and ABPBG monomers, respectively. These findings suggest that the biological and molecular function of Fel d 1 is similar to that of ABP in chemical communication, possibly via pheromone and/or steroid binding. PMID:29771985
International Nuclear Information System (INIS)
1977-12-01
This report provides a description of the Nuclear Regulatory Commission's Program for the Resolution of Generic Issues Related to Nuclear Power Plants. The NRC program is of considerably broader scope than the ''Unresolved Safety Issues Plan'' required by Section 210. The NRC program does include plans for the resolution of ''Unresolved Safety Issues''; however, in addition, it includes generic tasks for the resolution of environmental issues, for the development of improvements in the reactor licensing process and for consideration of less conservative design criteria or operating limitations in areas where over conservatisms may be unnecessarily restrictive or costly
Reid, Anna-Jean M; Budge, Suzanne M
2015-01-01
Heightened awareness of the health benefits of fish oil consumption has led to a great increase in the number of fish oil supplements available to the consumer. Therefore manufacturers are continually looking for ways to distinguish their products from those of competitors. Minimally refined or virgin fish oils provide a unique feature; however, petroleum hydrocarbon contamination from oil spills is a reality in the world's oceans. The question arises whether oil produced from fish species caught in these polluted areas is free of petroleum hydrocarbons, with particular interest in unresolved complex mixtures (UCMs). This study investigates the presence of UCMs in commercially available fish oil supplements advertised as being virgin, as well as refined. Weathered petroleum hydrocarbons in the form of a UCM were found at 523 µg g(-1) in a virgin Alaskan salmon oil supplement. Supplements that were refined were free of this contamination. Fish used in the production of fish oil supplements appear to have accumulated petrogenic hydrocarbons in their tissues which were not removed by minimal oil refining. Further study is required to determine if there are any health implications associated with long-term consumption of these contaminated supplements. © 2014 Society of Chemical Industry.
Wilson, Mark A.; Amour, Courtney V. St.; Collins, Jennifer L.; Ringe, Dagmar; Petsko, Gregory A.
2004-01-01
The yeast gene YDR533C encodes a protein belonging to the DJ-1/ThiJ/PfpI superfamily. This family includes the human protein DJ-1, which is mutated in autosomal recessive early-onset Parkinson's disease. The function of DJ-1 and its yeast homologue YDR533Cp is unknown. We report here the crystal structure of YDR533Cp at 1.8-Å resolution. The structure indicates that the closest relative to YDR533Cp is the Escherichia coli heat shock protein Hsp31 (YedU), which has both chaperone and protease activity. As expected, the overall fold of the core domain of YDR533Cp is also similar to that of DJ-1 and the bacterial protease PfpI. YDR533Cp contains a possible catalytic triad analogous to that of Hsp31 and an additional domain that is present in Hsp31 but is not seen in DJ-1 and other members of the family. The cysteine in this triad (Cys-138) is oxidized in this crystal structure, similar to modifications seen in the corresponding cysteine in the crystal structure of DJ-1. YDR533Cp appears to be a dimer both in solution and the crystal, but this dimer is formed by a different interface than that found in Hsp31 or other members of the superfamily. PMID:14745011
An analytic approach to probability tables for the unresolved resonance region
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Brown David
2017-01-01
Full Text Available The Unresolved Resonance Region (URR connects the fast neutron region with the Resolved Resonance Region (RRR. The URR is problematic since resonances are not resolvable experimentally yet the fluctuations in the neutron cross sections play a discernible and technologically important role: the URR in a typical nucleus is in the 100 keV – 2 MeV window where the typical fission spectrum peaks. The URR also represents the transition between R-matrix theory used to described isolated resonances and Hauser-Feshbach theory which accurately describes the average cross sections. In practice, only average or systematic features of the resonances in the URR are known and are tabulated in evaluations in a nuclear data library such as ENDF/B-VII.1. Codes such as AMPX and NJOY can compute the probability distribution of the cross section in the URR under some assumptions using Monte Carlo realizations of sets of resonances. These probability distributions are stored in the so-called PURR tables. In our work, we begin to develop a scheme for computing the covariance of the cross section probability distribution analytically. Our approach offers the possibility of defining the limits of applicability of Hauser-Feshbach theory and suggests a way to calculate PURR tables directly from systematics for nuclei whose RRR is unknown, provided one makes appropriate assumptions about the shape of the cross section probability distribution.
Svrbicka, Alexandra; Toth Hervay, Nora; Gbelska, Yvetta
2016-03-01
Boron is an essential micronutrient for living cells, yet its excess causes toxicity. To date, the mechanisms of boron toxicity are poorly understood. Recently, the ScATR1 gene has been identified encoding the main boron efflux pump in Saccharomyces cerevisiae. In this study, we analyzed the ScATR1 ortholog in Kluyveromyces lactis--the KNQ1 gene, to understand whether it participates in boron stress tolerance. We found that the KNQ1 gene, encoding a permease belonging to the major facilitator superfamily, is required for K. lactis boron tolerance. Deletion of the KNQ1 gene led to boron sensitivity and its overexpression increased K. lactis boron tolerance. The KNQ1 expression was induced by boron and the intracellular boron concentration was controlled by Knq1p. The KNQ1 promoter contains two putative binding motifs for the AP-1-like transcription factor KlYap1p playing a central role in oxidative stress defense. Our results indicate that the induction of the KNQ1 expression requires the presence of KlYap1p and that Knq1p like its ortholog ScAtr1p in S. cerevisiae functions as a boron efflux pump providing boron resistance in K. lactis.
Sun, Miao-Miao; Han, Liang; Zhang, Fu-Kai; Zhou, Dong-Hui; Wang, Shu-Qing; Ma, Jun; Zhu, Xing-Quan; Liu, Guo-Hua
2018-01-01
Marshallagia marshalli (Nematoda: Trichostrongylidae) infection can lead to serious parasitic gastroenteritis in sheep, goat, and wild ruminant, causing significant socioeconomic losses worldwide. Up to now, the study concerning the molecular biology of M. marshalli is limited. Herein, we sequenced the complete mitochondrial (mt) genome of M. marshalli and examined its phylogenetic relationship with selected members of the superfamily Trichostrongyloidea using Bayesian inference (BI) based on concatenated mt amino acid sequence datasets. The complete mt genome sequence of M. marshalli is 13,891 bp, including 12 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes. All protein-coding genes are transcribed in the same direction. Phylogenetic analyses based on concatenated amino acid sequences of the 12 protein-coding genes supported the monophylies of the families Haemonchidae, Molineidae, and Dictyocaulidae with strong statistical support, but rejected the monophyly of the family Trichostrongylidae. The determination of the complete mt genome sequence of M. marshalli provides novel genetic markers for studying the systematics, population genetics, and molecular epidemiology of M. marshalli and its congeners.
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Chiguang Feng
2017-06-01
Full Text Available Neuraminidases (NAs are critical virulence factors for several microbial pathogens. With a highly conserved catalytic domain, a microbial NA “superfamily” has been proposed. We previously reported that murine polymorphonuclear leukocyte (PMN sialidase activity was important in leukocyte trafficking to inflamed sites and that antibodies to Clostridium perfringens NA recognized a cell surface molecule(s, presumed to be a sialidase of eukaryotic origin on interleukin-8-stimulated human and murine PMNs. These antibodies also inhibited cell sialidase activity both in vitro and, in the latter instance, in vivo. We therefore hypothesized that mammalian sialidases share structural homology and epitopes with microbial NAs. We now report that antibodies to one of the isoforms of C. perfringens NA, as well as anti-influenza virus NA serum, recognize human NEU3 but not NEU1 and that antibodies to C. perfringens NA inhibit NEU3 enzymatic activity. We conclude that the previously described microbial NA superfamily extends to human sialidases. Strategies designed to therapeutically inhibit microbial NA may need to consider potential compromising effects on human sialidases, particularly those expressed in cells of the immune system.
Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques
Günther, Torsten; Valdiosera, Cristina; Malmström, Helena; Ureña, Irene; Rodriguez-Varela, Ricardo; Sverrisdóttir, Óddny Osk; Daskalaki, Evangelia A.; Skoglund, Pontus; Naidoo, Thijessen; Svensson, Emma M.; Bermúdez de Castro, José María; Carbonell, Eudald; Dunn, Michael; Storå, Jan; Iriarte, Eneko; Arsuaga, Juan Luis; Carretero, José-Miguel; Götherström, Anders; Jakobsson, Mattias
2015-01-01
The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modern-day people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, the first genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history of Iberia and Europe and reveal how prehistoric groups relate to modern-day people. PMID:26351665
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Acely Garza-Garcia
Full Text Available BACKGROUND: Following the amputation of a limb, newts and salamanders have the capability to regenerate the lost tissues via a complex process that takes place at the site of injury. Initially these cells undergo dedifferentiation to a state competent to regenerate the missing limb structures. Crucially, dedifferentiated cells have memory of their level of origin along the proximodistal (PD axis of the limb, a property known as positional identity. Notophthalmus viridescens Prod1 is a cell-surface molecule of the three-finger protein (TFP superfamily involved in the specification of newt limb PD identity. The TFP superfamily is a highly diverse group of metazoan proteins that includes snake venom toxins, mammalian transmembrane receptors and miscellaneous signaling molecules. METHODOLOGY/PRINCIPAL FINDINGS: With the aim of identifying potential orthologs of Prod1, we have solved its 3D structure and compared it to other known TFPs using phylogenetic techniques. The analysis shows that TFP 3D structures group in different categories according to function. Prod1 clusters with other cell surface protein TFP domains including the complement regulator CD59 and the C-terminal domain of urokinase-type plasminogen activator. To infer orthology, a structure-based multiple sequence alignment of representative TFP family members was built and analyzed by phylogenetic methods. Prod1 has been proposed to be the salamander CD59 but our analysis fails to support this association. Prod1 is not a good match for any of the TFP families present in mammals and this result was further supported by the identification of the putative orthologs of both CD59 and N. viridescens Prod1 in sequence data for the salamander Ambystoma tigrinum. CONCLUSIONS/SIGNIFICANCE: The available data suggest that Prod1, and thereby its role in encoding PD identity, is restricted to salamanders. The lack of comparable limb-regenerative capability in other adult vertebrates could be
Unresolved transition array based water window soft x-ray source by laser-produced high-Z plasma
International Nuclear Information System (INIS)
Higashiguchi, Takeshi; Dunne, Padraig; O'Sullivan, Gerry
2013-01-01
We demonstrate a table-top broadband emission water window source based on laser-produced high-Z plasmas. resonance emission from multiply charged ions merges to produce intense unresolved transition arrays (UTAs) in the 2 to 4 nm region, extending below the carbon K edge (4.37 nm). Arrays resulting from n=4-n=4 transitions are overlaid with n=4-n=5 emission and shift to shorter wavelength with increasing atomic number. An outline of a microscope design for single-shot live cell imaging is proposed based on a bismuth plasma UTA source, coupled to multilayer mirror optics. At power densities available from 'table-top' solid-state lasers, comparison of emission from a number of targets has shown that 3d-4f UTA in zirconium plasmas have highest overall brightness and in an imaging system based on reflective multilayer mirrors, may, depending on bandwidth, have superior performance than either line or broader-band sources. (author)
International Nuclear Information System (INIS)
Rubin, A.M.
1986-01-01
''Station Blackout'' is the complete loss of alternating current (ac) electric power to the essential and nonessential buses in a nuclear power plant; it results when both offsite power and the onsite emergency ac power systems are unavailable. Because many safety systems required for reactor core decay heat removal and containment heat removal depend on ac power, the consequences of a station blackout could be severe. Because of the concern about the frequency of loss of offsite power, the number of failures of emergency diesel generators, and the potentially severe consequences of a loss of all ac power, ''Station Blackout'' was designated as Unresolved Safety Issue (USI) A-44. This report presents the regulatory analysis for USI A-44. It includes: (1) a summary of the issue, (2) the proposed technical resolution, (3) alternative resolutions considered by the Nuclear Regulatory Commission (NRC) staff, (4) an assessment of the benefits and costs of the recommended resolution, (5) the decision rationale, and (6) the relationship between USI A-44 and other NRC programs and requirements
Jones, Jason D; Cassidy, Jude; Shaver, Phillip R
2015-02-01
For decades, attachment scholars have been investigating how parents' adult attachment orientations relate to the ways in which they parent. Traditionally, this research has been conducted by developmental and clinical psychologists who typically employ the Adult Attachment Interview (AAI) to measure adult attachment. However, dating back to the mid-1990s, social and personality psychologists have been investigating how self-reported adult attachment styles relate to various facets of parenting. The literature on self-reported attachment and parenting has received less attention than AAI research on the same topic and, to date, there is no comprehensive review of this literature. In this article, we review more than 60 studies of the links between self-reported attachment styles and parenting, integrate the findings to reach general conclusions, discuss unresolved questions, and suggest future directions. Finally, we discuss the potential benefits to the study of parenting of collaborations among researchers from the developmental and social attachment research traditions. © 2014 by the Society for Personality and Social Psychology, Inc.
Jones, Jason D.; Cassidy, Jude; Shaver, Phillip. R.
2014-01-01
For decades, attachment scholars have been investigating how parents’ adult attachment orientations relate to the ways in which they parent. Traditionally, this research has been conducted by developmental and clinical psychologists who typically employ the Adult Attachment Interview (AAI) to measure adult attachment. However, dating back to the mid-1990s, social and personality psychologists have been investigating how self-reported adult attachment styles relate to various facets of parenting. The literature on self-reported attachment and parenting has received less attention than AAI research on the same topic and, to date, there is no comprehensive review of this literature. In this article, we review over 60 studies of the links between self-reported attachment styles and parenting, integrate the findings to reach general conclusions, discuss unresolved questions, and suggest future directions. Finally, we discuss the potential benefits to the study of parenting of collaborations among researchers from the developmental and social attachment research traditions. PMID:25024278
Could a Change in Diet Revitalize Children Who Suffer from Unresolved Fatigue?
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Tessa Gerjanne Steenbruggen
2015-03-01
Full Text Available Many children deal with fatigue for which no proper treatment can be given. A possible explanation for their fatigue is a micro deficiency of minerals and vitamins. In this non-randomized controlled trial, we clinically evaluated symptoms of fatigue in children for whom a nutrient-rich diet was advised. A group of 98 children (2–18 years old with unexplained symptoms of fatigue was examined. The dietary modifications consisted of green vegetables, beef, whole milk and full-fat butter. Children in the intervention group were asked to follow the diet for three months, whereas the control-group followed their normal diet. The primary outcome was symptoms of fatigue, as determined by a PedsQL Multidimensional Fatigue Scale, and secondary outcomes were compliance with the diet and BMI. Children, who followed the diet showed a significant decrease in the need to sleep (CI 0.83; 14.86, p = 0.03. They slept better through the night and took fewer naps. When analyzing components of the advised diet separately, a significant larger decrease in cognitive fatigue symptoms was seen for eating green vegetables according to the diet guidelines (CI 2.27; 30.63, p = 0.024. Furthermore, a lower need to sleep was seen when whole milk was consumed almost daily (CI 0.02; 14.62, p = 0.049. Our study showed that nutritional advice is an elegant, and effective method for decreasing some symptoms of medically unresolved fatigue in children.
Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude
2011-06-20
One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.
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Martin Juliette
2011-06-01
Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.
Ersoy, Baran A; Tarun, Akansha; D'Aquino, Katharine; Hancer, Nancy J; Ukomadu, Chinweike; White, Morris F; Michel, Thomas; Manning, Brendan D; Cohen, David E
2013-07-30
Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenced by insulin-independent IRS2 activation after knockdown, genetic ablation, or chemical inhibition of PC-TP. In addition, IRS2 was activated after knockdown of THEM2, providing support for a role for the interaction of PC-TP with THEM2 in suppressing insulin signaling. Additionally, we showed that PC-TP bound to tuberous sclerosis complex 2 (TSC2) and stabilized the components of the TSC1-TSC2 complex, which functions to inhibit mTORC1. Preventing phosphatidylcholine from binding to PC-TP disrupted interactions of PC-TP with THEM2 and TSC2, and disruption of the PC-TP-THEM2 complex was associated with increased activation of both IRS2 and mTORC1. In livers of mice with genetic ablation of PC-TP or that had been treated with a PC-TP inhibitor, steady-state amounts of IRS2 were increased, whereas those of TSC2 were decreased. These findings reveal a phospholipid-dependent mechanism that suppresses insulin signaling downstream of its receptor.
Endolysosomal Cation Channels and Cancer—A Link with Great Potential
Grimm, Christian; Bartel, Karin; Vollmar, Angelika M.; Biel, Martin
2018-01-01
The endolysosomal system (ES) consists of lysosomes; early, late, and recycling endosomes; and autophagosomes. It is a key regulator not only of macromolecule degradation and recycling, plasma membrane repair, homeostasis, and lipid storage, but also of antigen presentation, immune defense, cell motility, cell death signaling, tumor growth, and cancer progression. In addition, it plays a critical role in autophagy, and the autophagy-lysosome pathway is intimately associated with the hallmarks of cancer, such as escaping cell death pathways, evading immune surveillance, and deregulating metabolism. The function of endolysosomes is critically dependent on both soluble and endolysosomal membrane proteins such as ion channels and transporters. Cation channels found in the ES include members of the TRP (transient receptor potential) channel superfamily, namely TRPML channels (mucolipins) as well as two-pore channels (TPCs). In recent studies, these channels have been found to play crucial roles in endolysosomal trafficking, lysosomal exocytosis, and autophagy. Mutation or loss of these channel proteins can impact multiple endolysosomal trafficking pathways. A role for TPCs in cancer cell migration and metastasis, linked to distinct defects in endolysosomal trafficking such as integrin trafficking, has been recently established. In this review, we give an overview on the function of lysosomes in cancer with a particular focus on the roles which TPCs and TRPML channels play in the ES and how this can affect cancer cells. PMID:29303993
Endolysosomal Cation Channels and Cancer-A Link with Great Potential.
Grimm, Christian; Bartel, Karin; Vollmar, Angelika M; Biel, Martin
2018-01-05
The endolysosomal system (ES) consists of lysosomes; early, late, and recycling endosomes; and autophagosomes. It is a key regulator not only of macromolecule degradation and recycling, plasma membrane repair, homeostasis, and lipid storage, but also of antigen presentation, immune defense, cell motility, cell death signaling, tumor growth, and cancer progression. In addition, it plays a critical role in autophagy, and the autophagy-lysosome pathway is intimately associated with the hallmarks of cancer, such as escaping cell death pathways, evading immune surveillance, and deregulating metabolism. The function of endolysosomes is critically dependent on both soluble and endolysosomal membrane proteins such as ion channels and transporters. Cation channels found in the ES include members of the TRP (transient receptor potential) channel superfamily, namely TRPML channels (mucolipins) as well as two-pore channels (TPCs). In recent studies, these channels have been found to play crucial roles in endolysosomal trafficking, lysosomal exocytosis, and autophagy. Mutation or loss of these channel proteins can impact multiple endolysosomal trafficking pathways. A role for TPCs in cancer cell migration and metastasis, linked to distinct defects in endolysosomal trafficking such as integrin trafficking, has been recently established. In this review, we give an overview on the function of lysosomes in cancer with a particular focus on the roles which TPCs and TRPML channels play in the ES and how this can affect cancer cells.
Expanding Horizons and Unresolved Conundrums: Language Testing and Assessment
Leung, Constant; Lewkowicz, Jo
2006-01-01
Since the last "TESOL Quarterly" commemorative issue 15 years ago, there have been too many important developments in language testing and assessment for all of them to be discussed in a single article. Therefore, this article focuses on issues that we believe are integrally linked to pedagogic and curriculum concerns of English language teaching.…
Quiles-Puchalt, Nuria; Tormo-Más, María Ángeles; Campoy, Susana; Toledo-Arana, Alejandro; Monedero, Vicente; Lasa, Íñigo; Novick, Richard P.; Christie, Gail E.; Penadés, José R.
2013-01-01
The propagation of bacteriophages and other mobile genetic elements requires exploitation of the phage mechanisms involved in virion assembly and DNA packaging. Here, we identified and characterized four different families of phage-encoded proteins that function as activators required for transcription of the late operons (morphogenetic and lysis genes) in a large group of phages infecting Gram-positive bacteria. These regulators constitute a super-family of proteins, here named late transcriptional regulators (Ltr), which share common structural, biochemical and functional characteristics and are unique to this group of phages. They are all small basic proteins, encoded by genes present at the end of the early gene cluster in their respective phage genomes and expressed under cI repressor control. To control expression of the late operon, the Ltr proteins bind to a DNA repeat region situated upstream of the terS gene, activating its transcription. This involves the C-terminal part of the Ltr proteins, which control specificity for the DNA repeat region. Finally, we show that the Ltr proteins are the only phage-encoded proteins required for the activation of the packaging and lysis modules. In summary, we provide evidence that phage packaging and lysis is a conserved mechanism in Siphoviridae infecting a wide variety of Gram-positive bacteria. PMID:23771138
Ma, Xueyan; Koepke, Juergen; Bayer, Anja; Linhard, Verena; Fritzsch, Günter; Zhang, Bin; Michel, Hartmut; Stöckigt, Joachim
2004-09-01
Crystals of vinorine synthase (VS) from medicinal plant Rauvolfia serpentina expressed in Escherichia coli have been obtained by the hanging-drop technique at 305 K with ammonium sulfate and PEG 400 as precipitants. The enzyme is involved in the biosynthesis of the antiarrhythmic drug ajmaline and is a member of the BAHD superfamily of acyltransferases. So far, no three-dimensional structure of a member of this enzyme family is known. The crystals belong to the space group P2(1)2(1)2(1) with cell dimensions of a=82.3 A, b=89.6 A and c=136.2 A. Under cryoconditions (120 K), a complete data set up to 2.8 A was collected at a synchrotron source.
International Nuclear Information System (INIS)
1985-10-01
This report summarizes key technical findings related to Unresolved Safety Issue (USI) A-43, Containment Emergency Sump Performance. Both BWRs and PWRs are considered in this report. Emergency core cooling systems require a clean, reliable water source to maintain long-term recirculation following a loss-of-coolant accident (LOCA). PWRs rely on the containment emergency sump to provide such a water supply to residual heat removal pumps and containment spray pumps. BWRs rely on pump suction intakes in the suppression pool or wet well to provide water to residual heat removal and core spray systems. Thus, the technical findings in this report provide information on post-LOCA recirculation. These findings have been derived from extensive experimental studies, generic plant studies, and assessments of sumps used for long-term cooling. Results of hydraulic tests have shown that the potential for air ingestion is less severe than previously hypothesized. The effects of debris blockage on NPSH margin must be dealt with on a plant-specific basis. These findings have been used to develop revisions to Regulatory Guide 1.82 and Standard Review Plan Section 6.2.2 (NUREG-0800)
Arturi, F; Scarpelli, D; Coco, A; Sacco, R; Bruno, R; Filetti, S; Russo, D
2003-04-01
Ten years after the first description of activating mutations in the thyroid stimulating hormone receptor (TSHR) gene in sporadic autonomous hyperfunctioning thyroid adenomas, there is general agreement in assigning a major pathogenic role of this genetic abnormality, acting via the constitutive activation of the cAMP pathway, in both the growth and functional characteristic of these tumours. From the beginning, however, the pathophysiological and clinical relevance of somatic TSHR mutations has been debated and some arguments still exist against a fully causative role of these mutations and the practical value of detecting these mutations for the diagnosis, treatment and prognosis of thyroid hot nodules. Some major issues will be examined herein, including (a) the frequency of TSHR alterations in various reports showing that the genetic abnormality underlying the pathogenesis of a substantial subset of thyroid tumours has yet to be identified; (b) the limitations of the present experimental models, which suggest greater caution in the interpretation of in vitro results; (c) the still unresolved question of absence of genotype-phenotype correlation. Clarification of these issues may hopefully provide new and useful tools for improving the clinical management of this disease.
Steering Through: How organizations negotiate permanent uncertainty and unresolvable choices
P.V. Poruthiyil (Prabhir Vishnu)
2011-01-01
textabstractIt is easy to observe instances of contradictions and dilemmas that multinational companies, public bureaucracies, and individuals encounter as they seek resources and markets in a globally-linked world. The default condition for such entities is that they are being constantly stretched
Energy Technology Data Exchange (ETDEWEB)
Brooks, David H. [College of Science, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States); Reep, Jeffrey W.; Warren, Harry P. [Space Science Division, Naval Research Laboratory, Washington, DC 20375 (United States)
2016-08-01
Recent observations from the Interface Region Imaging Spectrograph ( IRIS ) have discovered a new class of numerous low-lying dynamic loop structures, and it has been argued that they are the long-postulated unresolved fine structures (UFSs) that dominate the emission of the solar transition region. In this letter, we combine IRIS measurements of the properties of a sample of 108 UFSs (intensities, lengths, widths, lifetimes) with one-dimensional non-equilibrium ionization simulations, using the HYDRAD hydrodynamic model to examine whether the UFSs are now truly spatially resolved in the sense of being individual structures rather than being composed of multiple magnetic threads. We find that a simulation of an impulsively heated single strand can reproduce most of the observed properties, suggesting that the UFSs may be resolved, and the distribution of UFS widths implies that they are structured on a spatial scale of 133 km on average. Spatial scales of a few hundred kilometers appear to be typical for a range of chromospheric and coronal structures, and we conjecture that this could be an important clue for understanding the coronal heating process.
Desimone, Marcelo; Catoni, Elisabetta; Ludewig, Uwe; Hilpert, Melanie; Schneider, Anja; Kunze, Reinhard; Tegeder, Mechthild; Frommer, Wolf Bernd; Schumacher, Karin
2002-01-01
A wide spectrum of soil heterocyclic nitrogen compounds are potential nutrients for plants. Here, it is shown that Arabidopsis plants are able to use allantoin as sole nitrogen source. By functional complementation of a yeast mutant defective in allantoin uptake, an Arabidopsis transporter, AtUPS1 (Arabidopsis thaliana ureide permease 1), was identified. AtUPS1 belongs to a novel superfamily of plant membrane proteins with five open reading frames in Arabidopsis (identity, 64 to 82%). UPS proteins have 10 putative transmembrane domains with a large cytosolic central domain containing a “Walker A” motif. Transport of 14C-labeled allantoin by AtUPS1 in yeast exhibited saturation kinetics (Km ∼ 52 μM), was dependent on Glc and a proton gradient, and was stimulated by acidic pH. AtUPS1 transports uric acid and xanthine, besides allantoin, but not adenine. Protons are cosubstrates in allantoin transport by AtUPS1, as demonstrated by expression in Xenopus laevis oocytes. In plants, AtUPS1 gene expression was dependent on the nitrogen source. Therefore, AtUPS1 presumably is involved in the uptake of allantoin and other purine degradation products when primary sources are limiting. PMID:11971139
Energy Technology Data Exchange (ETDEWEB)
Calinisan, Venice; Gravem, Dana; Chen, Ray Ping-Hsu; Brittin,Sachi; Mohandas, Narla; Lecomte, Marie-Christine; Gascard, Philippe
2005-06-17
Members of the protein 4.1 family of adapter proteins are expressed in a broad panel of tissues including various epithelia where they likely play an important role in maintenance of cell architecture and polarity and in control of cell proliferation. We have recently characterized the structure and distribution of three members of the protein 4.1 family, 4.1B, 4.1R and 4.1N, in mouse kidney. We describe here binding partners for renal 4.1 proteins, identified through the screening of a rat kidney yeast two-hybrid system cDNA library. The identification of putative protein 4.1-based complexes enables us to envision potential functions for 4.1 proteins in kidney: organization of signaling complexes, response to osmotic stress, protein trafficking, and control of cell proliferation. We discuss the relevance of these protein 4.1-based interactions in kidney physio-pathology in the context of their previously identified functions in other cells and tissues. Specifically, we will focus on renal 4.1 protein interactions with beta amyloid precursor protein (beta-APP), 14-3-3 proteins, and the cell swelling-activated chloride channel pICln. We also discuss the functional relevance of another member of the protein 4.1 superfamily, ezrin, in kidney physiopathology.
Zarzycki, Jan; Kerfeld, Cheryl A
2013-11-09
Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases). Here we report the first crystal structures of MCLs from two different phylogenetic subgroups in apo- and substrate-bound forms. Both the C. aurantiacus and the R. sphaeroides MCL contain elaborations on the canonical β8/α8 TIM barrel fold and form hexameric assemblies. Upon ligand binding, changes in the C-terminal domains of the MCLs result in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer. The distinctive features of the two MCL subgroups were compared to known structures of other CitE-like superfamily enzymes and to malate synthases, providing insight into the structural subtleties that underlie the functional versatility of these enzymes. Although the C. aurantiacus and the R. sphaeroides MCLs have divergent primary structures (~37% identical), their tertiary and quaternary structures are very similar. It can be assumed that the C-C bond formation catalyzed by the MCLs occurs as proposed for
DEFF Research Database (Denmark)
Døssing, Arne; Hopper, J.R.; Olesen, Arne Vestergaard
2013-01-01
The tectonic history of the Arctic Ocean remains poorly resolved and highly controversial. Details regarding break up of the Lomonosov Ridge from the Barents-Kara shelf margins and the establishment of seafloor spreading in the Cenozoic Eurasia Basin are unresolved. Significantly, the plate...... tectonic evolution of the Mesozoic Amerasia Basin is essentially unknown. The Arctic Ocean north of Greenland is at a critical juncture that formed at the locus of a Mesozoic three-plate setting between the Lomonosov Ridge, Greenland, and North America. In addition, the area is close to the European plate...... plateau against an important fault zone north of Greenland. Our results provide new constraints for Cretaceous-Cenozoic plate reconstructions of the Arctic. Key Points Presentation of the largest aero-gravity survey acquired over the Arctic Ocean Plate tectonic link between Atlantic and Arctic spreading...
International Nuclear Information System (INIS)
1981-03-01
As a result of NRC staff review and extended collegial consultations and investigations within the NRC, the Commission has designated four new Unresolved Safety Issues (USIs). This report describes the process used to evaluate the large number of concerns and recommendations which resulted from the major investigations of the Three Mile Island-2 accident as well as other events and investigations of the past year, and the report identifies the four new USIs selected as follows: (1) Shutdown decay heat removal requirements (Task A-45); (2) Seismic qualification of equipment in operating plants (Task A-46); (3) Safety implications of control systems (Task A-47); and (4) Hydrogen control measures and effects of hydrogen burns on safety equipment (Task A-48). Appendix A of the report presents an expanded discussion of each new USI including issue definition, a preliminary discussion of the action plan and a basis for continued plant operations and licensing. Appendix B of the report provides a brief discussion of each of the candidate safety issues not designated as an USI
International Nuclear Information System (INIS)
Chang, T.Y.; Anderson, N.R.
1987-02-01
The margin of safety provided in existing nuclear power plant equipment to resist seismically induced loads and perform required safety functions may vary considerably, because of significant changes in design criteria and methods for the seismic qualification of equipment over the years. Therefore, the seismic qualification of equipment in operating plants must be reassessed to determine whether requalification is necessary. The objective of technical studies performed under Task Action Plan A-46 was to establish an explicit set of guidelines and acceptance criteria to judge the adequacy of equipment under seismic loading at all operating plants, in lieu of requiring these plants to meet the criteria that are applied to new plants. This report presents the regulatory analysis for Unresolved Safety Issue (USI) A-46. It includes: Statement of the Problem; the Objective of USI A-46; a Summary of A-46 Tasks; a Proposed Implementation Procedure; a Value-Impact Analysis; Application of the Backfit Rule; 10 CFR 50.109; Implementation; and Operating Plants To Be Reviewed to USI A-46 Requirements
International Nuclear Information System (INIS)
1992-12-01
This report is to provide a comprehensive description of the implementation and verification status of Three Mile Island (TMI) Action Plan requirements, safety issues designated as Unresolved Safety Issues (USIs), Generic Safety Issues(GSIs), and other Multiplant Actions (MPAs) that have been resolved and involve implementation of an action or actions by licensees. This report makes the information available to other interested parties, including the public. An additional purpose of this NUREG report is to serve as a follow-on to NUREG-0933, ''A Prioritization of Generic Safety Issues,'' which tracks safety issues up until requirements are approved for imposition at licensed plants or until the NRC issues a request for action by licensees
Directory of Open Access Journals (Sweden)
Reitzel Adam M
2011-02-01
Full Text Available Abstract Background Nuclear receptors (NRs are an ancient superfamily of metazoan transcription factors that play critical roles in regulation of reproduction, development, and energetic homeostasis. Although the evolutionary relationships among NRs are well-described in two prominent clades of animals (deuterostomes and protostomes, comparatively little information has been reported on the diversity of NRs in early diverging metazoans. Here, we identified NRs from the phylum Ctenophora and used a phylogenomic approach to explore the emergence of the NR superfamily in the animal kingdom. In addition, to gain insight into conserved or novel functions, we examined NR expression during ctenophore development. Results We report the first described NRs from the phylum Ctenophora: two from Mnemiopsis leidyi and one from Pleurobrachia pileus. All ctenophore NRs contained a ligand-binding domain and grouped with NRs from the subfamily NR2A (HNF4. Surprisingly, all the ctenophore NRs lacked the highly conserved DNA-binding domain (DBD. NRs from Mnemiopsis were expressed in different regions of developing ctenophores. One was broadly expressed in the endoderm during gastrulation. The second was initially expressed in the ectoderm during gastrulation, in regions corresponding to the future tentacles; subsequent expression was restricted to the apical organ. Phylogenetic analyses of NRs from ctenophores, sponges, cnidarians, and a placozoan support the hypothesis that expansion of the superfamily occurred in a step-wise fashion, with initial radiations in NR family 2, followed by representatives of NR families 3, 6, and 1/4 originating prior to the appearance of the bilaterian ancestor. Conclusions Our study provides the first description of NRs from ctenophores, including the full complement from Mnemiopsis. Ctenophores have the least diverse NR complement of any animal phylum with representatives that cluster with only one subfamily (NR2A. Ctenophores and
Singh, Dinkar; Yadav, Narendra Singh; Tiwari, Vivekanand; Agarwal, Pradeep K; Jha, Bhavanath
2016-01-01
About 1000 salt-responsive ESTs were identified from an extreme halophyte Salicornia brachiata. Among these, a novel salt-inducible gene SbSLSP (Salicornia brachiata SNARE-like superfamily protein), showed up-regulation upon salinity and dehydration stress. The presence of cis-regulatory motifs related to abiotic stress in the putative promoter region supports our finding that SbSLSP gene is inducible by abiotic stress. The SbSLSP protein showed a high sequence identity to hypothetical/uncharacterized proteins from Beta vulgaris, Spinacia oleracea, Eucalyptus grandis, and Prunus persica and with SNARE-like superfamily proteins from Zostera marina and Arabidopsis thaliana. Bioinformatics analysis predicted a clathrin adaptor complex small-chain domain and N-myristoylation site in the SbSLSP protein. Subcellular localization studies indicated that the SbSLSP protein is mainly localized in the plasma membrane. Using transgenic tobacco lines, we establish that overexpression of SbSLSP resulted in elevated tolerance to salt and drought stress. The improved tolerance was confirmed by alterations in a range of physiological parameters, including high germination and survival rate, higher leaf chlorophyll contents, and reduced accumulation of Na(+) ion and reactive oxygen species (ROS). Furthermore, overexpressing lines also showed lower water loss, higher cell membrane stability, and increased accumulation of proline and ROS-scavenging enzymes. Overexpression of SbSLSP also enhanced the transcript levels of ROS-scavenging and signaling enzyme genes. This study is the first investigation of the function of the SbSLSP gene as a novel determinant of salinity/drought tolerance. The results suggest that SbSLSP could be a potential candidate to increase salinity and drought tolerance in crop plants for sustainable agriculture in semi-arid saline soil.
Directory of Open Access Journals (Sweden)
Dinkar eSingh
2016-06-01
Full Text Available About 1000 salt-responsive ESTs were identified from an extreme halophyte Salicornia brachiata. Among these, a novel salt-inducible gene SbSLSP, (Salicornia brachiata SNARE-like superfamily protein showed up-regulation upon salinity and dehydration stress. The presence of cis-regulatory motifs related to abiotic stress in the putative promoter region supports our finding that SbSLSP gene is inducible by abiotic stress. The SbSLSP protein showed a high sequence identity to hypothetical/uncharacterised proteins from Beta vulgaris, Spinacia oleracea, Eucalyptus grandis and Prunus persica and with SNARE-like superfamily proteins from Zostera marina and Arabidopsis thaliana. Bioinformatics analysis predicted a clathrin adaptor complex small-chain domain and N-myristoylation site in the SbSLSP protein. Subcellular localisation studies indicated that the SbSLSP protein is mainly localised in the plasma membrane. Using transgenic tobacco lines, we establish that overexpression of SbSLSP resulted in elevated tolerance to salt and drought stress. The improved tolerance was confirmed by alterations in a range of physiological parameters, including high germination and survival rate, higher leaf chlorophyll contents, and reduced accumulation of Na+ ion and reactive oxygen species (ROS. Furthermore, overexpressing lines also showed lower water loss, higher cell membrane stability and increased accumulation of proline and ROS-scavenging enzymes. Overexpression of SbSLSP also enhanced the transcript levels of ROS-scavenging and signalling enzyme genes. This study is the first investigation of the function of the SbSLSP gene as a novel determinant of salinity/drought tolerance. The results suggest that SbSLSP could be a potential candidate to increase salinity and drought tolerance in crop plants for sustainable agriculture in semi-arid saline soil.
Molecular basis of androgen insensitivity
Brinkmann, A.; Jenster, G.; Ris-Stalpers, C.; van der Korput, H.; Brüggenwirth, H.; Boehmer, A.; Trapman, J.
1996-01-01
Male sexual differentiation and development proceed under direct control of androgens. Androgen action is mediated by the intracellular androgen receptor, which belongs to the superfamily of ligand-dependent transcription factors. In the X-linked androgen insensitivity syndrome, defects in the
Matsunaga, James; Barocchi, Michele A.; Croda, Julio; Young, Tracy A.; Sanchez, Yolanda; Siqueira, Isadora; Bolin, Carole A.; Reis, Mitermayer G.; Riley, Lee W.; Haake, David A.; Ko, Albert I.
2005-01-01
Summary Proteins with bacterial immunoglobulin-like (Big) domains, such as the Yersinia pseudotuberculosis invasin and Escherichia coli intimin, are surface-expressed proteins that mediate host mammalian cell invasion or attachment. Here, we report the identification and characterization of a new family of Big domain proteins, referred to as Lig (leptospiral Ig-like) proteins, in pathogenic Leptospira. Screening of L. interrogans and L. kirschneri expression libraries with sera from leptospirosis patients identified 13 lambda phage clones that encode tandem repeats of the 90 amino acid Big domain. Two lig genes, designated ligA and ligB, and one pseudo-gene, ligC, were identified. The ligA and ligB genes encode amino-terminal lipoprotein signal peptides followed by 10 or 11 Big domain repeats and, in the case of ligB, a unique carboxy-terminal non-repeat domain. The organization of ligC is similar to that of ligB but contains mutations that disrupt the reading frame. The lig sequences are present in pathogenic but not saprophytic Leptospira species. LigA and LigB are expressed by a variety of virulent leptospiral strains. Loss of Lig protein and RNA transcript expression is correlated with the observed loss of virulence during culture attenuation of pathogenic strains. High-pressure freeze substitution followed by immunocytochemical electron microscopy confirmed that the Lig proteins were localized to the bacterial surface. Immunoblot studies with patient sera found that the Lig proteins are a major antigen recognized during the acute host infection. These observations demonstrate that the Lig proteins are a newly identified surface protein of pathogenic Leptospira, which by analogy to other bacterial immunoglobulin superfamily virulence factors, may play a role in host cell attachment and invasion during leptospiral pathogenesis. PMID:12890019
Directory of Open Access Journals (Sweden)
Yulia Sokurenko
2016-01-01
Full Text Available The N1/T1 RNase superfamily comprises enzymes with well-established antitumor effects, such as ribotoxins secreted by fungi, primarily by Aspergillus and Penicillium species, and bacterial RNase secreted by B. pumilus (binase and B. amyloliquefaciens (barnase. RNase is regarded as an alternative to classical chemotherapeutic agents due to its selective cytotoxicity towards tumor cells. New RNase with a high degree of structural similarity with binase (73% and barnase (74% was isolated and purified from Bacillus licheniformis (balifase, calculated molecular weight 12421.9 Da, pI 8.91. The protein sample with enzymatic activity of 1.5 × 106 units/A280 was obtained. The physicochemical properties of balifase are similar to those of barnase. However, in terms of its gene organization and promoter activity, balifase is closer to binase. The unique feature of balifase gene organization consists in the fact that genes of RNase and its inhibitor are located in one operon. Similarly to biosynthesis of binase, balifase synthesis is induced under phosphate starvation; however, in contrast to binase, balifase does not form dimers under natural conditions. We propose that the highest stability of balifase among analyzed RNase types allows the protein to retain its structure without oligomerization.
International Nuclear Information System (INIS)
Burks, Elizabeth A.; Fleming, Christopher D.; Mesecar, Andrew D.; Whitman, Christian P.; Pegan, Scott D.
2010-01-01
4-Oxalocrotonate tautomerase (4-OT) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. These enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where Pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the C-5 position of the product. 4-OT, a homohexamer from Pseudomonas putida mt-2, is the most extensively studied 4-OT isozyme and the founding member of the tautomerase superfamily. A search of five thermophilic bacterial genomes identified a coded amino acid sequence in each that had been annotated as a tautomerase-like protein but lacked Pro-1. However, a nearby sequence has Pro-1, but the sequence is not annotated as a tautomerase-like protein. To characterize this group of proteins, two genes from Chloroflexus aurantiacus J-10-fl were cloned, and the corresponding proteins were expressed. Kinetic, biochemical, and X-ray structural analyses show that the two expressed proteins form a functional heterohexamer 4-OT (hh4-OT), composed of three αβ dimers. Like the P. putida enzyme, hh4-OT requires the amino-terminal proline and two arginines for the conversion of 2-hydroxymuconate to the product, implicating an analogous mechanism. In contrast to 4-OT, hh4-OT does not exhibit the low-level activity of another tautomerase superfamily member, the heterohexamer trans-3-chloroacrylic acid dehalogenase (CaaD). Characterization of hh4-OT enables functional assignment of the related enzymes, highlights the diverse ways the β-α-β building block can be assembled into an active enzyme, and provides further insight into the molecular basis of the low-level CaaD activity in 4-OT.
Steering Through: How organizations negotiate permanent uncertainty and unresolvable choices
Poruthiyil, Prabhir Vishnu
2011-01-01
textabstractIt is easy to observe instances of contradictions and dilemmas that multinational companies, public bureaucracies, and individuals encounter as they seek resources and markets in a globally-linked world. The default condition for such entities is that they are being constantly stretched apart by global and local processes that are multiple, intertwined, contradictory and irreconcilable. Through qualitative studies of two such organizational environments, this thesis describes its ...
Sukhwal, Anshul; Sowdhamini, Ramanathan
2013-07-01
and its remote homologue-interacting partner pair. We found that, in exceptional cases, homologous proteins belonging to the same superfamily, but with remote sequence similarity, can share similar interfaces.
A Decade of e-Cigarettes: Limited Research & Unresolved Safety Concerns
Kaisar, Mohammad Abul; Prasad, Shikha; Liles, Tylor; Cucullo, Luca
2016-01-01
It is well known that tobacco consumption is a leading cause of preventable deaths worldwide and has been linked to major diseases ranging from cancer to chronic obstructive pulmonary disease, atherosclerosis, stroke and a host of neurological/neurodegenerative disorders. In the past decade a number of alternative vaping products have hit the market, rapidly gaining consumers especially among the younger population. Electronic nicotine delivery systems or e-cigarettes have become the sought-a...
Specificity of drug transport mediated by CaMDR1: a major facilitator ...
Indian Academy of Sciences (India)
Unknown
CaMDR1 encodes a major facilitator superfamily (MFS) protein in Candida albicans whose expression has been linked to .... by plaque assay and the integration of CaMDR1 at the ... with recombinant virus, vAcCaMDR1 and cells infected.
Single liposome analysis of peptide translocation by the ABC transporter TAPL
Zollmann, Tina; Moiset Coll, Gemma; Tumulka, Franz; Tampé, Robert; Poolman, Bert; Abele, Rupert
2015-01-01
ATP-binding cassette (ABC) transporters use ATP to drive solute transport across biological membranes. Members of this superfamily have crucial roles in cell physiology, and some of the transporters are linked to severe diseases. However, understanding of the transport mechanism, especially of human
Rosenthal, Cindy; Mueller, Uwe; Panjikar, Santosh; Sun, Lianli; Ruppert, Martin; Zhao, Yu; Stöckigt, Joachim
2006-01-01
Perakine reductase (PR) is a novel member of the aldo-keto reductase enzyme superfamily from higher plants. PR from the plant Rauvolfia serpentina is involved in the biosynthesis of monoterpenoid indole alkaloids by performing NADPH-dependent reduction of perakine, yielding raucaffrinoline. However, PR can also reduce cinnamic aldehyde and some of its derivatives. After heterologous expression of a triple mutant of PR in Escherichia coli, crystals of the purified and methylated enzyme were obtained by the hanging-drop vapour-diffusion technique at 293 K with 100 mM sodium citrate pH 5.6 and 27% PEG 4000 as precipitant. Crystals belong to space group C2221 and diffract to 2.0 Å, with unit-cell parameters a = 58.9, b = 93.0, c = 143.4 Å. PMID:17142919
Glenohumeral abduction contracture in children with unresolved neonatal brachial plexus palsy.
Eismann, Emily A; Little, Kevin J; Laor, Tal; Cornwall, Roger
2015-01-21
Following neonatal brachial plexus palsy, the Putti sign-obligatory tilt of the scapula with brachiothoracic adduction-suggests the presence of glenohumeral abduction contracture. In the present study, we utilized magnetic resonance imaging (MRI) to quantify this glenohumeral abduction contracture and evaluate its relationship to shoulder joint deformity, muscle atrophy, and function. We retrospectively reviewed MRIs of the thorax and shoulders obtained before and after shoulder rebalancing surgery (internal rotation contracture release and external rotation tendon transfer) for twenty-eight children with unresolved neonatal brachial plexus palsy. Two raters measured the coronal positions of the scapula, thoracic spine, and humeral shaft bilaterally on coronal images, correcting trigonometrically for scapular protraction on axial images. Supraspinatus, deltoid, and latissimus dorsi muscle atrophy was assessed, blinded to other measures. Correlations between glenohumeral abduction contracture and glenoid version, humeral head subluxation, passive external rotation, and Mallet shoulder function before and after surgery were performed. MRI measurements were highly reliable between raters. Glenohumeral abduction contractures were present in twenty-five of twenty-eight patients, averaging 33° (range, 10° to 65°). Among those patients, abductor atrophy was present in twenty-three of twenty-five, with adductor atrophy in twelve of twenty-five. Preoperatively, greater abduction contracture severity correlated with greater Mallet global abduction and hand-to-neck function. Abduction contracture severity did not correlate preoperatively with axial measurements of glenohumeral dysplasia, but greater glenoid retroversion was associated with worse abduction contractures postoperatively. Surgery improved passive external rotation, active abduction, and hand-to-neck function, but did not change the abduction contracture. A majority of patients with persistent shoulder weakness
Directory of Open Access Journals (Sweden)
Andrade-Navarro Miguel A
2007-11-01
Full Text Available Abstract Background Genetic variants in the FTO (fat mass and obesity associated gene have been associated with an increased risk of obesity. However, the function of its protein product has not been experimentally studied and previously reported sequence similarity analyses suggested the absence of homologs in existing protein databases. Here, we present the first detailed computational analysis of the sequence and predicted structure of the protein encoded by FTO. Results We performed a sequence similarity search using the human FTO protein as query and then generated a profile using the multiple sequence alignment of the homologous sequences. Profile-to-sequence and profile-to-profile based comparisons identified remote homologs of the non-heme dioxygenase family. Conclusion Our analysis suggests that human FTO is a member of the non-heme dioxygenase (Fe(II- and 2-oxoglutarate-dependent dioxygenases superfamily. Amino acid conservation patterns support this hypothesis and indicate that both 2-oxoglutarate and iron should be important for FTO function. This computational prediction of the function of FTO should suggest further steps for its experimental characterization and help to formulate hypothesis about the mechanisms by which it relates to obesity in humans.
Wu, S-F; Yu, H-Y; Jiang, T-T; Gao, C-F; Shen, J-L
2015-08-01
G protein-coupled receptors (GPCRs) are the largest and most versatile superfamily of cell membrane proteins, which mediate various physiological processes including reproduction, development and behaviour. The diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae), is one of the most notorious insect pests, preferentially feeding on cruciferous plants. P. xylostella is not only one of the world's most widespread lepidopteran insects, but has also developed resistance to nearly all classes of insecticides. Although the mechanisms of insecticide resistance have been studied extensively in many insect species, few investigations have been carried out on GPCRs in P. xylostella. In the present study, we identified 95 putative GPCRs in the P. xylostella genome. The identified GPCRs were compared with their homologues in Bombyx mori and Drosophila melanogaster. Our results suggest that GPCRs in different insect species may have evolved by a birth-and-death process. One of the differences among compared insects is the duplication of short neuropeptide F receptor and adipokinetic hormone receptors in P. xylostella and B. mori. Another divergence is the decrease in quantity and diversity of the stress-tolerance gene, Mth, in P. xylostella. The evolution by the birth-and-death process is probably involved in adaptation to the feeding behaviour, reproduction and stress responses of P. xylostella. Some of the genes identified in the present study could be potential targets for the development of novel pesticides. © 2015 The Royal Entomological Society.
Exploring the role of cellular homologous of the 30K-superfamily of plant virus movement proteins.
Carrasco, José L; Sánchez-Navarro, Jesús A; Elena, Santiago F
2018-02-21
Genes orthologous to the 30K-superfamily of movement proteins (MP) from plant viruses have been recently discovered by bioinformatics analyses as integrated elements in the genome of most vascular plants. However, their functional relevance for plants is still unclear. Here, we undertake some preliminary steps into the functional characterization of one of these putative MP genes found in Arabidopsis thaliana. We found that the AtMP gene is expressed at different stages of the plant development, with accumulation being highest in flowers but lowest in mature siliques. We also found down-regulation of the gene may result in a small delay in plant development and in an exacerbation of the negative effect of salinity in germination efficiency. We have also explored whether changes in expression of the endogenous AtMP have any effect on susceptibility to infection with several viruses, and found that the infectivity of tobacco rattle tobravirus was strongly dependent on the expression of the endogenous AtMP. Finally, we have cloned the endogenous MP from four different plant species into an expression vector that allows for specifically assessing their activity as cell-to-cell movement proteins and have shown that though some may still retain the ancestral activity, they do so in a quite inefficient manner, thus suggesting they have acquired a novel function during adaptation to the host genome. Copyright © 2018 Elsevier B.V. All rights reserved.
THE SPITZER INFRARED SPECTROGRAPH DEBRIS DISK CATALOG. I. CONTINUUM ANALYSIS OF UNRESOLVED TARGETS
Energy Technology Data Exchange (ETDEWEB)
Chen, Christine H. [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Mittal, Tushar [Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA 94720-4767 (United States); Kuchner, Marc [NASA Goddard Space Flight Center, Exoplanets and Stellar Astrophysics Laboratory, Code 667, Greenbelt, MD 20771 (United States); Forrest, William J.; Watson, Dan M. [Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627 (United States); Lisse, Carey M. [Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723 (United States); Manoj, P. [Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005 (India); Sargent, Benjamin A., E-mail: cchen@stsci.edu [Center for Imaging Science and Laboratory for Multiwavelength Astrophysics, Rochester Institute of Technology, 54 Lomb Memorial Drive, Rochester, NY 14623 (United States)
2014-04-01
During the Spitzer Space Telescope cryogenic mission, Guaranteed Time Observers, Legacy Teams, and General Observers obtained Infrared Spectrograph (IRS) observations of hundreds of debris disk candidates. We calibrated the spectra of 571 candidates, including 64 new IRAS and Multiband Imaging Photometer for Spitzer (MIPS) debris disks candidates, modeled their stellar photospheres, and produced a catalog of excess spectra for unresolved debris disks. For 499 targets with IRS excess but without strong spectral features (and a subset of 420 targets with additional MIPS 70 μm observations), we modeled the IRS (and MIPS data) assuming that the dust thermal emission was well-described using either a one- or two-temperature blackbody model. We calculated the probability for each model and computed the average probability to select among models. We found that the spectral energy distributions for the majority of objects (∼66%) were better described using a two-temperature model with warm (T {sub gr} ∼ 100-500 K) and cold (T {sub gr} ∼ 50-150 K) dust populations analogous to zodiacal and Kuiper Belt dust, suggesting that planetary systems are common in debris disks and zodiacal dust is common around host stars with ages up to ∼1 Gyr. We found that younger stars generally have disks with larger fractional infrared luminosities and higher grain temperatures and that higher-mass stars have disks with higher grain temperatures. We show that the increasing distance of dust around debris disks is inconsistent with self-stirred disk models, expected if these systems possess planets at 30-150 AU. Finally, we illustrate how observations of debris disks may be used to constrain the radial dependence of material in the minimum mass solar nebula.
Effects of mixing on resolved and unresolved scales on stratospheric age of air
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S. Dietmüller
2017-06-01
Full Text Available Mean age of air (AoA is a widely used metric to describe the transport along the Brewer–Dobson circulation. We seek to untangle the effects of different processes on the simulation of AoA, using the chemistry–climate model EMAC (ECHAM/MESSy Atmospheric Chemistry and the Chemical Lagrangian Model of the Stratosphere (CLaMS. Here, the effects of residual transport and two-way mixing on AoA are calculated. To do so, we calculate the residual circulation transit time (RCTT. The difference of AoA and RCTT is defined as aging by mixing. However, as diffusion is also included in this difference, we further use a method to directly calculate aging by mixing on resolved scales. Comparing these two methods of calculating aging by mixing allows for separating the effect of unresolved aging by mixing (which we term aging by diffusion in the following in EMAC and CLaMS. We find that diffusion impacts AoA by making air older, but its contribution plays a minor role (order of 10 % in all simulations. However, due to the different advection schemes of the two models, aging by diffusion has a larger effect on AoA and mixing efficiency in EMAC, compared to CLaMS. Regarding the trends in AoA, in CLaMS the AoA trend is negative throughout the stratosphere except in the Northern Hemisphere middle stratosphere, consistent with observations. This slight positive trend is neither reproduced in a free-running nor in a nudged simulation with EMAC – in both simulations the AoA trend is negative throughout the stratosphere. Trends in AoA are mainly driven by the contributions of RCTT and aging by mixing, whereas the contribution of aging by diffusion plays a minor role.
Yakovleva, Lyudmila; Shuman, Stewart
2012-08-01
Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.
GH97 is a new family of glycoside hydrolases, which is related to the α-galactosidase superfamily
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Naumoff Daniil G
2005-08-01
Full Text Available Abstract Background As a rule, about 1% of genes in a given genome encode glycoside hydrolases and their homologues. On the basis of sequence similarity they have been grouped into more than ninety GH families during the last 15 years. The GH97 family has been established very recently and initially included only 18 bacterial proteins. However, the evolutionary relationship of the genes encoding proteins of this family remains unclear, as well as their distribution among main groups of the living organisms. Results The extensive search of the current databases allowed us to double the number of GH97 family proteins. Five subfamilies were distinguished on the basis of pairwise sequence comparison and phylogenetic analysis. Iterative sequence analysis revealed the relationship of the GH97 family with the GH27, GH31, and GH36 families of glycosidases, which belong to the α-galactosidase superfamily, as well as a more distant relationship with some other glycosidase families (GH13 and GH20. Conclusion The results of this study show an unexpected sequence similarity of GH97 family proteins with glycoside hydrolases from several other families, that have (β/α8-barrel fold of the catalytic domain and a retaining mechanism of the glycoside bond hydrolysis. These data suggest a common evolutionary origin of glycosidases representing different families and clans.
DEFF Research Database (Denmark)
Bikker, Floris J; Ligtenberg, Antoon J M; Nazmi, Kamran
2002-01-01
Salivary agglutinin is encoded by DMBT1 and identical to gp-340, a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Salivary agglutinin/DMBT1 is known for its Streptococcus mutans agglutinating properties. This 300-400 kDa glycoprotein is composed of conserved peptide motifs: 14...... containing exclusively SRCR and SID domains that binds to S. mutans. To define more closely the S. mutans-binding domain, consensus-based peptides of the SRCR domains and SIDs were designed and synthesized. Only one of the SRCR peptides, designated SRCRP2, and none of the SID peptides bound to S. mutans....... Strikingly, this peptide was also able to induce agglutination of S. mutans and a number of other bacteria. The repeated presence of this peptide in the native molecule endows agglutinin/DMBT1 with a general bacterial binding feature with a multivalent character. Moreover, our studies demonstrate...
Karshikoff, Andrey; Nilsson, Lennart; Foloppe, Nicolas
2013-08-27
E. coli DsbA is an intensively studied enzyme of the thioredoxin superfamily of thiol-disulfide oxidoreductases. DsbA catalyzes the disulfide bond formation and folding of proteins in the bacterial periplasm. DsbA and its mutants have highlighted the strong and puzzling influence of the -C-X1-X2-C- active site variants, found across the thioredoxin superfamily, on the ionization and redox properties of this site. However, the interpretation of these observations remains wanting, largely due to a dearth of structural information. Here, molecular dynamics simulations are used to provide extensive information on the structure and dynamics of reduced -C30-X31-X32-C33- motifs in wild type DsbA and 13 of its mutants. These simulations are combined with calculations of the pK of H32 and of the very low pK of the catalytic cysteine C30. In wild type DsbA, the titrations of C30 and H32 are shown to be coupled; the protonation states and dynamics of H32 are examined. The thiolate of C30 is stabilized by hydrogen bonds with the protein. Modulation of these hydrogen bonds by alteration of residue X32 has the greatest impact on the pK of C30, which rationalizes its higher pK in thioredoxin and tryparedoxin. Because of structural constrains, residue X31 has only an indirect and weak influence on the pK of C30. The dynamics of C30 is clearly related to its stabilizing interactions and pK value. Although relatively small differences between pKs were not reproduced in the calculations, the major trends are explained, adding new insights to our understanding of enzymes in this family.
Discovery of a distinct superfamily of Kunitz-type toxin (KTT from tarantulas.
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Chun-Hua Yuan
Full Text Available BACKGROUND: Kuntiz-type toxins (KTTs have been found in the venom of animals such as snake, cone snail and sea anemone. The main ancestral function of Kunitz-type proteins was the inhibition of a diverse array of serine proteases, while toxic activities (such as ion-channel blocking were developed under a variety of Darwinian selection pressures. How new functions were grafted onto an old protein scaffold and what effect Darwinian selection pressures had on KTT evolution remains a puzzle. PRINCIPAL FINDINGS: Here we report the presence of a new superfamily of ktts in spiders (TARANTULAS: Ornithoctonus huwena and Ornithoctonus hainana, which share low sequence similarity to known KTTs and is clustered in a distinct clade in the phylogenetic tree of KTT evolution. The representative molecule of spider KTTs, HWTX-XI, purified from the venom of O. huwena, is a bi-functional protein which is a very potent trypsin inhibitor (about 30-fold more strong than BPTI as well as a weak Kv1.1 potassium channel blocker. Structural analysis of HWTX-XI in 3-D by NMR together with comparative function analysis of 18 expressed mutants of this toxin revealed two separate sites, corresponding to these two activities, located on the two ends of the cone-shape molecule of HWTX-XI. Comparison of non-synonymous/synonymous mutation ratios (omega for each site in spider and snake KTTs, as well as PBTI like body Kunitz proteins revealed high Darwinian selection pressure on the binding sites for Kv channels and serine proteases in snake, while only on the proteases in spider and none detected in body proteins, suggesting different rates and patterns of evolution among them. The results also revealed a series of key events in the history of spider KTT evolution, including the formation of a novel KTT family (named sub-Kuntiz-type toxins derived from the ancestral native KTTs with the loss of the second disulfide bridge accompanied by several dramatic sequence modifications
Too Many Links in the Horizon; What is Next? Linked Views and Linked History
E. Liarou (Erietta); S. Idreos (Stratos)
2011-01-01
textabstractThe trend for more online linked data becomes stronger. Foreseeing a future where ``everything" will be online and linked, we ask the critical question; what is next? We envision that managing, querying and storing large amounts of links and data is far from yet another query
Sayedyahossein, Samar; Rudkouskaya, Alena; Leclerc, Valerie; Dagnino, Lina
2016-02-01
A functional permeability barrier is essential to prevent the passage of water and electrolytes, macromolecules, and pathogens through the epidermis. This is accomplished in terminally differentiated keratinocytes through formation of a cornified envelope and the assembly of tight intercellular junctions. Integrin-linked kinase (ILK) is a scaffold protein essential for hair follicle morphogenesis and epidermal attachment to the basement membrane. However, the biological functions of ILK in differentiated keratinocytes remain poorly understood. Furthermore, whether ILK is implicated in keratinocyte differentiation and intercellular junction formation has remained an unresolved issue. Here we describe a pivotal role for ILK in keratinocyte differentiation responses to increased extracellular Ca(2+), regulation of adherens and tight junction assembly, and the formation of an outside-in permeability barrier toward macromolecules. In the absence of ILK, the calcium sensing receptor, E-cadherin, and ZO-1 fail to translocate to the cell membrane, through mechanisms that involve abnormalities in microtubules and in RhoA activation. In situ, ILK-deficient epidermis exhibits reduced tight junction formation and increased outside-in permeability to a dextran tracer, indicating reduced barrier properties toward macromolecules. Therefore, ILK is an essential component of keratinocyte differentiation programs that contribute to epidermal integrity and the establishment of its barrier properties. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
Nikolaidis, Nikolas; Nei, Masatoshi
2004-03-01
We have identified the Hsp70 gene superfamily of the nematode Caenorhabditis briggsae and investigated the evolution of these genes in comparison with Hsp70 genes from C. elegans, Drosophila, and yeast. The Hsp70 genes are classified into three monophyletic groups according to their subcellular localization, namely, cytoplasm (CYT), endoplasmic reticulum (ER), and mitochondria (MT). The Hsp110 genes can be classified into the polyphyletic CYT group and the monophyletic ER group. The different Hsp70 and Hsp110 groups appeared to evolve following the model of divergent evolution. This model can also explain the evolution of the ER and MT genes. On the other hand, the CYT genes are divided into heat-inducible and constitutively expressed genes. The constitutively expressed genes have evolved more or less following the birth-and-death process, and the rates of gene birth and gene death are different between the two nematode species. By contrast, some heat-inducible genes show an intraspecies phylogenetic clustering. This suggests that they are subject to sequence homogenization resulting from gene conversion-like events. In addition, the heat-inducible genes show high levels of sequence conservation in both intra-species and inter-species comparisons, and in most cases, amino acid sequence similarity is higher than nucleotide sequence similarity. This indicates that purifying selection also plays an important role in maintaining high sequence similarity among paralogous Hsp70 genes. Therefore, we suggest that the CYT heat-inducible genes have been subjected to a combination of purifying selection, birth-and-death process, and gene conversion-like events.
Directory of Open Access Journals (Sweden)
Elena V. Savvateeva-Popova
2017-09-01
Full Text Available Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV with small insertions and deletions (INDELs sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS with LIM-kinase 1-dependent cognitive defects. The Drosophila melanogaster mutant agnts3 has unusual architecture of the agnostic locus harboring LIMK1: it is a hotspot of chromosome breaks, ectopic contacts, underreplication, and recombination. Here, we present the analysis of LIMK1-containing locus sequencing data in agnts3 and three D. melanogaster wild-type strains—Canton-S, Berlin, and Oregon-R. We found multiple strain-specific SVs, namely, single base changes and small INDEls. The specific feature of agnts3 is 28 bp A/T-rich insertion in intron 1 of LIMK1 and the insertion of mobile S-element from Tc1/mariner superfamily residing ~460 bp downstream LIMK1 3′UTR. Neither of SVs leads to amino acid substitutions in agnts3 LIMK1. However, they apparently affect the nucleosome distribution, non-canonical DNA structure formation and transcriptional factors binding. Interestingly, the overall expression of miRNAs including the biomarkers for human neurological diseases, is drastically reduced in agnts3 relative to the wild-type strains. Thus, LIMK1 DNA structure per se, as well as the pronounced changes in total miRNAs profile, probably lead to LIMK1 dysregulation and complex behavioral dysfunctions observed in agnts3 making this mutant a simple plausible Drosophila model for WBS.
Yan, Fan; Di, Shaokang; Takahashi, Ryoji
2015-08-01
The R gene of soybean, presumably encoding a MYB transcription factor, controls seed coat color. The gene consists of multiple alleles, R (black), r-m (black spots and (or) concentric streaks on brown seed), and r (brown seed). This study was conducted to determine the structure of the MYB transcription factor gene in a near-isogenic line (NIL) having r-m allele. PCR amplification of a fragment of the candidate gene Glyma.09G235100 generated a fragment of about 1 kb in the soybean cultivar Clark, whereas a fragment of about 14 kb in addition to fragments of 1 and 1.4 kb were produced in L72-2040, a Clark 63 NIL with the r-m allele. Clark 63 is a NIL of Clark with the rxp and Rps1 alleles. A DNA fragment of 13 060 bp was inserted in the intron of Glyma.09G235100 in L72-2040. The fragment had the CACTA motif at both ends, imperfect terminal inverted repeats (TIR), inverse repetition of short sequence motifs close to the 5' and 3' ends, and a duplication of three nucleotides at the site of integration, indicating that it belongs to a CACTA-superfamily transposable element. We designated the element as Tgm11. Overall nucleotide sequence, motifs of TIR, and subterminal repeats were similar to those of Tgm1 and Tgs1, suggesting that these elements comprise a family.
Hose, Katja; Schenkel, Ralf
2014-01-01
Linked Data Management presents techniques for querying and managing Linked Data that is available on today’s Web. The book shows how the abundance of Linked Data can serve as fertile ground for research and commercial applications. The text focuses on aspects of managing large-scale collections of Linked Data. It offers a detailed introduction to Linked Data and related standards, including the main principles distinguishing Linked Data from standard database technology. Chapters also describe how to generate links between datasets and explain the overall architecture of data integration systems based on Linked Data. A large part of the text is devoted to query processing in different setups. After presenting methods to publish relational data as Linked Data and efficient centralized processing, the book explores lookup-based, distributed, and parallel solutions. It then addresses advanced topics, such as reasoning, and discusses work related to read-write Linked Data for system interoperation. Desp...
S-LINK, a data link interface specification for the LHC era
International Nuclear Information System (INIS)
Bij, H.C. van der; McLaren, R.A.; Boyle, O.
1996-01-01
In the Technical Proposals for ATLAS, CMS and ALICE there is a requirement for several thousand data links. Although there is an obvious need for standardization, this seems difficult to achieve as the links run at different speeds, over different distances and have various constraints of power consumption, size and radiation hardness. An additional complication is that today we cannot decide which will be the most cost effective technology for the implementation of the final links. Furthermore, we must allow designers of boards at each end of the link, for example readout electronics and input buffers, to work in parallel with the development of the links. The S-LINK is a new concept which should provide the benefits of standardization without the limitations. The S-LINK specification defines, at both ends of the link, a simple FIFO-like user interface which remains independent of the technology used to implement the physical link. The physical link provides transfer of event data and control words, error detection, optional flow control and test facilities. This paper describes the S-LINK specification and gives examples of the use of the S-LINK, the physical links being designed, and the test equipment that is being developed
LinkED: A Novel Methodology for Publishing Linked Enterprise Data
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Shreyas Suresh Rao
2017-01-01
Full Text Available Semantic Web technologies have redefined and strengthened the Enterprise-Web interoperability over the last decade. Linked Open Data (LOD refers to a set of best practices that empower enterprises to publish and interlink their data using existing ontologies on the World Wide Web. Current research in LOD focuses on expert search, the creation of unified information space and augmentation of core data from an enterprise context. However, existing approaches for publication of enterprise data as LOD are domain-specific, ad-hoc and suffer from lack of uniform representation across domains. The paper proposes a novel methodology called LinkED that contributes towards LOD literature in two ways: (a streamlines the publishing process through five stages of cleaning, triplification, interlinking, storage and visualization; (b addresses the latest challenges in LOD publication, namely: inadequate links, inconsistencies in the quality of the dataset and replicability of the LOD publication process. Further, the methodology is demonstrated via the publication of digital repository data as LOD in a university setting, which is evaluated based on two semantic standards: Five-Star model and data quality metrics. Overall, the paper provides a generic LOD publication process that is applicable across various domains such as healthcare, e-governance, banking, and tourism, to name a few.
Differential substrate specificities of human ABCD1 and ABCD2 in peroxisomal fatty acid β-oxidation
van Roermund, Carlo W. T.; Visser, Wouter F.; Ijlst, Lodewijk; Waterham, Hans R.; Wanders, Ronald J. A.
2011-01-01
The gene mutated in X-linked adrenoleukodystrophy (X-ALD) codes for the HsABCD1 protein, also named ALDP, which is a member of the superfamily of ATP-binding cassette (ABC) transporters and required for fatty acid transport across the peroxisomal membrane. Although a defective HsABCD1 results in the
Chronic toxicity of unresolved complex mixtures (UCM) of hydrocarbons in marine sediments
Energy Technology Data Exchange (ETDEWEB)
Scarlett, A.; Galloway, T.S. [Plymouth Univ., Drake Circus (United Kingdom). School of Biological Sciences; Rowland, S.J. [Plymouth Univ., Drake Circus (United Kingdom). School of Earth, Ocean and Environmental Sciences
2007-08-15
Background, Aim and Scope: Unresolved complex mixtures (UCM) of hydrocarbons, containing many thousands of compounds which cannot be resolved by conventional gas chromatography (GC), are common contaminants of sediments but little is known of their potential to affect sediment-dwelling organisms. Evidence exists for reduced health status in mussels, arising from aqueous exposure to aromatic UCM components acting through a narcotic mode of action. However, UCM contaminants in sediments may not be sufficiently bioavailable to elicit toxic effects. The aim of our study was therefore to measure the sublethal effects of chronic exposure to model UCM-dominated oils at environmentally realistic concentrations and compare this to effects produced by a UCM containing weathered crude oil. A further aim was to determine which, if any, fractions of the oils were responsible for any observed toxicity. Materials and Methods: Whole oils were spiked into estuarine sediment to give nominal concentrations of 500 {mu}g g-1 dry weight. Juveniles of the estuarine amphipod Corophium volutator were exposed to the contaminated sediment for 35 days and their survival, growth rate and reproductive success quantified. Using an effect-directed fractionation approach, the oils were fractionated into aliphatic and two aromatic fractions by open column chromatography and their toxicity assessed by further chronic exposures using juvenile C. volutator. Results: The growth rates of amphipods were reduced following exposure to the oils although this was only statistically significant for the weathered oil; reproductive success was reduced by all oil exposures. Sediment spiked with UCM fractions also caused reduced growth and reproduction but no particular fraction was found to be responsible for the observed toxicity. Survivorship was not affected by any oil or fraction. Discussion: The study showed that chronic exposure to sediments contaminated by UCM-dominated oils could have population level
Interactions of relativistic heavy ions in thick heavy element targets and some unresolved problems
International Nuclear Information System (INIS)
Brandt, R.; Ditlov, V.A.; Pozharova, E.A.; Smirnitskij, V.A.
2005-01-01
Interactions of relativistic heavy ions with total energies above 30 GeV in thick Cu and Pb targets (≥2 cm) have been studied with various techniques. Radiochemical irradiation experiments using thick Cu targets, both in a compact form or as diluted '2π-Cu targets' have been carried out with several relativistic heavy ions, such as 44 GeV 12 C (JINR, Dubna) and 72 GeV 40 Ar (LBL, Berkeley, USA). Neutron measuring experiments using thick targets irradiated with various relativistic heavy ions up to 44 GeV 12 C have been performed at JINR. In addition, the number of 'black prongs' in nuclear interactions (due to protons with energies less than 30 MeV and emitted from the target-like interaction partner at rest) produced with 72 GeV 22 Ne ions in nuclear emulsion plates has been measured in the first nuclear interaction of the primary 22 Ne ion and in the following second nuclear interaction of the secondary heavy (Z>1) ion. Some essential results have been obtained. 1) Spallation products produced by relativistic secondary fragments in interactions ([44 GeV 12 C or 72 GeV 40 Ar]+Cu) within thick copper yield less products close to the target and much more products far away from the target as compared to primary beam interactions. This applies also to secondary particles emitted into large angles (Θ>10deg). 2) The neutron production of 44 GeV 12 C within thick Cu and Pb targets is beyond the estimated yield as based on experiments with 12 GeV 12 C. These rather independent experimental results cannot be understood with well-accepted nuclear reaction models. They appear to present unresolved problems
Inheritance - sex-linked dominant; Genetics - sex-linked dominant; X-linked dominant; Y-linked dominant ... can be either an autosomal chromosome or a sex chromosome. It also depends on whether the trait ...
NCX-DB: a unified resource for integrative analysis of the sodium calcium exchanger super-family.
Bode, Katrin; O'Halloran, Damien M
2018-04-13
Na + /Ca 2+ exchangers are low-affinity high-capacity transporters that mediate Ca 2+ extrusion by coupling Ca 2+ efflux to the influx of Na + ions. The Na + /Ca 2+ exchangers form a super-family comprised of three branches each differing in ion-substrate selectivity: Na + /Ca 2+ exchangers (NCX), Na + /Ca 2+ /K + exchangers, and Ca 2+ /cation exchangers. Their primary function is to maintain Ca 2+ homeostasis and play a particularly important role in excitable cells that experience transient Ca 2+ fluxes. Research into the role and activity of Na + /Ca 2+ exchangers has focused extensively on the cardio-vascular system, however, growing evidence suggests that Na + /Ca 2+ exchangers play a key role in neuronal processes such as memory formation, learning, oligodendrocyte differentiation, neuroprotection during brain ischemia and axon guidance. They have also been implicated in pathologies such as Alzheimer's disease, Parkinson's disease, Multiple Sclerosis and Epilepsy, however, a clear understanding of their mechanism during disease is lacking. To date, there has never been a central resource or database for Na + /Ca 2+ exchangers. With clear disease relevance and ever-increasing research on Na + /Ca 2+ exchangers from both model and non-model species, a database that unifies the data on Na + /Ca 2+ exchangers is needed for future research. NCX-DB is a publicly available database with a web interface that enables users to explore various Na + /Ca 2+ exchangers, perform cross-species sequence comparison, identify new exchangers, and stay-up to date with recent literature. NCX-DB is available on the web via an interactive user interface with an intuitive design, which is applicable for the identification and comparison of Na + /Ca 2+ exchanger proteins across diverse species.
Characterization of a novel wheat endosperm protein belonging to the prolamin superfamily
Starch granule surface-associated proteins were separated by HPLC and identified by direct protein sequencing. Among the proteins identified was one that consisted of two polypeptide chains of 11 kDa and 19 kDa linked by disulfide bonds. Sequencing of tryptic peptides from each of the polypeptide ch...
International Nuclear Information System (INIS)
Leal, L.C.; de Saussure, G.; Perez, R.B.
1990-01-01
The URR computer code has been developed to calculate cross-section probability tables, Bondarenko self-shielding factors, and self-indication ratios for fertile and fissile isotopes in the unresolved resonance region. Monte Carlo methods are utilized to select appropriate resonance parameters and to compute the cross sections at the desired reference energy. The neutron cross sections are calculated by the single-level Breit-Wigner formalism with s-, p-, and d-wave contributions. The cross-section probability tables are constructed by sampling by Doppler broadened cross-sections. The various self-shielding factors are computer numerically as Lebesgue integrals over the cross-section probability tables
International Nuclear Information System (INIS)
Baranowsky, P.W.
1985-05-01
''Station Blackout,'' which is the complete loss of alternating current (ac) electrical power in a nuclear power plant, has been designated as Unresolved Safety Issue A-44. Because many safety systems required for reactor core decay heat removal and containment heat removal depend on ac power, the consequences of a station blackout could be severe. This report documents the findings of technical studies performed as part of the program to resolve this issue. The important factors analyzed include: the frequency of loss of offsite power; the probability that emergency or onsite ac power supplies would be unavailable; the capability and reliability of decay heat removal systems independent of ac power; and the likelihood that offsite power would be restored before systems that cannot operate for extended periods without ac power fail, thus resulting in core damage. This report also addresses effects of different designs, locations, and operational features on the estimated frequency of core damage resulting from station blackout events
Directory of Open Access Journals (Sweden)
Buchmeier Michael J
2001-02-01
Full Text Available Abstract Background Recent studies of viral entry proteins from influenza, measles, human immunodeficiency virus, type 1 (HIV-1, and Ebola virus have shown, first with molecular modeling, and then X-ray crystallographic or other biophysical studies, that these disparate viruses share a coiled-coil type of entry protein. Results Structural models of the transmembrane glycoproteins (GP-2 of the Arenaviruses, lymphochoriomeningitis virus (LCMV and Lassa fever virus, are presented, based on consistent structural propensities despite variation in the amino acid sequence. The principal features of the model, a hydrophobic amino terminus, and two antiparallel helices separated by a glycosylated, antigenic apex, are common to a number of otherwise disparate families of enveloped RNA viruses. Within the first amphipathic helix, demonstrable by circular dichroism of a peptide fragment, there is a highly conserved heptad repeat pattern proposed to mediate multimerization by coiled-coil interactions. The amino terminal 18 amino acids are 28% identical and 50% highly similar to the corresponding region of Ebola, a member of the Filovirus family. Within the second, charged helix just prior to membrane insertion there is also high similarity over the central 18 amino acids in corresponding regions of Lassa and Ebola, which may be further related to the similar region of HIV-1 defining a potent antiviral peptide analogue. Conclusions These findings indicate a common pattern of structure and function among viral transmembrane fusion proteins from a number of virus families. Such a pattern may define a viral transmembrane superfamily that evolved from a common precursor eons ago.
Directory of Open Access Journals (Sweden)
Sierra M Li
Full Text Available Monoallelic expression is an integral component of regulation of a number of essential genes and gene families. To probe for allele-specific expression in cells of CNS origin, we used next-generation sequencing (RNA-seq to analyze four clonal neural stem cell (NSC lines derived from Mus musculus C57BL/6 (B6×Mus musculus molossinus (JF1 adult female mice. We established a JF1 cSNP library, then ascertained transcriptome-wide expression from B6 vs. JF1 alleles in the NSC lines. Validating the assay, we found that 262 of 268 X-linked genes evaluable in at least one cell line showed monoallelic expression (at least 85% expression of the predominant allele, p-value<0.05. For autosomal genes 170 of 7,198 genes (2.4% of the total showed monoallelic expression in at least 2 evaluable cell lines. The group included eight known imprinted genes with the expected pattern of allele-specific expression. Among the other autosomal genes with monoallelic expression were five members of the glutathione transferase gene superfamily, which processes xenobiotic compounds as well as carcinogens and cancer therapeutic agents. Monoallelic expression within this superfamily thus may play a functional role in the response to diverse and potentially lethal exogenous factors, as is the case for the immunoglobulin and olfactory receptor superfamilies. Other genes and gene families showing monoallelic expression include the annexin gene family and the Thy1 gene, both linked to inflammation and cancer, as well as genes linked to alcohol dependence (Gabrg1 and epilepsy (Kcnma1. The annotated set of genes will provide a resource for investigation of mechanisms underlying certain cases of these and other major disorders.
Deploying Linked Open Vocabulary (LOV to Enhance Library Linked Data
Directory of Open Access Journals (Sweden)
Oh, Sam Gyun
2015-06-01
Full Text Available Since the advent of Linked Data (LD as a method for building webs of data, there have been many attempts to apply and implement LD in various settings. Efforts have been made to convert bibliographic data in libraries into Linked Data, thereby generating Library Linked Data (LLD. However, when memory institutions have tried to link their data with external sources based on principles suggested by Tim Berners-Lee, identifying appropriate vocabularies for use in describing their bibliographic data has proved challenging. The objective of this paper is to discuss the potential role of Linked Open Vocabularies (LOV in providing better access to various open datasets and facilitating effective linking. The paper will also examine the ways in which memory institutions can utilize LOV to enhance the quality of LLD and LLD-based ontology design.
International Nuclear Information System (INIS)
Shibata, Yasuaki; Tsukazaki, Tomoo; Hirata, Kazunari; Xin Cheng; Yamaguchi, Akira
2004-01-01
Bone regeneration is critically regulated by various molecules. To identify the new genes involved in bone regeneration, we performed microarray-based gene expression analysis using a mouse bone regeneration model. We identified a new member of the IGFBP superfamily, designated IGFBP-rP10, whose expression is up-regulated at the early phase of bone regeneration. IGFBP-rP10 consists of an IGFBP homologous domain followed by a Kazal-type protein inhibitor domain and an immunoglobulin G-like domain. A real-time-based RT-PCR analysis demonstrated that various tissues including bone expressed IGFBP-rP10 mRNA in various degrees, and confirmed an up-regulation at the early phase of bone regeneration. In situ hybridization revealed that osteoblastic cells expressed IGFPB-rP10 mRNA during bone regeneration. Bone morphogenetic protein-2 increased the expression level of IGFBP-rP10 mRNA in various cells including C3H10T1/2, MC3T3-E1, C2C12, and primary murine osteoblastic cells. The addition of recombinant mouse IGFBP-rP10 promoted the proliferation of these cells but failed to stimulate alkaline phosphatase activity. These results suggest that IGFBP-rP10 is involved in the proliferation of osteoblasts during bone formation and bone regeneration
Directory of Open Access Journals (Sweden)
Sophia S Wang
Full Text Available A promoter polymorphism in the pro-inflammatory cytokine tumor necrosis factor (TNF (TNF G-308A is associated with increased non-Hodgkin lymphoma (NHL risk. The protein product, TNF-alpha, activates the nuclear factor kappa beta (NF-kappaB transcription factor, and is critical for inflammatory and apoptotic responses in cancer progression. We hypothesized that the TNF and NF-kappaB pathways are important for NHL and that gene variations across the pathways may alter NHL risk.We genotyped 500 tag single nucleotide polymorphisms (SNPs from 48 candidate gene regions (defined as 20 kb 5', 10 kb 3' in the TNF and TNF receptor superfamilies and the NF-kappaB and related transcription factors, in 1946 NHL cases and 1808 controls pooled from three independent population-based case-control studies. We obtained a gene region-level summary of association by computing the minimum p-value ("minP test". We used logistic regression to compute odds ratios and 95% confidence intervals for NHL and four major NHL subtypes in relation to SNP genotypes and haplotypes. For NHL, the tail strength statistic supported an overall relationship between the TNF/NF-kappaB pathway and NHL (p = 0.02. We confirmed the association between TNF/LTA on chromosome 6p21.3 with NHL and found the LTA rs2844484 SNP most significantly and specifically associated with the major subtype, diffuse large B-cell lymphoma (DLBCL (p-trend = 0.001. We also implicated for the first time, variants in NFKBIL1 on chromosome 6p21.3, associated with NHL. Other gene regions identified as statistically significantly associated with NHL included FAS, IRF4, TNFSF13B, TANK, TNFSF7 and TNFRSF13C. Accordingly, the single most significant SNPs associated with NHL were FAS rs4934436 (p-trend = 0.0024, IRF4 rs12211228 (p-trend = 0.0026, TNFSF13B rs2582869 (p-trend = 0.0055, TANK rs1921310 (p-trend = 0.0025, TNFSF7 rs16994592 (p-trend = 0.0024, and TNFRSF13C rs6002551 (p-trend = 0.0074. All associations were
National Research Council Canada - National Science Library
Jager, Sheila M
2007-01-01
... of memory, identity, and nationalism. The potential for violent military clashes in the Taiwan Strait and the Korean peninsula largely involve disputes over history and territory, linked as they are to the unresolved legacies of the Cold War...
Role of TGF-β signaling in inherited and acquired myopathies
Directory of Open Access Journals (Sweden)
Burks Tyesha N
2011-05-01
Full Text Available Abstract The transforming growth factor-beta (TGF-β superfamily consists of a variety of cytokines expressed in many different cell types including skeletal muscle. Members of this superfamily that are of particular importance in skeletal muscle are TGF-β1, mitogen-activated protein kinases (MAPKs, and myostatin. These signaling molecules play important roles in skeletal muscle homeostasis and in a variety of inherited and acquired neuromuscular disorders. Expression of these molecules is linked to normal processes in skeletal muscle such as growth, differentiation, regeneration, and stress response. However, chronic elevation of TGF-β1, MAPKs, and myostatin is linked to various features of muscle pathology, including impaired regeneration and atrophy. In this review, we focus on the aberrant signaling of TGF-β in various disorders such as Marfan syndrome, muscular dystrophies, sarcopenia, and critical illness myopathy. We also discuss how the inhibition of several members of the TGF-β signaling pathway has been implicated in ameliorating disease phenotypes, opening up novel therapeutic avenues for a large group of neuromuscular disorders.
The link between atmospheric radicals and newly formed particles at a spruce forest site in Germany
DEFF Research Database (Denmark)
Bonn, B.; Bourtsoukidis, E.; Sun, T. S.
2014-01-01
It has been claimed for more than a century that atmospheric new particle formation is primarily influenced by the presence of sulfuricacid. However, the activation process of sulfuric acid related clusters into detectable particles is still an unresolved topic. In this study we focus onthe PARAD...
The link between atmospheric radicals and newly formed particles at a spruce forest site in Germany
DEFF Research Database (Denmark)
Bonn, B.; Bourtsoukidis, E.; Sun, T. S.
2013-01-01
It has been claimed for more than a century that atmospheric new particle formation is primarily influenced by the presence of sulphuric acid. However, the activation process of sulphuric acid related clusters into detectable particles is still an unresolved topic. In this study we focus on the P...
DEFF Research Database (Denmark)
Wistoft, Karen; Højlund, Holger
2012-01-01
educational goals, learning content, or value clarification. Health pedagogy is often a matter of retrospective rationalization rather than the starting point of planning. Health and risk behaviour approaches override health educational approaches. Conclusions: Operational links between health education......, health professionalism, and management strategies pose the foremost challenge. Operational links indicates cooperative levels that facilitate a creative and innovative effort across traditional professional boundaries. It is proposed that such links are supported by network structures, shared semantics...
Mouse RC/BTB2, a Member of the RCC1 Superfamily, Localizes to Spermatid Acrosomal Vesicles
Shen, Xuening; Nagarkatti-Gude, David R.; Hess, Rex A.; Henderson, Scott C.; Strauss, Jerome F.; Zhang, Zhibing
2012-01-01
Mouse RC/BTB2 is an unstudied protein of the RCC1 (Regulator of Chromosome Condensation) superfamily. Because of the significant remodeling of chromatin that occurs during spermiogenesis, we characterized the expression and localization of mouse RC/BTB2 in the testis and male germ cells. The Rc/btb2 gene yields two major transcripts: 2.3 kb Rc/btb2-s, present in most somatic tissues examined; and 2.5 kb Rc/btb2-t, which contains a unique non-translated exon in its 5′-UTR that is only detected in the testis. During the first wave of spermatogenesis, Rc/btb2-t mRNA is expressed from day 8 after birth, reaching highest levels of expression at day 30 after birth. The full-length protein contains three RCC1 domains in the N-terminus, and a BTB domain in the C-terminus. In the testis, the protein is detectable from day 12, but is progressively up-regulated to day 30 and day 42 after birth. In spermatids, some of the protein co-localizes with acrosomal markers sp56 and peanut lectin, indicating that it is an acrosomal protein. A GFP-tagged RCC1 domain is present throughout the cytoplasm of transfected CHO cells. However, both GFP-tagged, full-length RC/BTB2 and a GFP-tagged BTB domain localize to vesicles in close proximity to the nuclear membrane, suggesting that the BTB domain might play a role in mediating full-length RC/BTB2 localization. Since RCC1 domains associate with Ran, a small GTPase that regulates molecular trafficking, it is possible that RC/BTB2 plays a role in transporting proteins during acrosome formation. PMID:22768142
Link-N: The missing link towards intervertebral disc repair is species-specific.
Directory of Open Access Journals (Sweden)
Frances C Bach
Full Text Available Degeneration of the intervertebral disc (IVD is a frequent cause for back pain in humans and dogs. Link-N stabilizes proteoglycan aggregates in cartilaginous tissues and exerts growth factor-like effects. The human variant of Link-N facilitates IVD regeneration in several species in vitro by inducing Smad1 signaling, but it is not clear whether this is species specific. Dogs with IVD disease could possibly benefit from Link-N treatment, but Link-N has not been tested on canine IVD cells. If Link-N appears to be effective in canines, this would facilitate translation of Link-N into the clinic using the dog as an in vivo large animal model for human IVD degeneration.This study's objective was to determine the effect of the human and canine variant of Link-N and short (s Link-N on canine chondrocyte-like cells (CLCs and compare this to those on already studied species, i.e. human and bovine CLCs. Extracellular matrix (ECM production was determined by measuring glycosaminoglycan (GAG content and histological evaluation. Additionally, the micro-aggregates' DNA content was measured. Phosphorylated (p Smad1 and -2 levels were determined using ELISA.Human (sLink-N induced GAG deposition in human and bovine CLCs, as expected. In contrast, canine (sLink-N did not affect ECM production in human CLCs, while it mainly induced collagen type I and II deposition in bovine CLCs. In canine CLCs, both canine and human (sLink-N induced negligible GAG deposition. Surprisingly, human and canine (sLink-N did not induce Smad signaling in human and bovine CLCs. Human and canine (sLink-N only mildly increased pSmad1 and Smad2 levels in canine CLCs.Human and canine (sLink-N exerted species-specific effects on CLCs from early degenerated IVDs. Both variants, however, lacked the potency as canine IVD regeneration agent. While these studies demonstrate the challenges of translational studies in large animal models, (sLink-N still holds a regenerative potential for humans.
International Nuclear Information System (INIS)
Leal, L.C.; de Saussure, G.; Perez, R.B.
1989-01-01
The URR computer code has been developed to calculate cross-section probability tables, Bondarenko self-shielding factors, and self- indication ratios for fertile and fissile isotopes in the unresolved resonance region. Monte Carlo methods are utilized to select appropriate resonance parameters and to compute the cross sections at the desired reference energy. The neutron cross sections are calculated by the single-level Breit-Wigner formalism with s-, p-, and d-wave contributions. The cross-section probability tables are constructed by sampling the Doppler broadened cross-section. The various shelf-shielded factors are computed numerically as Lebesgue integrals over the cross-section probability tables. 6 refs
Light-induced cross-linking and post-cross-linking modification of polyglycidol.
Marquardt, F; Bruns, M; Keul, H; Yagci, Y; Möller, M
2018-02-08
The photoinduced radical generation process has received renewed interest due to its economic and ecological appeal. Herein the light-induced cross-linking of functional polyglycidol and its post-cross-linking modification are presented. Linear polyglycidol was first functionalized with a tertiary amine in a two-step reaction. Dimethylaminopropyl functional polyglycidol was cross-linked in a UV-light mediated reaction with camphorquinone as a type II photoinitiator. The cross-linked polyglycidol was further functionalized by quaternization with various organoiodine compounds. Aqueous dispersions of the cross-linked polymers were investigated by means of DLS and zeta potential measurements. Polymer films were evaluated by DSC and XPS.
International Nuclear Information System (INIS)
Silva, M.K.; Neill, R.H.
1994-09-01
The purpose of the Waste Isolation Pilot Plant (WIPP) is to dispose of 176,000 cubic meters of transuranic (TRU) waste generated by the defense activities of the US Government. The envisioned inventory contains approximately 6 million cubic feet of contact-handled transuranic (CH TRU) waste and 250,000 cubic feet of remote handled transuranic (RH TRU) waste. CH TRU emits less than 0.2 rem/hr at the container surface. Of the 250,000 cubic feet of RH TRU waste, 5% by volume can emit up to 1,000 rem/hr at the container surface. The remainder of RH TRU waste must emit less than 100 rem/hr. These are major unresolved problems with the intended disposal of RH TRU waste in the WIPP. (1) The WIPP design requires the canisters of RH TRU waste to be emplaced in the walls (ribs) of each repository room. Each room will then be filled with drums of CH TRU waste. However, the RH TRU waste will not be available for shipment and disposal until after several rooms have already been filled with drums of CH TRU waste. RH TRU disposal capacity will be loss for each room that is first filled with CH TRU waste. (2) Complete RH TRU waste characterization data will not be available for performance assessment because the facilities needed for waste handling, waste treatment, waste packaging, and waste characterization do not yet exist. (3) The DOE does not have a transportation cask for RH TRU waste certified by the US Nuclear Regulatory Commission (NRC). These issues are discussed along with possible solutions and consequences from these solutions. 46 refs
Marzo, Mar; Puig, Marta; Ruiz, Alfredo
2008-02-26
Galileo is the only transposable element (TE) known to have generated natural chromosomal inversions in the genus Drosophila. It was discovered in Drosophila buzzatii and classified as a Foldback-like element because of its long, internally repetitive, terminal inverted repeats (TIRs) and lack of coding capacity. Here, we characterized a seemingly complete copy of Galileo from the D. buzzatii genome. It is 5,406 bp long, possesses 1,229-bp TIRs, and encodes a 912-aa transposase similar to those of the Drosophila melanogaster 1360 (Hoppel) and P elements. We also searched the recently available genome sequences of 12 Drosophila species for elements similar to Dbuz\\Galileo by using bioinformatic tools. Galileo was found in six species (ananassae, willistoni, peudoobscura, persimilis, virilis, and mojavensis) from the two main lineages within the Drosophila genus. Our observations place Galileo within the P superfamily of cut-and-paste transposons and extend considerably its phylogenetic distribution. The interspecific distribution of Galileo indicates an ancient presence in the genus, but the phylogenetic tree built with the transposase amino acid sequences contrasts significantly with that of the species, indicating lineage sorting and/or horizontal transfer events. Our results also suggest that Foldback-like elements such as Galileo may evolve from DNA-based transposon ancestors by loss of the transposase gene and disproportionate elongation of TIRs.
Use of link to mammography screening information and link sharing strategies
DEFF Research Database (Denmark)
Mukai, Thomas; Bro, Flemming; Olesen, Frede
2011-01-01
-43%) reported use of the link. The difference between the two strategies was 15% (95% CI: 8-22%) (Pused the link prior to the screening event, and 37% (95% CI: 30-43%) used the link afterwards. The difference was 9% (95% CI: 0-17%) (P=0.035). Among the GPs in group 1, 40% (95% CI......Introduction: The Internet is increasingly being used for disseminating knowledge in health care. Often this is done through a ‘Uniform Resource Locator’ (URL), better known as a link. There are three ways of sharing a link: verbally, in print or electronically. Furthermore, timing and exposure...... in Central Denmark Region, we constructed a website containing screening programme information for GPs. We inserted the link to this website in different media and divided the GPs into three groups: Group 1 received a letter prior to the screening event and an electronic test result after the screening...
Wallops Low Elevation Link Analysis for the Constellation Launch/Ascent Links
Cheung, Keith; Ho, C.; Kantak, A.; Lee, C.; Tye, R.; Richards, E.; Sham, C.; Schlesinger, A.; Barritt, B.
2011-01-01
To execute the President's Vision for Space Exploration, the Constellation Program (CxP) was formed to build the next generation spacecraft Orion and launch vehicles Ares, to transport human and cargo to International Space Station (ISS), moon, and Mars. This paper focuses on the detailed link analysis for Orion/Ares s launch and ascent links with Wallops 11.3m antenna (1) Orion's Dissimilar Voice link: 10.24 Kbps, 2-way (2) Ares Developmental Flight Instrument link, 20 Mbps, downlink. Three launch trajectories are considered: TD7-E, F (Feb), and G (Aug). In certain launch scenarios, the critical events of main engine cutoff (MECO) and Separation occur during the low elevation regime of WFF s downrange -- less than 5 degree elevation angle. The goal of the study is to access if there is enough link margins for WFF to track the DV and DFI links.
On the specification of bus voltages and radial link transfer impedance modes
Energy Technology Data Exchange (ETDEWEB)
El-Sadik, F.M. [Khartoum Univ., Aljamaa, Khartoum (Sudan)
2010-07-01
No algebraic equation has been derived for the steady-state stability limit (SSSL) of radial power system components in terms of their resistive sectional impedance elements and associated scalar node voltage constraints. While many criterion have been developed in the literature for the steady state angle and voltage stability limits of systems with losses, speculation exists about certain advocated metrics for these systems in terms of stability reserve margins as a measure of the risk of blackout and the representation of reactance modes associated with Putman's model for synchronous machines. This paper presented the results of a generalized algebraic statement for the reactance modes under stability conditions in voltage-specified power system components cited in the single machine-infinite bus (SMIB) and the radial power link (RPL) systems. The direct analytical solution to the problem enabled the identification of 2 different constraint relations for the sending (E) and receiving-end voltage regulator (VR) voltages. The paper discussed the general SSSL function plan, conditions for SMIB system reactances, and index results for the voltage stability of radial lines. The results for the R2 influence and influence on radial compensation levels were also presented. Index results for non-operational reactance zones were provided. It was concluded that the algebraic solution in a full representation of system losses would enable identification of additional function discontinuities that might not reveal in a step-by-step numerical algorithm and that may account for the many unresolved transmission system phenomenon associated with SSSL predictions and capacitance compensation schemes. 11 refs., 1 tab., 5 figs., 3 appendices.
Greifender, Elke; Seadle, Michael
2013-01-01
Linked Data (LD), Linked Open Data (LOD) and generating a web of data, present the new knowledge sharing frontier. In a philosophical context, LD is an evolving environment that reflects humankinds' desire to understand the world by drawing on the latest technologies and capabilities of the time. LD, while seemingly a new phenomenon did not emerge overnight; rather it represents the natural progression by which knowledge structures are developed, used, and shared. Linked Open Vocabularies is a significant trajectory of LD. Linked Open Vocabularies targets vocabularies that have traditionally b
Horton, John R; Engstrom, Amanda; Zoeller, Elizabeth L; Liu, Xu; Shanks, John R; Zhang, Xing; Johns, Margaret A; Vertino, Paula M; Fu, Haian; Cheng, Xiaodong
2016-02-05
The KDM5/JARID1 family of Fe(II)- and α-ketoglutarate-dependent demethylases remove methyl groups from tri- and dimethylated lysine 4 of histone H3. Accumulating evidence from primary tumors and model systems supports a role for KDM5A (JARID1A/RBP2) and KDM5B (JARID1B/PLU1) as oncogenic drivers. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC). Here we demonstrate that internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes. We present a crystal structure of the linked JmjN-JmjC domain from KDM5A, which reveals that the linked domain fully reconstitutes the cofactor (metal ion and α-ketoglutarate) binding characteristics of other structurally characterized Jumonji domain demethylases. Docking studies with GSK-J1, a selective inhibitor of the KDM6/KDM5 subfamilies, identify critical residues for binding of the inhibitor to the reconstituted KDM5 Jumonji domain. Further, we found that GSK-J1 inhibited the demethylase activity of KDM5C with 8.5-fold increased potency compared with that of KDM5B at 1 mm α-ketoglutarate. In contrast, JIB-04 (a pan-inhibitor of the Jumonji demethylase superfamily) had the opposite effect and was ~8-fold more potent against KDM5B than against KDM5C. Interestingly, the relative selectivity of JIB-04 toward KDM5B over KDM5C in vitro translates to a ~10-50-fold greater growth-inhibitory activity against breast cancer cell lines. These data define the minimal requirements for enzymatic activity of the KDM5 family to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain and provide structural characterization of the linked JmjN-JmjC domain for the KDM5 family, which should prove useful in the
Effect of Link Flexibility on tip position of a single link robotic arm
Madhusudan Raju, E.; Siva Rama Krishna, L.; Mouli, Y. Sharath Chandra; Nageswara Rao, V.
2015-12-01
The flexible robots are widely used in space applications due to their quick response, lower energy consumption, lower overall mass and operation at high speed compared to conventional industrial rigid link robots. These robots are inherently flexible, so that the kinematics of flexible robots can't be solved with rigid body assumptions. The flexibility in links and joints affects end-point positioning accuracy of the robot. It is important to model the link kinematics with precision which in turn simplifies modelling of dynamics of flexible robots. The main objective of this paper is to evaluate the effect of link flexibility on a tip position of a single link robotic arm for a given motion. The joint is assumed to be rigid and only link flexibility is considered. The kinematics of flexible link problem is evaluated by Assumed Modes Method (AMM) using MAT LAB Programming. To evaluate the effect of link flexibility (with and without payload) of robotic arm, the normalized tip deviation is found for flexible link with respect to a rigid link. Finally, the limiting inertia for payload mass is found if the allowable tip deviation is 5%.
Leadbetter, Adam; Arko, Robert; Chandler, Cynthia; Shepherd, Adam
2014-05-01
"Linked Data" is a term used in Computer Science to encapsulate a methodology for publishing data and metadata in a structured format so that links may be created and exploited between objects. Berners-Lee (2006) outlines the following four design principles of a Linked Data system: Use Uniform Resource Identifiers (URIs) as names for things. Use HyperText Transfer Protocol (HTTP) URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (Resource Description Framework [RDF] and the RDF query language [SPARQL]). Include links to other URIs so that they can discover more things. In 2010, Berners-Lee revisited his original design plan for Linked Data to encourage data owners along a path to "good Linked Data". This revision involved the creation of a five star rating system for Linked Data outlined below. One star: Available on the web (in any format). Two stars: Available as machine-readable structured data (e.g. An Excel spreadsheet instead of an image scan of a table). Three stars: As two stars plus the use of a non-proprietary format (e.g. Comma Separated Values instead of Excel). Four stars: As three stars plus the use of open standards from the World Wide Web Commission (W3C) (i.e. RDF and SPARQL) to identify things, so that people can point to your data and metadata. Five stars: All the above plus link your data to other people's data to provide context Here we present work building on the SeaDataNet common vocabularies served by the NERC Vocabulary Server, connecting projects such as the Rolling Deck to Repository (R2R) and the Biological and Chemical Oceanography Data Management Office (BCO-DMO) and other vocabularies such as the Marine Metadata Interoperability Ontology Register and Repository and the NASA Global Change Master Directory to create a Linked Ocean Data cloud. Publishing the vocabularies and metadata in standard RDF XML and exposing SPARQL endpoints renders them five-star Linked
Novel members of the adipokinetic hormone family in beetles of the superfamily Scarabaeoidea
Czech Academy of Sciences Publication Activity Database
Gäde, G.; Šimek, Petr; Marco, H. G.
2016-01-01
Roč. 48, č. 12 (2016), s. 2785-2798 ISSN 0939-4451 R&D Projects: GA ČR GA13-18509S Institutional support: RVO:60077344 Keywords : insects * beetles * Scarabaeidae Subject RIV: ED - Physiology Impact factor: 3.173, year: 2016 http://link.springer.com/article/10.1007%2Fs00726-016-2314-0
Visualisierung von typisierten Links in Linked Data
Directory of Open Access Journals (Sweden)
Georg Neubauer
2017-09-01
Full Text Available Das Themengebiet der Arbeit behandelt Visualisierungen von typisierten Links in Linked Data. Die wissenschaftlichen Gebiete, die im Allgemeinen den Inhalt des Beitrags abgrenzen, sind das Semantic Web, das Web of Data und Informationsvisualisierung. Das Semantic Web, das von Tim Berners Lee 2001 erfunden wurde, stellt eine Erweiterung zum World Wide Web (Web 2.0 dar. Aktuelle Forschungen beziehen sich auf die Verknüpfbarkeit von Informationen im World Wide Web. Um es zu ermöglichen, solche Verbindungen wahrnehmen und verarbeiten zu können sind Visualisierungen die wichtigsten Anforderungen als Hauptteil der Datenverarbeitung. Im Zusammenhang mit dem Sematic Web werden Repräsentationen von zuhammenhängenden Informationen anhand von Graphen gehandhabt. Der Grund des Entstehens dieser Arbeit ist in erster Linie die Beschreibung der Gestaltung von Linked Data-Visualisierungskonzepten, deren Prinzipien im Rahmen einer theoretischen Annäherung eingeführt werden. Anhand des Kontexts führt eine schrittweise Erweiterung der Informationen mit dem Ziel, praktische Richtlinien anzubieten, zur Vernetzung dieser ausgearbeiteten Gestaltungsrichtlinien. Indem die Entwürfe zweier alternativer Visualisierungen einer standardisierten Webapplikation beschrieben werden, die Linked Data als Netzwerk visualisiert, konnte ein Test durchgeführt werden, der deren Kompatibilität zum Inhalt hatte. Der praktische Teil behandelt daher die Designphase, die Resultate, und zukünftige Anforderungen des Projektes, die durch die Testung ausgearbeitet wurden.
International Nuclear Information System (INIS)
Ferrell, C.M.; Soffer, L.
1989-09-01
Unresolved Safety Issue (USI) A-48 arose as a result of the large amount of hydrogen generated and burned within containment during the Three Mile Island accident. This issue covers hydrogen control measures for recoverable degraded-core accidents for all boiling-water reactors (BWRs) and those pressurized-water reactors (PWRs) with ice-condenser containments. The Commission and the nuclear industry have sponsored extensive research in this area, which has led to significant revision of the Commission's hydrogen control regulations, given in Title 10, Code of Federal Regulations, Part 50 (10 CFR 50), Section 50.44. BWRs having Mark I and II containments are presently required to operate with inerted containment atmospheres that effectively prevent hydrogen combustion. BWRs with Mark III containments and PWRs with ice-condenser containments are now required to be equipped with hydrogen control systems to protect containment integrity and safety systems inside containment. Industry has chosen to use hydrogen igniter systems to burn hydrogen produced in a controlled fashion to prevent damage. An independent review by a Committee of the National Research Council concluded that, for most accident scenarios, current regulatory requirements make it highly unlikely that hydrogen detonation would be the cause of containment failure. On the basis of the extensive research effort conducted and current regulatory requirements, including their implementation, the staff concludes that no new regulatory guidance on hydrogen control for recoverable degraded-core accidents for these types of plants is necessary and that USI A-48 is resolved
Directory of Open Access Journals (Sweden)
Kürster M.
2011-07-01
Full Text Available From radial velocity (RV detections alone one does not get all orbital parameters needed to derive the true mass of a non-transiting, unresolved substellar companion to a star. Additional astrometric measurements are needed to calculate the inclination and the longitude of the ascending node. Until today only few true substellar companion masses have been determined by this method with the HST fine guidance sensor [1, 2]. We aim to derive the true mass of a brown dwarf candidate companion to an early M 2.5V dwarf with groundbased high-resolution astrometry aided by adaptive optics. We found this unique brown dwarf desert object, whose distance to the host star is only 0.42 AU, in our UVES precision RV survey of M dwarfs, inferring a minimum companion mass of 27 Jupiter masses [3]. Combining the data with HIPPARCOS astrometry, we found a probability of only 2.9% that the companion is stellar. We therefore observed the host star together with a reference star within a monitoring program with VLT/NACO to derive the true mass of the companion and establish its nature (brown dwarf vs. star. Simultaneous observations of a reference field in a globular cluster are performed to determine the stability of the adaptive optics (AO plus detector system and check its suitability for such high-precision astrometric measurements over several epochs which are needed to find and analyse extrasolar planet systems.
LinkMind: Link Optimization in Swarming Mobile Sensor Networks
DEFF Research Database (Denmark)
Ngo, Trung Dung
2012-01-01
of the most advantageous properties of the swarming wireless sensor network is that mobile nodes can work cooperatively to organize an ad-hoc network and optimize the network link capacity to maximize the transmission of gathered data from a source to a target. This paper describes a new method of link...... optimization of swarming mobile sensor networks. The new method is based on combination of the artificial potential force guaranteeing connectivities of the mobile sensor nodes and the max-flow min-cut theorem of graph theory ensuring optimization of the network link capacity. The developed algorithm...
Yu, Jingyin; Tehrim, Sadia; Wang, Linhai; Dossa, Komivi; Zhang, Xiurong; Ke, Tao; Liao, Boshou
2017-09-18
The cytochrome P450 monooxygenase (P450) superfamily is involved in the biosynthesis of various primary and secondary metabolites. However, little is known about the effects of whole genome duplication (WGD) and tandem duplication (TD) events on the evolutionary history and functional divergence of P450s in Brassica after splitting from a common ancestor with Arabidopsis thaliana. Using Hidden Markov Model search and manual curation, we detected that Brassica species have nearly 1.4-fold as many P450 members as A. thaliana. Most P450s in A. thaliana and Brassica species were located on pseudo-chromosomes. The inferred phylogeny indicated that all P450s were clustered into two different subgroups. Analysis of WGD event revealed that different P450 gene families had appeared after evolutionary events of species. For the TD event analyses, the P450s from TD events in Brassica species can be divided into ancient and recent parts. Our comparison of influence of WGD and TD events on the P450 gene superfamily between A. thaliana and Brassica species indicated that the family-specific evolution in the Brassica lineage can be attributed to both WGD and TD, whereas WGD was recognized as the major mechanism for the recent evolution of the P450 super gene family. Expression analysis of P450s from A. thaliana and Brassica species indicated that WGD-type P450s showed the same expression pattern but completely different expression with TD-type P450s across different tissues in Brassica species. Selection force analysis suggested that P450 orthologous gene pairs between A. thaliana and Brassica species underwent negative selection, but no significant differences were found between P450 orthologous gene pairs in A. thaliana-B. rapa and A. thaliana-B. oleracea lineages, as well as in different subgenomes in B. rapa or B. oleracea compared with A. thaliana. This study is the first to investigate the effects of WGD and TD on the evolutionary history and functional divergence of P450
Wallops' Low Elevation Link Analysis for the Constellation Launch/Ascent Links
Cheung, Kar-Ming; Ho, Christian; Kantak, Anil; Lee, Charles; Tye, Robert; Richards, Edger; Sham, Catherine; Schlesinger, Adam; Barritt, Brian
2011-01-01
Prior to the redirection of the Constellation Program, the Wallops 11.3-meter ground station was tasked to support the Orion's Dissimilar Voice (DV) link and the Ares's Development Flight Instrument (DFI) link. Detailed analysis of the launch trajectories indicates that during the launch and ascent operation, the critical events of Orion-Ares main engine cut off (MECO) and Separation occur at low elevation angle. We worked with engineers from both Wallops Flight Facility (WFF) and Johnson Space Center (JSC) to perform an intensive measurement and link analysis campaign on the DV and DFI links. The main results were as follows: (1) The DV links have more than 3 dB margin at MECO and Separation. (2) The DFI links have 0 dB margin at Separation during certain weather condition in summer season. (3) Tropospheric scintillation loss is the major impairment at low elevation angle. (4) The current scintillation models in the Recommendation ITU-R P.618 (Propagation data and prediction methods required for the design of Earth-space telecommunication systems), which are based on limited experimental and theoretical work, exhibit idiosyncratic behaviors. We developed an improved model based on the measurements of recent Shuttle mission launch and ascent links and the ITU propagation data. (5) Due to the attitude uncertainty of the Orion-Ares stack, the high dynamics of the launch and ascent trajectory, and the irregularity of the Orion and Ares antenna patterns, we employed new link analysis approach to model the spacecraft antenna gain. In this paper we discuss the details of the aforementioned results.
Khovanov homology of graph-links
Energy Technology Data Exchange (ETDEWEB)
Nikonov, Igor M [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)
2012-08-31
Graph-links arise as the intersection graphs of turning chord diagrams of links. Speaking informally, graph-links provide a combinatorial description of links up to mutations. Many link invariants can be reformulated in the language of graph-links. Khovanov homology, a well-known and useful knot invariant, is defined for graph-links in this paper (in the case of the ground field of characteristic two). Bibliography: 14 titles.
Directory of Open Access Journals (Sweden)
Ben L Phillips
Full Text Available Pathogen spread can cause population declines and even species extinctions. Nonetheless, in the absence of tailored monitoring schemes, documenting pathogen spread can be difficult. In the case of worldwide amphibian declines the best present understanding is that the chytrid fungus Batrachochytrium dendrobatidis (Bd has recently spread, causing amphibian declines and extinction in the process. However, good evidence demonstrating pathogen arrival followed by amphibian decline is rare, and analysis of putative evidence is often inadequate. Here we attempt to examine the relationship between Bd arrival and amphibian decline across north-eastern Australia, using sites where a wave-like pattern of amphibian decline was first noticed and at which intensive research has since been conducted. We develop an analytical framework that allows rigorous estimation of pathogen arrival date, which can then be used to test for a correlation between the time of pathogen arrival and amphibian decline across sites. Our results show that, with the current dataset, the earliest possible arrival date of Bd in north-eastern Australia is completely unresolved; Bd could have arrived immediately before sampling commenced or may have arrived thousands of years earlier, the present data simply cannot say. The currently available data are thus insufficient to assess the link between timing of pathogen arrival and population decline in this part of the world. This data insufficiency is surprising given that there have been decades of research on chytridiomycosis in Australia and that there is a general belief that the link between Bd arrival and population decline is well resolved in this region. The lack of data on Bd arrival currently acts as a major impediment to determining the role of environmental factors in driving the global amphibian declines, and should be a major focus of future research.
Li, Xiaoqin; Guo, Rongrong; Li, Jun; Singer, Stacy D; Zhang, Yucheng; Yin, Xiangjing; Zheng, Yi; Fan, Chonghui; Wang, Xiping
2013-10-01
Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encoding NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. In plants, they are involved in many biological processes and play a role in the response to environmental stress. In this study, a total of 39 ALDH genes from ten families were identified in the apple (Malus × domestica Borkh.) genome. Synteny analysis of the apple ALDH (MdALDH) genes indicated that segmental and tandem duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of these gene families in apple. Moreover, synteny analysis between apple and Arabidopsis demonstrated that several MdALDH genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes appeared before the divergence of lineages that led to apple and Arabidopsis. In addition, phylogenetic analysis, as well as comparisons of exon-intron and protein structures, provided further insight into both their evolutionary relationships and their putative functions. Tissue-specific expression analysis of the MdALDH genes demonstrated diverse spatiotemporal expression patterns, while their expression profiles under abiotic stress and various hormone treatments indicated that many MdALDH genes were responsive to high salinity and drought, as well as different plant hormones. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles, of the apple MdALDH genes will not only be useful for the further analysis of ALDH genes and their roles in stress response, but may also aid in the future improvement of apple stress tolerance. Copyright © 2013 Elsevier Masson SAS. All rights reserved.
Wongnate, Thanyaporn; Chaiyen, Pimchai
2013-07-01
Enzymes in the glucose-methanol-choline (GMC) oxidoreductase superfamily catalyze the oxidation of an alcohol moiety to the corresponding aldehyde. In this review, the current understanding of the sugar oxidation mechanism in the reaction of pyranose 2-oxidase (P2O) is highlighted and compared with that of other enzymes in the GMC family for which structural and mechanistic information is available, including glucose oxidase, choline oxidase, cholesterol oxidase, cellobiose dehydrogenase, aryl-alcohol oxidase, and pyridoxine 4-oxidase. Other enzymes in the family that have been newly discovered or for which less information is available are also discussed. A large primary kinetic isotope effect was observed for the flavin reduction when 2-d-D-glucose was used as a substrate, but no solvent kinetic isotope effect was detected for the flavin reduction step. The reaction of P2O is consistent with a hydride transfer mechanism in which there is stepwise formation of d-glucose alkoxide prior to the hydride transfer. Site-directed mutagenesis of P2O and pH-dependence studies indicated that His548 is a catalytic base that facilitates the deprotonation of C2-OH in D-glucose. This finding agrees with the current mechanistic model for aryl-alcohol oxidase, glucose oxidase, cellobiose dehydrogenase, methanol oxidase, and pyridoxine 4-oxidase, but is different from that of cholesterol oxidase and choline oxidase. Although all of the GMC enzymes share similar structural folding and use the hydride transfer mechanism for flavin reduction, they appear to have subtle differences in the fine-tuned details of how they catalyze substrate oxidation. © 2013 The Authors Journal compilation © 2013 FEBS.
Adiponectin in mice with altered GH action: links to insulin sensitivity and longevity?
Lubbers, Ellen R; List, Edward O; Jara, Adam; Sackman-Sala, Lucila; Cordoba-Chacon, Jose; Gahete, Manuel D; Kineman, Rhonda D; Boparai, Ravneet; Bartke, Andrzej; Kopchick, John J; Berryman, Darlene E
2013-03-01
Adiponectin is positively correlated with longevity and negatively correlated with many obesity-related diseases. While there are several circulating forms of adiponectin, the high-molecular-weight (HMW) version has been suggested to have the predominant bioactivity. Adiponectin gene expression and cognate serum protein levels are of particular interest in mice with altered GH signaling as these mice exhibit extremes in obesity that are positively associated with insulin sensitivity and lifespan as opposed to the typical negative association of these factors. While a few studies have reported total adiponectin levels in young adult mice with altered GH signaling, much remains unresolved, including changes in adiponectin levels with advancing age, proportion of total adiponectin in the HMW form, adipose depot of origin, and differential effects of GH vs IGF1. Therefore, the purpose of this study was to address these issues using assorted mouse lines with altered GH signaling. Our results show that adiponectin is generally negatively associated with GH activity, regardless of age. Further, the amount of HMW adiponectin is consistently linked with the level of total adiponectin and not necessarily with previously reported lifespan or insulin sensitivity of these mice. Interestingly, circulating adiponectin levels correlated strongly with inguinal fat mass, implying that the effects of GH on adiponectin are depot specific. Interestingly, rbGH, but not IGF1, decreased circulating total and HMW adiponectin levels. Taken together, these results fill important gaps in the literature related to GH and adiponectin and question the frequently reported associations of total and HMW adiponectin with insulin sensitivity and longevity.
Phosphorylation of human link proteins
International Nuclear Information System (INIS)
Oester, D.A.; Caterson, B.; Schwartz, E.R.
1986-01-01
Three link proteins of 48, 44 and 40 kDa were purified from human articular cartilage and identified with monoclonal anti-link protein antibody 8-A-4. Two sets of lower molecular weight proteins of 30-31 kDa and 24-26 kDa also contained link protein epitopes recognized by the monoclonal antibody and were most likely degradative products of the intact link proteins. The link proteins of 48 and 40 kDa were identified as phosphoproteins while the 44 kDa link protein did not contain 32 P. The phosphorylated 48 and 40 kDa link proteins contained approximately 2 moles PO 4 /mole link protein
Kanda, Atsuhiro; Satake, Honoo; Kawada, Tsuyoshi; Minakata, Hiroyuki
2004-01-01
The common octopus, Octopus vulgaris, is the first invertebrate species that was shown to possess two oxytocin/vasopressin (OT/VP) superfamily peptides, octopressin (OP) and cephalotocin (CT). Previously, we cloned a GPCR (G-protein-coupled receptor) specific to CT [CTR1 (CT receptor 1)]. In the present study, we have identified an additional CTR, CTR2, and a novel OP receptor, OPR. Both CTR2 and OPR include domains and motifs typical of GPCRs, and the intron– exon structures are in accord with those of OT/VP receptor genes. CTR2 and OPR expressed in Xenopus oocytes induced calcium-mediated inward chloride current in a CT- and OP-specific manner respectively. Several regions and residues, which are requisite for binding of the vertebrate OT/VP receptor family with their ligands, are highly conserved in CTRs, but not in OPR. These different sequences between CTRs and OPR, as well as the amino acid residues of OP and CT at positions 2–5, were presumed to play crucial roles in the binding selectivity to their receptors, whereas the difference in the polarity of OT/VP family peptide residues at position 8 confers OT and VP with the binding specificity in vertebrates. CTR2 mRNA was present in various peripheral tissues, and OPR mRNA was detected in both the nervous system and peripheral tissues. Our findings suggest that the CT and OP genes, similar to the OT/VP family, evolved through duplication, but the ligand–receptor selectivity were established through different evolutionary lineages from those of their vertebrate counterparts. PMID:15504101
Directory of Open Access Journals (Sweden)
Bua-In Saowaluck
2014-01-01
Full Text Available Cassumunar ginger (Zingiber montanum (Koenig Link ex Dietr. is a native Thai herb with a high content and large variety of terpenoids in its essential oil. Improving the essential oil content and quality of cassumunar ginger is difficult for a breeder due to its clonally propagated nature. In this research, we describe the isolation and expression level of the monoterpene synthase gene that controls the key step of essential oil synthesis in this plant and evaluate the mechanical wounding that may influence the transcription level of the monoterpene synthase gene. To isolate the gene, the selected clones from DNA derived from young leaves were sequenced and analyzed and the monoterpene synthase gene from cassumunar ginger (ZMM1 was identified. The ZMM1 CDS containing 1 773 bp (KF500399 is predicted to encode a protein of 590 amino acids. The deduced amino acid sequence is 40-74% identical with known sequences of other angiosperm monoterpene synthases belonging to the isoprenoid biosynthesis C1 superfamily. A transcript of ZMM1 was detected almost exclusively in the leaves and was related to leaf wounding. The results of this research offer insight into the control of monoterpene synthesis in this plant. This finding can be applied to breeding programs or crop management of cassumunar ginger for better yield and quality of essential oil.
The pulsar contribution to the diffuse galactic gamma-ray emission
DEFF Research Database (Denmark)
Pohl, M.; Kanbach, G.; Hunter, S.D.
1997-01-01
There is active interest in the extent to which unresolved gamma-ray pulsars contribute to the Galactic diffuse emission, and in whether unresolved gamma-ray pulsars could be responsible for the excess of diffuse Galactic emission above 1 GeV that has been observed by EGRET. The diffuse gamma......-ray intensity due to unresolved pulsars is directly linked to the number of objects that should be observed in the EGRET data. We can therefore use our knowledge of the unidentified EGRET sources to constrain model parameters like the pulsar birthrate and their beaming angle. This analysis is based only...... on the properties of the six pulsars that have been identified in the EGRET data and is independent of choice of a pulsar emission model. We find that pulsars contribute very little to the diffuse emission at lower energies, whereas above 1 GeV they can account for 18% of the observed intensity in selected regions...
Novel p47phox-related organizers regulate NADPH oxidase 1 (Nox1) activity and localization
Gianni, Davide; Diaz, Begoña; Taulet, Nicolas; Fowler, Bruce; Courtneidge, Sara A.; Bokoch, Gary M.
2010-01-01
The mechanisms that determine localized formation of reactive oxygen species (ROS) via NADPH oxidases (Nox) in nonphagocytic cells are unknown. We show that the c-Src substrate proteins Tks4 and Tks5 are functional members of a p47phox-related organizer superfamily. Tks proteins selectively support Nox1 and Nox3 (vs. Nox2 and Nox4) activity in reconstituted cellular systems, and interact with the NoxA1 activator protein through an SH3-mediated interaction. Endogenous Tks4 is required for Rac GTPase-dependent ROS production by DLD1 colon cancer cells. Tks4 recruits Nox1 to invadopodia that form in DLD1 cells in a Tks- and Nox-dependent fashion. We propose that Tks organizers represent novel members of an organizer superfamily that link Nox to localized ROS formation. PMID:19755710
TULIP: A Link-Level Protocol for Improving TCP over Wireless Links
National Research Council Canada - National Science Library
Parsa, Christina; Garcia-Luna-Aceves, J. J
1999-01-01
We present the transport unaware link improvement protocol (TULIP), which dramatically improves the performance of TCP over lossy wireless links, without competing with or modifying the transport- or network-layer protocols...
International Nuclear Information System (INIS)
Harada, Hiroo; Asai, Kiyoshi; Kihara, Kazuhisa.
1981-09-01
The purpose of dynamic link facility is to link a load module dynamically only when it is used in execution time. The facility is very useful for development, execution and maintenance of a large scale computer program which is too big to be saved as one load module in main memory, or it is poor economy to save it due to many unused subroutines depending on an input. It is also useful for standardization and common utilization of programs. Standard usage of dynamic link facility of FACOM M-200 computer system, a software tool which analyzes the effect of dynamic link facility and application of dynamic link to nuclear codes are described. (author)
Energy Technology Data Exchange (ETDEWEB)
Helton, Jon C. [Arizona State Univ., Tempe, AZ (United States); Brooks, Dusty Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sallaberry, Cedric Jean-Marie. [Engineering Mechanics Corp. of Columbus, OH (United States)
2018-02-01
Representations are developed and illustrated for the distribution of link property values at the time of link failure in the presence of aleatory uncertainty in link properties. The following topics are considered: (i) defining properties for weak links and strong links, (ii) cumulative distribution functions (CDFs) for link failure time, (iii) integral-based derivation of CDFs for link property at time of link failure, (iv) sampling-based approximation of CDFs for link property at time of link failure, (v) verification of integral-based and sampling-based determinations of CDFs for link property at time of link failure, (vi) distributions of link properties conditional on time of link failure, and (vii) equivalence of two different integral-based derivations of CDFs for link property at time of link failure.
A comprehensive comparison of network similarities for link prediction and spurious link elimination
Zhang, Peng; Qiu, Dan; Zeng, An; Xiao, Jinghua
2018-06-01
Identifying missing interactions in complex networks, known as link prediction, is realized by estimating the likelihood of the existence of a link between two nodes according to the observed links and nodes' attributes. Similar approaches have also been employed to identify and remove spurious links in networks which is crucial for improving the reliability of network data. In network science, the likelihood for two nodes having a connection strongly depends on their structural similarity. The key to address these two problems thus becomes how to objectively measure the similarity between nodes in networks. In the literature, numerous network similarity metrics have been proposed and their accuracy has been discussed independently in previous works. In this paper, we systematically compare the accuracy of 18 similarity metrics in both link prediction and spurious link elimination when the observed networks are very sparse or consist of inaccurate linking information. Interestingly, some methods have high prediction accuracy, they tend to perform low accuracy in identification spurious interaction. We further find that methods can be classified into several cluster according to their behaviors. This work is useful for guiding future use of these similarity metrics for different purposes.
Adiponectin in mice with altered growth hormone action: links to insulin sensitivity and longevity?
Lubbers, Ellen R.; List, Edward O.; Jara, Adam; Sackman-Sala, Lucila; Cordoba-Chacon, Jose; Gahete, Manuel D.; Kineman, Rhonda D.; Boparai, Ravneet; Bartke, Andrzej; Kopchick, John J.; Berryman, Darlene E.
2013-01-01
Adiponectin is positively correlated with longevity and negatively correlated with many obesity-related diseases. While there are several circulating forms of adiponectin, the high molecular weight (HMW) version has been suggested to have the predominant bioactivity. Adiponectin gene expression and cognate serum protein levels are of particular interest in mice with altered growth hormone (GH) signaling as these mice exhibit extremes in obesity that are positively associated with insulin sensitivity and lifespan as opposed to the typical negative association of these factors. While a few studies have reported total adiponectin levels in young adult mice with altered GH signaling, much remains unresolved, including changes in adiponectin levels with advancing age, proportion of total adiponectin in the HMW form, adipose depot of origin, and differential effects of GH versus IGF1. Therefore, the purpose of this study was to address these issues using assorted mouse lines with altered GH signaling. Our results show that adiponectin is generally negatively associated with GH activity, regardless of age. Further, the amount of HMW adiponectin is consistently linked with the level of total adiponectin and not necessarily with previously reported lifespan or insulin sensitivity of these mice. Interestingly, circulating adiponectin levels correlated strongly with inguinal fat mass, implying the effects of GH on adiponectin are depot-specific. Interestingly rbGH, but not IGF1, decreased circulating total and HMW adiponectin levels. Taken together, these results fill important gaps in the literature related to GH and adiponectin and question the frequently reported associations of total and HMW adiponectin with insulin sensitivity and longevity. PMID:23261955
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Wu, Zhihao; Lin, Youfang; Zhao, Yiji; Yan, Hongyan
2018-02-01
Networks can represent a wide range of complex systems, such as social, biological and technological systems. Link prediction is one of the most important problems in network analysis, and has attracted much research interest recently. Many link prediction methods have been proposed to solve this problem with various techniques. We can note that clustering information plays an important role in solving the link prediction problem. In previous literatures, we find node clustering coefficient appears frequently in many link prediction methods. However, node clustering coefficient is limited to describe the role of a common-neighbor in different local networks, because it cannot distinguish different clustering abilities of a node to different node pairs. In this paper, we shift our focus from nodes to links, and propose the concept of asymmetric link clustering (ALC) coefficient. Further, we improve three node clustering based link prediction methods via the concept of ALC. The experimental results demonstrate that ALC-based methods outperform node clustering based methods, especially achieving remarkable improvements on food web, hamster friendship and Internet networks. Besides, comparing with other methods, the performance of ALC-based methods are very stable in both globalized and personalized top-L link prediction tasks.
Directory of Open Access Journals (Sweden)
Stephanie E Hesselson
2009-09-01
Full Text Available Membrane transporters play crucial roles in the cellular uptake and efflux of an array of small molecules including nutrients, environmental toxins, and many clinically used drugs. We hypothesized that common genetic variation in the proximal promoter regions of transporter genes contribute to observed variation in drug response. A total of 579 polymorphisms were identified in the proximal promoters (-250 to +50 bp and flanking 5' sequence of 107 transporters in the ATP Binding Cassette (ABC and Solute Carrier (SLC superfamilies in 272 DNA samples from ethnically diverse populations. Many transporter promoters contained multiple common polymorphisms. Using a sliding window analysis, we observed that, on average, nucleotide diversity (pi was lowest at approximately 300 bp upstream of the transcription start site, suggesting that this region may harbor important functional elements. The proximal promoters of transporters that were highly expressed in the liver had greater nucleotide diversity than those that were highly expressed in the kidney consistent with greater negative selective pressure on the promoters of kidney transporters. Twenty-one promoters were evaluated for activity using reporter assays. Greater nucleotide diversity was observed in promoters with strong activity compared to promoters with weak activity, suggesting that weak promoters are under more negative selective pressure than promoters with high activity. Collectively, these results suggest that the proximal promoter region of membrane transporters is rich in variation and that variants in these regions may play a role in interindividual variation in drug disposition and response.
DC-Link Compensation Method for Slim DC Link Drives Fed by Soft Grid
DEFF Research Database (Denmark)
Mathe, Laszlo; Rosendahl Andersen, Henrik; Lazar, Radu
2010-01-01
Slim DC-link PWM (AC) drives for lowperformance applications are emerging on the market. Such drives equipped with a small DC-link capacitance exhibit instability tendencies, if installed on a soft line, giving a degraded performance. The total harmonic distortion (THD) and the partially weighted...... harmonic distortion (PWHD) of the line current are degraded, if resonance between the line impedance and the DC-link capacitance occurs. Likewise, the motor performance is affected negatively giving extra torque ripple, vibration and acoustic-noise emission. This paper proposes a novel DC-link compensation...
International Nuclear Information System (INIS)
Leal, L.; Shibata, K.; Iwamoto, O.; Chiba, G.; Noguere, G.; Saint Jean, C. de; Sirakov, I.; Capote, R.; Sublet, J.C.; Coste-Delclaux, M.; Jouanne, C.; MacFarlane, R.E.; Kahler, A.C. Jr.; Lubitz, C.R.; Cullen, D.; Herman, M.; Ribon, P.
2011-01-01
This report summarises the work performed under WPEC Subgroup 32 (SG32) on issues pertinent to the methodology used in the unresolved resonance region (URR). The main purpose of SG32 was to verify the validity of the Single-level Breit-Wigner (SLBW) cross-section representation in the URR for self-shielding calculations. While SG32 work was under way, several other developments related to the URR on this subject came into play that had a direct impact on the results of calculations. The work described in this report focuses on: - testing of the SLBW formalism in the URR for fissile and fertile isotopes; - URR covariance representation; - interpolation issue with a URR resonance parameter for the infinitely dilute cross-section calculations; - ENDF URR parameter representation based on the LSSF = 0 or LSSF = 1 option
Linked Data Reactor: a Framework for Building Reactive Linked Data Applications
Khalili, Ali
2016-01-01
This paper presents Linked Data Reactor (LD-Reactor or LD-R) as a framework for developing exible and reusable User Interface components for Linked Data applications. LD-Reactor utilizes Facebook's ReactJS components, Flux architecture and Yahoo's Fluxible framework for isomorphic Web applications.
Ma, Wen; Waffo-Téguo, Pierre; Alessandra Paissoni, Maria; Jourdes, Michäel; Teissedre, Pierre-Louis
2018-05-30
Polymeric tannins from grapes have always been reported as an unresolved broad peak in HPLC chromatograms, and this has severely limited their identification to date. This study aimed to disassemble this broad peak and explore the polymeric tannin molecules inside. By applying centrifugal partition chromatography (CPC), an efficient separation approach was developed to split the broad peak of grape seed tannins into fractions. Then, the fractions were analyzed by Q-ToF (quadrupole time-of-flight mass spectrometry) to determine the corresponding structures of the tannins. The results suggest that grape seed polymeric tannins were eluted consecutively according to their degree of polymerization (DP). Condensed tannins identified in wine grape seed have a range of DP and degree of galloylation (DG) up to 20 and 11, respectively. The molecular mass of the largest molecule detected was 6067. To our knowledge, this is the first report to offer an insight into the broad peak of polymeric tannins found with HPLC and to characterize the tannins with a DP up to 20 as shown by HRMS and MS/MS data. Copyright © 2018 Elsevier Ltd. All rights reserved.
EarthCube GeoLink: Semantics and Linked Data for the Geosciences
Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Ji, P.; Jones, M. B.; Krisnadhi, A.; Lehnert, K. A.; Mickle, A.; Narock, T.; O'Brien, M.; Raymond, L. M.; Schildhauer, M.; Shepherd, A.; Wiebe, P. H.
2015-12-01
The NSF EarthCube initiative is building next-generation cyberinfrastructure to aid geoscientists in collecting, accessing, analyzing, sharing, and visualizing their data and knowledge. The EarthCube GeoLink Building Block project focuses on a specific set of software protocols and vocabularies, often characterized as the Semantic Web and "Linked Data", to publish data online in a way that is easily discoverable, accessible, and interoperable. GeoLink brings together specialists from the computer science, geoscience, and library science domains, and includes data from a network of NSF-funded repositories that support scientific studies in marine geology, marine ecosystems, biogeochemistry, and paleoclimatology. We are working collaboratively with closely-related Building Block projects including EarthCollab and CINERGI, and solicit feedback from RCN projects including Cyberinfrastructure for Paleogeosciences (C4P) and iSamples. GeoLink has developed a modular ontology that describes essential geoscience research concepts; published data from seven collections (to date) on the Web as geospatially-enabled Linked Data using this ontology; matched and mapped data between collections using shared identifiers for investigators, repositories, datasets, funding awards, platforms, research cruises, physical specimens, and gazetteer features; and aggregated the results in a shared knowledgebase that can be queried via a standard SPARQL endpoint. Client applications have been built around the knowledgebase, including a Web/map-based data browser using the Leaflet JavaScript library and a simple query service using the OpenSearch format. Future development will include extending and refining the GeoLink ontology, adding content from additional repositories, developing semi-automated algorithms to enhance metadata, and further work on client applications.
International Nuclear Information System (INIS)
1991-12-01
As part of ongoing US Nuclear Regulatory Commission (NRC) efforts to ensure the quality and accountability of safety issue information, a program was established whereby an annual NUREG report would be published on the status of licensee implementation and NRC verification of safety issues in major NRC requirements areas. This information was compiled and reported in three NUREG volumes. Volume 1, published in March 1991, addressed the status of of Three Mile Island (TMI) Action Plan Requirements. Volume 2, published in May 1991, addressed the status of unresolved safety issues (USIs). Volume 3, published in June 1991, addressed the implementation and verification status of generic safety issues (GSIs). This annual NUREG report combines these volumes into a single report and provides updated information as of September 30, 1991. The data contained in these NUREG reports are a product of the NRC's Safety Issues Management System (SIMS) database, which is maintained by the Project Management Staff in the Office of Nuclear Reactor Regulation and by NRC regional personnel. This report is to provide a comprehensive description of the implementation and verification status of TMI Action Plan Requirements, safety issues designated as USIs, and GSIs that have been resolved and involve implementation of an action or actions by licensees. This report makes the information available to other interested parties, including the public. An additional purpose of this NUREG report is to serve as a follow-on to NUREG-0933, ''A Prioritization of Generic Safety Issues,'' which tracks safety issues up until requirements are approved for imposition at licensed plants or until the NRC issues a request for action by licensees
Linked Health Data: how linked data can help provide better health decisions.
Farinelli, Fernanda; Barcellos de Almeida, Maurício; Linhares de Souza, Yóris
2015-01-01
This paper provides a brief survey about the use of linked data in healthcare to foster better health decisions and increase health knowledge. We present real cases from the Brazilian experience and emphasize some issues in research. This paper is not intending to be fully comprehensive, we discuss some open issues and research challenges in linked data and the technologies involved. We conclude that even though linked data has been adopted in many countries, some challenges have to be overcome, for example, interoperability between different standards. A defined solution able to foster the semantic interoperability between different standards must be developed. Benefits contributed through linked health data involve better decision making on diagnostics, assertive treatments, knowledge acquisition, improvements in quality healthcare service to citizens.
LinkMind: link optimization in swarming mobile sensor networks.
Ngo, Trung Dung
2011-01-01
A swarming mobile sensor network is comprised of a swarm of wirelessly connected mobile robots equipped with various sensors. Such a network can be applied in an uncertain environment for services such as cooperative navigation and exploration, object identification and information gathering. One of the most advantageous properties of the swarming wireless sensor network is that mobile nodes can work cooperatively to organize an ad-hoc network and optimize the network link capacity to maximize the transmission of gathered data from a source to a target. This paper describes a new method of link optimization of swarming mobile sensor networks. The new method is based on combination of the artificial potential force guaranteeing connectivities of the mobile sensor nodes and the max-flow min-cut theorem of graph theory ensuring optimization of the network link capacity. The developed algorithm is demonstrated and evaluated in simulation.
LinkMind: Link Optimization in Swarming Mobile Sensor Networks
Directory of Open Access Journals (Sweden)
Trung Dung Ngo
2011-08-01
Full Text Available A swarming mobile sensor network is comprised of a swarm of wirelessly connected mobile robots equipped with various sensors. Such a network can be applied in an uncertain environment for services such as cooperative navigation and exploration, object identification and information gathering. One of the most advantageous properties of the swarming wireless sensor network is that mobile nodes can work cooperatively to organize an ad-hoc network and optimize the network link capacity to maximize the transmission of gathered data from a source to a target. This paper describes a new method of link optimization of swarming mobile sensor networks. The new method is based on combination of the artificial potential force guaranteeing connectivities of the mobile sensor nodes and the max-flow min-cut theorem of graph theory ensuring optimization of the network link capacity. The developed algorithm is demonstrated and evaluated in simulation.
Directory of Open Access Journals (Sweden)
Zhu Chen
Full Text Available Recent genomic sequencing of the foxtail millet, an abiotic, stress-tolerant crop, has provided a great opportunity for novel gene discovery and functional analysis of this popularly-grown grass. However, few stress-mediated gene families have been studied. Aldehyde dehydrogenases (ALDHs comprise a gene superfamily encoding NAD (P +-dependent enzymes that play the role of "aldehyde scavengers", which indirectly detoxify cellular ROS and reduce the effect of lipid peroxidation meditated cellular toxicity under various environmental stresses. In the current paper, we identified a total of 20 ALDH genes in the foxtail millet genome using a homology search and a phylogenetic analysis and grouped them into ten distinct families based on their amino acid sequence identity. Furthermore, evolutionary analysis of foxtail millet reveals that both tandem and segmental duplication contributed significantly to the expansion of its ALDH genes. The exon-intron structures of members of the same family in foxtail millet or the orthologous genes in rice display highly diverse distributions of their exonic and intronic regions. Also, synteny analysis shows that the majority of foxtail millet and rice ALDH gene homologs exist in the syntenic blocks between the two, implying that these ALDH genes arose before the divergence of cereals. Semi-quantitative and real-time quantitative PCR data reveals that a few SiALDH genes are expressed in an organ-specific manner and that the expression of a number of foxtail millet ALDH genes, such as, SiALDH7B1, SiALDH12A1 and SiALDH18B2 are up-regulated by osmotic stress, cold, H2O2, and phytohormone abscisic acid (ABA. Furthermore, the transformation of SiALDH2B2, SiALDH10A2, SiALDH5F1, SiALDH22A1, and SiALDH3E2 into Escherichia coli (E.coli was able to improve their salt tolerance. Taken together, our results show that genome-wide identification characteristics and expression analyses provide unique opportunities for assessing
Chen, Zhu; Chen, Ming; Xu, Zhao-shi; Li, Lian-cheng; Chen, Xue-ping; Ma, You-zhi
2014-01-01
Recent genomic sequencing of the foxtail millet, an abiotic, stress-tolerant crop, has provided a great opportunity for novel gene discovery and functional analysis of this popularly-grown grass. However, few stress-mediated gene families have been studied. Aldehyde dehydrogenases (ALDHs) comprise a gene superfamily encoding NAD (P) +-dependent enzymes that play the role of "aldehyde scavengers", which indirectly detoxify cellular ROS and reduce the effect of lipid peroxidation meditated cellular toxicity under various environmental stresses. In the current paper, we identified a total of 20 ALDH genes in the foxtail millet genome using a homology search and a phylogenetic analysis and grouped them into ten distinct families based on their amino acid sequence identity. Furthermore, evolutionary analysis of foxtail millet reveals that both tandem and segmental duplication contributed significantly to the expansion of its ALDH genes. The exon-intron structures of members of the same family in foxtail millet or the orthologous genes in rice display highly diverse distributions of their exonic and intronic regions. Also, synteny analysis shows that the majority of foxtail millet and rice ALDH gene homologs exist in the syntenic blocks between the two, implying that these ALDH genes arose before the divergence of cereals. Semi-quantitative and real-time quantitative PCR data reveals that a few SiALDH genes are expressed in an organ-specific manner and that the expression of a number of foxtail millet ALDH genes, such as, SiALDH7B1, SiALDH12A1 and SiALDH18B2 are up-regulated by osmotic stress, cold, H2O2, and phytohormone abscisic acid (ABA). Furthermore, the transformation of SiALDH2B2, SiALDH10A2, SiALDH5F1, SiALDH22A1, and SiALDH3E2 into Escherichia coli (E.coli) was able to improve their salt tolerance. Taken together, our results show that genome-wide identification characteristics and expression analyses provide unique opportunities for assessing the functional
Age differences in search of web pages: the effects of link size, link number, and clutter.
Grahame, Michael; Laberge, Jason; Scialfa, Charles T
2004-01-01
Reaction time, eye movements, and errors were measured during visual search of Web pages to determine age-related differences in performance as a function of link size, link number, link location, and clutter. Participants (15 young adults, M = 23 years; 14 older adults, M = 57 years) searched Web pages for target links that varied from trial to trial. During one half of the trials, links were enlarged from 10-point to 12-point font. Target location was distributed among the left, center, and bottom portions of the screen. Clutter was manipulated according to the percentage of used space, including graphics and text, and the number of potentially distracting nontarget links was varied. Increased link size improved performance, whereas increased clutter and links hampered search, especially for older adults. Results also showed that links located in the left region of the page were found most easily. Actual or potential applications of this research include Web site design to increase usability, particularly for older adults.
Unresolved theoretical problems
International Nuclear Information System (INIS)
Vogt, E.
1983-03-01
A summary is given of nuclear physics ideas which form the perspective within which the spin excitations in nuclei should be considered. Past work on the nuclear shell model, nuclear collective motion, cluster degrees of freedom and isobaric analogic resonances is reviewed. Indications of the future directions physicists should be taking are discussed. The importance of joining quantum chromodynamics with study of atomic nuclei, and in particular the GT resonance, is highlighted
DEFF Research Database (Denmark)
Wistoft, Karen; Højlund, Holger
2012-01-01
and have been the object of great expectations concerning the ability to incorporate health concerns into every welfare area through health promotion strategies. The paper draws on results and analyses of a collective research project funded by the Danish National Research Council and carried out...... links' that indicate cooperative levels which facilitate a creative and innovative effort in disease prevention and health promotion targeted at children and adolescents - across traditional professional boundaries. It is proposed that such links are supported by network structures, shared semantics...
Link prediction with node clustering coefficient
Wu, Zhihao; Lin, Youfang; Wang, Jing; Gregory, Steve
2016-06-01
Predicting missing links in incomplete complex networks efficiently and accurately is still a challenging problem. The recently proposed Cannistrai-Alanis-Ravai (CAR) index shows the power of local link/triangle information in improving link-prediction accuracy. Inspired by the idea of employing local link/triangle information, we propose a new similarity index with more local structure information. In our method, local link/triangle structure information can be conveyed by clustering coefficient of common-neighbors directly. The reason why clustering coefficient has good effectiveness in estimating the contribution of a common-neighbor is that it employs links existing between neighbors of a common-neighbor and these links have the same structural position with the candidate link to this common-neighbor. In our experiments, three estimators: precision, AUP and AUC are used to evaluate the accuracy of link prediction algorithms. Experimental results on ten tested networks drawn from various fields show that our new index is more effective in predicting missing links than CAR index, especially for networks with low correlation between number of common-neighbors and number of links between common-neighbors.
Abdoul-Azize, Souleymane; Selvakumar, Subramaniam; Sadou, Hassimi; Besnard, Philippe; Khan, Naim Akhtar
2014-01-01
Recent compelling evidences from rodent and human studies raise the possibility for an additional sixth taste modality devoted to oro-gustatory perception of dietary lipids. Understanding the mechanisms underlying oro-gustatory detection of dietary fat is critical for the prevention and treatment of obesity. A number of studies have suggested that lingual CD36, a glycoprotein, highly expressed by circumvallate papillae of the tongue, is implicated in the perception of dietary fat taste. G protein-coupled receptors (GPCRs) are important signaling molecules for many aspects of cellular functions. It has been shown that these receptors, particularly GPR120, are also involved in lipid taste perception. We have shown that dietary long-chain fatty acids (LCFAs), in CD36-positive taste bud cells (TBC), induce increases in free intracellular Ca(2+) concentrations, [Ca(2+)]i, by recruiting Ca(2+) from endoplasmic reticulum (ER) pool via inositol 1,4,5-triphosphate production, followed by Ca(2+) influx via opening of store-operated Ca(2+) (SOC) channels. GPR120 is also coupled to increases in [Ca(2+)]i by dietary fatty acids. We observed that stromal interaction molecule 1 (STIM1), a sensor of Ca(2+) depletion in the ER, mediated fatty acid-induced Ca(2+) signaling and spontaneous preference for fat in the mouse. In this review article, we discuss the recent advances and unresolved roles of CD36 and GPR120 in lipid taste signaling in taste bud cells. Copyright © 2013 Elsevier Masson SAS. All rights reserved.
The Independence Pipeline project : ANR's supply link - Independence Pipeline, Transco's market link
International Nuclear Information System (INIS)
Persells, T.
1998-01-01
An overview of the Independence Pipeline project was presented. The project offers access from Chicago to the U.S. Midwest market, as well as to Ontario via MichCon, Consumers Power, Great Lakes and Panhandle. The project has three components: ANR's Supply Link, the Independence Pipeline and Transco's MarketLink. The three components are budgeted at $ 1.332 billion dollars and projected for completion between Nov 1999 and Nov 2000. Each component (services, access advantages, market links, rates, storage services, etc ) are described separately. figs
Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.
Directory of Open Access Journals (Sweden)
Apiruck Watthanasurorot
2013-03-01
Full Text Available Daily, circadian rhythms influence essentially all living organisms and affect many physiological processes from sleep and nutrition to immunity. This ability to respond to environmental daily rhythms has been conserved along evolution, and it is found among species from bacteria to mammals. The hematopoietic process of the crayfish Pacifastacus leniusculus is under circadian control and is tightly regulated by astakines, a new family of cytokines sharing a prokineticin (PROK domain. The expression of AST1 and AST2 are light-dependent, and this suggests an evolutionarily conserved function for PROK domain proteins in mediating circadian rhythms. Vertebrate PROKs are transmitters of circadian rhythms of the suprachiasmatic nucleus (SCN in the brain of mammals, but the mechanism by which they function is unknown. Here we demonstrate that high AST2 expression is induced by melatonin in the brain. We identify RACK1 as a binding protein of AST2 and further provide evidence that a complex between AST2 and RACK1 functions as a negative-feedback regulator of the circadian clock. By DNA mobility shift assay, we showed that the AST2-RACK1 complex will interfere with the binding between BMAL1 and CLK and inhibit the E-box binding activity of the complex BMAL1-CLK. Finally, we demonstrate by gene knockdown that AST2 is necessary for melatonin-induced inhibition of the complex formation between BMAL1 and CLK during the dark period. In summary, we provide evidence that melatonin regulates AST2 expression and thereby affects the core clock of the crustacean brain. This process may be very important in all animals that have AST2 molecules, i.e. spiders, ticks, crustaceans, scorpions, several insect groups such as Hymenoptera, Hemiptera, and Blattodea, but not Diptera and Coleoptera. Our findings further reveal an ancient evolutionary role for the prokineticin superfamily protein that links melatonin to direct regulation of the core clock gene feedback loops.
Seismic link at plate boundary
Indian Academy of Sciences (India)
time series to determine the causality and related orientation. The resulting link ... Triggering causes changes in the Coulomb stress on a specified fault, which is ... work link shows that the alignment of the links is parallel to the Honshu Trench ...
Hacking 360 Link: A hybrid approach
Directory of Open Access Journals (Sweden)
John Durno
2012-10-01
Full Text Available When the University of Victoria Libraries switched from a locally-hosted link resolver (SFX to a vendor-hosted link resolver (360Link, new strategies were required to effectively integrate the vendor-hosted link resolver with the Libraries' other systems and services. Custom javascript is used to add links to the 360Link page; these links then point at local PHP code running on UVic servers, which can then redirect to appropriate local service or display a form directly. An open source PHP OpenURL parser class is announced. Consideration is given to the importance of maintaining open protocols and standards in the transition to vendor-hosted services.
Zhang, Yaqing; Zhang, Xiangmei; Xu, Ling; Wei, Shicheng; Zhai, Maolin
2015-01-01
Ionizing radiation effectively cross-links collagen into network with enhanced anti-degradability and biocompatibility, while radiation-cross-linked collagen scaffold lacks flexibility, satisfactory surface appearance, and performs poor in cell penetration and ingrowth. To make the radiation-cross-linked collagen scaffold to serve as an ideal artificial dermis, dextran was incorporated into collagen. Scaffolds with the collagen/dextran (Col/Dex) ratios of 10/0, 7/3, and 5/5 were fabricated via (60)Co γ-irradiation cross-linking, followed by lyophilization. The morphology, microstructure, physicochemical, and biological properties were investigated. Compared with pure collagen, scaffolds with dextran demonstrated more porous appearance, enhanced hydrophilicity while the cross-linking density was lower with the consequence of larger pore size, higher water uptake, as well as reduced stiffness. Accelerated degradation was observed when dextran was incorporated in both the in vitro and in vivo assays, which led to earlier integration with cell and host tissue. The effect of dextran on degradation was ascribed to the decreased cross-linking density, looser microstructure, more porous and hydrophilic surface. Considering the better appearance, softness, moderate degradation rate due to controllable cross-linking degree and good biocompatibility as well, radiation-cross-linked collagen/dextran scaffolds are expected to serve as promising artificial dermal substitutes.
International Nuclear Information System (INIS)
Bera, Asim K.; Atanasova, Vesna; Gamage, Swarna; Robinson, Howard; Parsons, James F.
2010-01-01
The structure of EhpF from P. agglomerans has been solved alone and in complex with phenazine-1,6-dicarboxylate. Apo EhpF was solved and refined in two different space groups at 1.95 and 2.3 Å resolution and the EhpF–phenazine-1,6-dicarboxylate complex structure was determined at 2.8 Å resolution. The structure of EhpF, a 41 kDa protein that functions in the biosynthetic pathway leading to the broad-spectrum antimicrobial compound d-alanylgriseoluteic acid (AGA), is reported. A cluster of approximately 16 genes, including ehpF, located on a 200 kbp plasmid native to certain strains of Pantoea agglomerans encodes the proteins that are required for the conversion of chorismic acid to AGA. Phenazine-1,6-dicarboxylate has been identified as an intermediate in AGA biosynthesis and deletion of ehpF results in accumulation of this compound in vivo. The crystallographic data presented here reveal that EhpF is an atypical member of the acyl-CoA synthase or ANL superfamily of adenylating enzymes. These enzymes typically catalyze two-step reactions involving adenylation of a carboxylate substrate followed by transfer of the substrate from AMP to coenzyme A or another phosphopantetheine. EhpF is distinguished by the absence of the C-terminal domain that is characteristic of enzymes from this family and is involved in phosphopantetheine binding and in the second half of the canonical two-step reaction that is typically observed. Based on the structure of EhpF and a bioinformatic analysis, it is proposed that EhpF and EhpG convert phenazine-1,6-dicarboxylate to 6-formylphenazine-1-carboxylate via an adenylyl intermediate
Directory of Open Access Journals (Sweden)
Kosuke Okada
2016-05-01
Full Text Available Objective: Non-shivering thermogenesis in brown adipose tissue (BAT plays a central role in energy homeostasis. Thioesterase superfamily member 1 (Them1, a BAT-enriched long chain fatty acyl-CoA thioesterase, is upregulated by cold and downregulated by warm ambient temperatures. Them1−/− mice exhibit increased energy expenditure and resistance to diet-induced obesity and diabetes, but the mechanistic contribution of Them1 to the regulation of cold thermogenesis remains unknown. Methods: Them1−/− and Them1+/+ mice were subjected to continuous metabolic monitoring to quantify the effects of ambient temperatures ranging from thermoneutrality (30 °C to cold (4 °C on energy expenditure, core body temperature, physical activity and food intake. The effects of Them1 expression on O2 consumption rates, thermogenic gene expression and lipolytic protein activation were determined ex vivo in BAT and in primary brown adipocytes. Results: Them1 suppressed thermogenesis in mice even in the setting of ongoing cold exposure. Without affecting thermogenic gene transcription, Them1 reduced O2 consumption rates in both isolated BAT and primary brown adipocytes. This was attributable to decreased mitochondrial oxidation of endogenous but not exogenous fatty acids. Conclusions: These results show that Them1 may act as a break on uncontrolled heat production and limit the extent of energy expenditure. Pharmacologic inhibition of Them1 could provide a targeted strategy for the management of metabolic disorders via activation of brown fat. Keywords: Energy expenditure, Fatty acyl-CoA, Acyl-CoA thioesterase, Mitochondria, Obesity
Goo, Stephen M.; Cho, Soochin
2013-01-01
The ribonuclease (RNase) A superfamily is a vertebrate-specific gene family. Because of a massive expansion that occurred during the early mammalian evolution, extant mammals in general have much more RNase genes than nonmammalian vertebrates. Mammalian RNases have been associated with diverse physiological functions including digestion, cytotoxicity, angiogenesis, male reproduction, and host defense. However, it is still uncertain when their expansion occurred and how a wide array of functions arose during their evolution. To answer these questions, we generate a compendium of all RNase genes identified in 20 complete mammalian genomes including the platypus, Ornithorhynchus anatinus. Using this, we delineate 13 ancient RNase gene lineages that arose before the divergence between the monotreme and the other mammals (∼220 Ma). These 13 ancient gene lineages are differentially retained in the 20 mammals, and the rate of protein sequence evolution is highly variable among them, which suggest that they have undergone extensive functional diversification. In addition, we identify 22 episodes of recent expansion of RNase genes, many of which have signatures of adaptive functional differentiation. Exemplifying this, bursts of gene duplication occurred for the RNase1, RNase4, and RNase5 genes of the little brown bat (Myotis lucifugus), which might have contributed to the species’ effective defense against heavier pathogen loads caused by its communal roosting behavior. Our study illustrates how host-defense systems can generate new functions efficiently by employing a multigene family, which is crucial for a host organism to adapt to its ever-changing pathogen environment. PMID:24162010
Thermophilic P-loop transport ATPases : Enzyme function and energetics at high temperature
Pretz, Monika Gyöngyi
2007-01-01
Primary transport ATPases are divided into several superfamilies; amongst others including ATPases of the ABC transporter superfamily, the F-ATPase superfamily or the motor ATPases of the General Secretory (Sec) pathway. Motor proteins from these superfamilies show a low sequence similarity, except
Cascade of links in complex networks
Energy Technology Data Exchange (ETDEWEB)
Feng, Yeqian; Sun, Bihui [Department of Management Science, School of Government, Beijing Normal University, 100875 Beijing (China); Zeng, An, E-mail: anzeng@bnu.edu.cn [School of Systems Science, Beijing Normal University, 100875 Beijing (China)
2017-01-30
Cascading failure is an important process which has been widely used to model catastrophic events such as blackouts and financial crisis in real systems. However, so far most of the studies in the literature focus on the cascading process on nodes, leaving the possibility of link cascade overlooked. In many real cases, the catastrophic events are actually formed by the successive disappearance of links. Examples exist in the financial systems where the firms and banks (i.e. nodes) still exist but many financial trades (i.e. links) are gone during the crisis, and the air transportation systems where the airports (i.e. nodes) are still functional but many airlines (i.e. links) stop operating during bad weather. In this letter, we develop a link cascade model in complex networks. With this model, we find that both artificial and real networks tend to collapse even if a few links are initially attacked. However, the link cascading process can be effectively terminated by setting a few strong nodes in the network which do not respond to any link reduction. Finally, a simulated annealing algorithm is used to optimize the location of these strong nodes, which significantly improves the robustness of the networks against the link cascade. - Highlights: • We propose a link cascade model in complex networks. • Both artificial and real networks tend to collapse even if a few links are initially attacked. • The link cascading process can be effectively terminated by setting a few strong nodes. • A simulated annealing algorithm is used to optimize the location of these strong nodes.
Cascade of links in complex networks
International Nuclear Information System (INIS)
Feng, Yeqian; Sun, Bihui; Zeng, An
2017-01-01
Cascading failure is an important process which has been widely used to model catastrophic events such as blackouts and financial crisis in real systems. However, so far most of the studies in the literature focus on the cascading process on nodes, leaving the possibility of link cascade overlooked. In many real cases, the catastrophic events are actually formed by the successive disappearance of links. Examples exist in the financial systems where the firms and banks (i.e. nodes) still exist but many financial trades (i.e. links) are gone during the crisis, and the air transportation systems where the airports (i.e. nodes) are still functional but many airlines (i.e. links) stop operating during bad weather. In this letter, we develop a link cascade model in complex networks. With this model, we find that both artificial and real networks tend to collapse even if a few links are initially attacked. However, the link cascading process can be effectively terminated by setting a few strong nodes in the network which do not respond to any link reduction. Finally, a simulated annealing algorithm is used to optimize the location of these strong nodes, which significantly improves the robustness of the networks against the link cascade. - Highlights: • We propose a link cascade model in complex networks. • Both artificial and real networks tend to collapse even if a few links are initially attacked. • The link cascading process can be effectively terminated by setting a few strong nodes. • A simulated annealing algorithm is used to optimize the location of these strong nodes.
Cross-linking of polymeric materials
International Nuclear Information System (INIS)
Bloom, L.I.; Du Plessis, T.A.; Meij, G.O.
1991-01-01
The invention provides a method of producing a cured polymeric artifact from a polymeric thermoplastic starting material, the material of the artifact having reduced thermoplasticity relative to the starting material and exhibiting an enhanced degree of cross-linking relative to the starting material. The method includes subjecting a polymeric thermoplastic starting material, which is capable of being cross-linked by irradiation, to sufficient irradiation partially to cross-linked the starting material to produce a thermoplastic partially cross-linked intermediate material. The thermoplasticity of the intermediate material is then reduced by heating it to raise its melting point. The invention also provides a method of making a partially cross-linked feedstocks and a master batch for use in making such artifacts
Novel p47(phox)-related organizers regulate localized NADPH oxidase 1 (Nox1) activity.
Gianni, Davide; Diaz, Begoña; Taulet, Nicolas; Fowler, Bruce; Courtneidge, Sara A; Bokoch, Gary M
2009-09-15
The mechanisms that determine localized formation of reactive oxygen species (ROS) through NADPH (reduced form of nicotinamide adenine dinucleotide phosphate) oxidase (Nox) family members in nonphagocytic cells are unknown. We show that the c-Src substrate proteins Tks4 (tyrosine kinase substrate with four SH3 domains) and Tks5 are functional members of a p47(phox)-related organizer superfamily. Tks proteins selectively support Nox1 and Nox3 (and not Nox2 and Nox4) activity in reconstituted cellular systems and interact with the NoxA1 activator protein through an Src homology 3 domain-mediated interaction. Endogenous Tks4 is required for Rac guanosine triphosphatase- and Nox1-dependent ROS production by DLD1 colon cancer cells. Our results are consistent with the Tks-mediated recruitment of Nox1 to invadopodia that form in DLD1 cells in a Tks- and Nox-dependent fashion. We propose that Tks organizers represent previously unrecognized members of an organizer superfamily that link Nox to localized ROS formation.
Crystal structure of the potassium-importing KdpFABC membrane complex
Energy Technology Data Exchange (ETDEWEB)
Huang, Ching-Shin; Pedersen, Bjørn Panyella; Stokes, David L.
2017-06-21
Cellular potassium import systems play a fundamental role in osmoregulation, pH homeostasis and membrane potential in all domains of life. In bacteria, the kdp operon encodes a four-subunit potassium pump that maintains intracellular homeostasis, cell shape and turgor under conditions in which potassium is limiting1. This membrane complex, called KdpFABC, has one channel-like subunit (KdpA) belonging to the superfamily of potassium transporters and another pump-like subunit (KdpB) belonging to the superfamily of P-type ATPases. Although there is considerable structural and functional information about members of both superfamilies, the mechanism by which uphill potassium transport through KdpA is coupled with ATP hydrolysis by KdpB remains poorly understood. Here we report the 2.9 Å X-ray structure of the complete Escherichia coli KdpFABC complex with a potassium ion within the selectivity filter of KdpA and a water molecule at a canonical cation site in the transmembrane domain of KdpB. The structure also reveals two structural elements that appear to mediate the coupling between these two subunits. Specifically, a protein-embedded tunnel runs between these potassium and water sites and a helix controlling the cytoplasmic gate of KdpA is linked to the phosphorylation domain of KdpB. On the basis of these observations, we propose a mechanism that repurposes protein channel architecture for active transport across biomembranes.
International Nuclear Information System (INIS)
Geissler, Kerstin; Metchev, Stanimir; Kirkpatrick, J. Davy; Berriman, G. Bruce; Looper, Dagny
2011-01-01
We present the completion of a program to cross-correlate the Sloan Digital Sky Survey Data Release 1 (SDSS DR1) and Two-Micron All-Sky Survey (2MASS) Point Source Catalog in search for extremely red L and T dwarfs. The program was initiated by Metchev and collaborators, who presented the findings on all newly identified T dwarfs in SDSS DR1 and estimated the space density of isolated T0-T8 dwarfs in the solar neighborhood. In the current work, we present most of the L dwarf discoveries. Our red-sensitive (z - J ≥ 2.75 mag) cross-match proves to be efficient in detecting peculiarly red L dwarfs, adding two new ones, including one of the reddest known L dwarfs. Our search also nets a new peculiarly blue L7 dwarf and, surprisingly, two M8 dwarfs. We further broaden our analysis to detect unresolved binary L or T dwarfs through spectral template fitting to all L and T dwarfs presented here and in the earlier work by Metchev and collaborators. We identify nine probable binaries, six of which are new and eight harbor likely T dwarf secondaries. We combine this result with current knowledge of the mass ratio distribution and frequency of substellar companions to estimate an overall space density of 0.005-0.05 pc -3 for individual T0-T8 dwarfs.
Multi-Functional Fibre-Optic Microwave Links
DEFF Research Database (Denmark)
Gliese, Ulrik Bo
1998-01-01
The multi-functionality of microwave links based on remote heterodyne detection of signals from a dual-frequency laser transmitter is discussed and experimentally demonstrated in this paper. Typically, direct detection in conjunction with optical intensity modulation is used to implement fibre......-optic microwave links. The resulting links are inherently transparent and mainly used for signal transmission. As opposed to direct detection links, remote heterodyne detection links can directly perform functionalities such as modulation, frequency conversion, and transparent signal recovery in addition...
ITK optical links backup document
Huffman, B T; The ATLAS collaboration; Flick, T; Ye, J
2013-01-01
This document describes the proposed optical links to be used for the ITK in the phase II upgrade. The current R&D for optical links pursued in the Versatile Link group is reviewed. In particular the results demonstrating the radiation tolerance of all the on-detector components are documented. The bandwidth requirements and the resulting numerology are given.
Full Text Available ... for young people, parents and teachers, and the media with links to our latest research findings and news updates. Read on to Learn the Link between ... to this site at: http://www.drugabuse.gov/news-events/public-education-projects/learn-link-drugs-hiv . ... Social Media Send the message to young people and to ...
Gueret, C.D.M.; de Boer, V.; Schlobach, K.S.
2014-01-01
Open data policies and linked data publication are powerful tools for increasing transparency, participatory governance, and accountability. The linked data community proudly emphasizes the economic and societal impact such technology shows. But a closer look proves that the design and deployment of
Gueret, Christophe; de Boer, Victor; Schlobach, Stefan
2014-01-01
Open data policies and linked data publication are powerful tools for increasing transparency, participatory governance, and accountability. A closer look at linked data technologies, however, proves that their design and deployment exclude the majority of the world’s population. It will take small
BG1 has a major role in MHC-linked resistance to malignant lymphoma in the chicken.
Goto, Ronald M; Wang, Yujun; Taylor, Robert L; Wakenell, Patricia S; Hosomichi, Kazuyoshi; Shiina, Takashi; Blackmore, Craig S; Briles, W Elwood; Miller, Marcia M
2009-09-29
Pathogen selection is postulated to drive MHC allelic diversity at loci for antigen presentation. However, readily apparent MHC infectious disease associations are rare in most species. The strong link between MHC-B haplotype and the occurrence of virally induced tumors in the chicken provides a means for defining the relationship between pathogen selection and MHC polymorphism. Here, we verified a significant difference in resistance to gallid herpesvirus-2 (GaHV-2)-induced lymphomas (Marek's disease) conferred by two closely-related recombinant MHC-B haplotypes. We mapped the crossover breakpoints that distinguish these haplotypes to the highly polymorphic BG1 locus. BG1 encodes an Ig-superfamily type I transmembrane receptor-like protein that contains an immunoreceptor tyrosine-based inhibition motif (ITIM), which undergoes phosphorylation and is recognized by Src homology 2 domain-containing protein tyrosine phosphatase (SHP-2). The recombinant haplotypes are identical, except for differences within the BG1 3'-untranslated region (3'-UTR). The 3'-UTR of the BG1 allele associated with increased lymphoma contains a 225-bp insert of retroviral origin and showed greater inhibition of luciferase reporter gene translation compared to the other allele. These findings suggest that BG1 could affect the outcome of GaHV-2 infection through modulation of the lymphoid cell responsiveness to infection, a condition that is critical for GaHV-2 replication and in which the MHC-B haplotype has been previously implicated. This work provides a mechanism by which MHC-B region genetics contributes to the incidence of GaHV-2-induced malignant lymphoma in the chicken and invites consideration of the possibility that similar mechanisms might affect the incidence of lymphomas associated with other oncogenic viral infections.
Montossi, F; Font-i-Furnols, M; del Campo, M; San Julián, R; Brito, G; Sañudo, C
2013-12-01
There are increasing concerns of society towards the consumption of animal products which have been produced and transformed in a sustainable manner. This trend influences consumer purchasing decision making, particularly in developed countries. On the other hand, in the next years, the pressure to increase the volume and efficiency of meat production will be much higher to cope with the expected unsatisfied demand. At least in part, current and future technologies could contribute to solve this challenge. However, the use of some of these innovations could have a negative effect on consumer preferences. There is no consensus in our society about this dilemma. The objective of this paper is to review the scientific evidence related to these topics and to analyze and discuss the effect of some of the extrinsic and intrinsic factors linked with the sheep industry which could affect the acceptability of lamb meat by consumers. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.
Weierstrass polynomials for links
DEFF Research Database (Denmark)
Hansen, Vagn Lundsgaard
1997-01-01
There is a natural way of identifying links in3-space with polynomial covering spaces over thecircle. Thereby any link in 3-space can be definedby a Weierstrass polynomial over the circle. Theequivalence relation for covering spaces over thecircle is, however, completely different from...
Kato, Takafumi; Tsuchiya, Eri; Kubota, Soichi; Miyagawa, Yoshiyuki
JST, cooperated with several national institutes, is currently developing “Japan Link Center”, which manages Japanese electronic scholarly contents (journal articles, books, dissertations etc.) in an integrated fashion using Digital Object Identifier (DOI). Japan Link Center will manage metadata and whereabouts information of the contents in the digital environment and provide domestic and international linking information, cite/cited information to activate dissemination of S&T information, furthermore, to strengthen transmission of S&T information from Japan. Japan Link Center is expected to be appointed as the 9th DOI registration agency (RA) in the world by the International DOI Foundation (IDF) this spring.
DEFF Research Database (Denmark)
Schultz, Laura Luise
2014-01-01
Paper presented at A Valentine to Gertrude Stein. The Reception of Gertrude Stein in the Arts and Humanities, held at the University of Copenhagen 8. - 10. May 2014, in collaboration with the universities of Ghent and Linköping......Paper presented at A Valentine to Gertrude Stein. The Reception of Gertrude Stein in the Arts and Humanities, held at the University of Copenhagen 8. - 10. May 2014, in collaboration with the universities of Ghent and Linköping...
DEFF Research Database (Denmark)
Bervild, Charlotte
2015-01-01
Link til læringsobjekter/undervisningsportalhttp://videoportal.ucc.dk/channel/10492641/charlotte-bervilds-undervisninghttp://videoportal.ucc.dk/video/8248508/3d-printer-v-lektor-charlotte-bervildFotoblog:http://charlottebervild.blogspot.dk/2008/10/fotocollager-af-charlotte-bervild.html......Link til læringsobjekter/undervisningsportalhttp://videoportal.ucc.dk/channel/10492641/charlotte-bervilds-undervisninghttp://videoportal.ucc.dk/video/8248508/3d-printer-v-lektor-charlotte-bervildFotoblog:http://charlottebervild.blogspot.dk/2008/10/fotocollager-af-charlotte-bervild.html...
Lu, Zhibing; Feng, Xiaohua; Song, Ling; Han, Ying; Kim, Alexander; Herzberg, Osnat; Woodson, William R; Martin, Brian M; Mariano, Patrick S; Dunaway-Mariano, Debra
2005-12-20
The work described in this paper was carried out to define the chemical function a new member of the isocitrate lyase enzyme family derived from the flowering plant Dianthus caryophyllus. This protein (Swiss-Prot entry Q05957) is synthesized in the senescent flower petals and is named the "petal death protein" or "PDP". On the basis of an analysis of the structural contexts of sequence markers common to the C-C bond lyases of the isocitrate lyase/phosphoenolpyruvate mutase superfamily, a substrate screen that employed a (2R)-malate core structure was designed. Accordingly, stereochemically defined C(2)- and C(3)-substituted malates were synthesized and tested as substrates for PDP-catalyzed cleavage of the C(2)-C(3) bond. The screen identified (2R)-ethyl, (3S)-methylmalate, and oxaloacetate [likely to bind as the hydrate, C(2)(OH)(2) gem-diol] as the most active substrates (for each, k(cat)/K(m) = 2 x 10(4) M(-)(1) s(-)(1)). In contrast to the stringent substrate specificities previously observed for the Escherichia coli isocitrate and 2-methylisocitrate lyases, the PDP tolerated hydrogen, methyl, and to a much lesser extent acetate substituents at the C(3) position (S configuration only) and hydoxyl, methyl, ethyl, propyl, and to a much lesser extent isobutyl substituents at C(2) (R configuration only). It is hypothesized that PDP functions in oxalate production in Ca(2+) sequestering and/or in carbon scavenging from alpha-hydroxycarboxylate catabolites during the biochemical transition accompanying petal senescence.
[Sex-linked juvenile retinoschisis].
François, P; Turut, P; Soltysik, C; Hache, J C
1976-02-01
About 13 observations of sexe linked juvenile retinoschisis, the authors describe the ophthalmoscopic, fluorographic and functional aspects of the disease whose caracteristics are:--its sexe linked recessive heredity; --its clinical characterestics associating: a microcystic macular degeneration, peripheral retinal lesions, vitreous body alterations, --an electroretinogram of the negative type.
Materializing the web of linked data
Konstantinou, Nikolaos
2015-01-01
This book explains the Linked Data domain by adopting a bottom-up approach: it introduces the fundamental Semantic Web technologies and building blocks, which are then combined into methodologies and end-to-end examples for publishing datasets as Linked Data, and use cases that harness scholarly information and sensor data. It presents how Linked Data is used for web-scale data integration, information management and search. Special emphasis is given to the publication of Linked Data from relational databases as well as from real-time sensor data streams. The authors also trace the transformation from the document-based World Wide Web into a Web of Data. Materializing the Web of Linked Data is addressed to researchers and professionals studying software technologies, tools and approaches that drive the Linked Data ecosystem, and the Web in general.
Microprocessor-controlled CAMAC data link module
International Nuclear Information System (INIS)
Potter, J.M.
1978-05-01
Communication between the central control computer and remote, satellite data-acquisition/control stations at the Clinton P. Anderson Meson Physics Facility (LAMPF) is presently accomplished through the use of CAMAC-based Data Link modules. With the advent of the microprocessor, a new philosophy for digital data communications has evolved. Data Link modules containing microprocessor controllers provide link management and communication network protocol through algorithms executed in the Data Link microprocessor. 13 figures
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Linked data for libraries, archives and museums how to clean, link and publish your metadata
Hooland, Seth van
2014-01-01
This highly practical handbook teaches you how to unlock the value of your existing metadata through cleaning, reconciliation, enrichment and linking and how to streamline the process of new metadata creation. Libraries, archives and museums are facing up to the challenge of providing access to fast growing collections whilst managing cuts to budgets. Key to this is the creation, linking and publishing of good quality metadata as Linked Data that will allow their collections to be discovered, accessed and disseminated in a sustainable manner. This highly practical handbook teaches you how to unlock the value of your existing metadata through cleaning, reconciliation, enrichment and linking and how to streamline the process of new metadata creation. Metadata experts Seth van Hooland and Ruben Verborgh introduce the key concepts of metadata standards and Linked Data and how they can be practically applied to existing metadata, giving readers the tools and understanding to achieve maximum results with limited re...
Opisthorchiasis and cholangiocarcinoma in Southeast Asia: an unresolved problem
Directory of Open Access Journals (Sweden)
Hughes T
2017-08-01
Full Text Available Thomas Hughes,1,* Thomas O’Connor,1,* Anchalee Techasen,2,3 Nisana Namwat,2,3 Watcharin Loilome,2,3 Ross H Andrews,2–4 Narong Khuntikeo,3,5 Puangrat Yongvanit,3,6 Paiboon Sithithaworn,3,7 Simon D Taylor-Robinson1 1Division of Digestive Health, Department of Surgery and Cancer, Imperial College London, London, UK; 2Department of Biochemistry, Faculty of Medicine, Liver Fluke and Cholangiocarcinoma Centre, 3Cholangiocarcinoma Screening and Care Program (CASCAP, Khon Kaen University, Khon Kaen, Thailand; 4Faculty of Medicine, St Mary’s Campus, Imperial College, London, UK; 5Department of Surgery, 6Department of Biochemistry, 7Department of Parasitology, Faculty of Medicine, Liver Fluke and Cholangiocarcinoma Centre, Khon Kaen University, Khon Kaen, Thailand *These authors contributed equally to this work Abstract: The prevalence of cholangiocarcinoma (CCA in Southeast Asia is much higher than other areas of the world. Eating raw, fermented, or undercooked cyprinid fish, infected with the liver fluke, Opisthorchis viverrini sensu lato (sl, results in chronic biliary inflammation, periductal fibrosis, and increased cancer risk. There may be associated glomerulonephritis. The process of infection is difficult to disrupt because eating practices have proven extremely difficult to change, and the life cycle of the fluke cannot be broken due to high prevalence in canine and feline reservoir hosts. Fecal analysis and enzyme-linked immunosorbent assay tests can be used to diagnose opisthorchiasis. Diagnosis of CCA is complex, partly due to the lack of definitive imaging characteristics but also due to the difficulty of obtaining samples for cytology or histology. This cancer has proven to be resistant to common chemotherapy treatments and so the two avenues of treatment available are surgical resection and liver transplantation, both requiring early detection of the tumor for the best chances of success. Late presentation of symptoms reduces the
ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.
Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala
2017-01-01
Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.
Holthuis, L.B.
1955-01-01
CONTENTS Introduction.......... 1 Supersection Natantia ...... 2 Section Caridea....... . 7 Superfamily Oplophoroida ... 12 Family Oplophoridae .... 12 Family Nematocarcinidae . . 17 Family Atyidae ..... 18 Superfamily Stylodactyloida . . 31 Family Stylodactylidae ... 31 Superfamily Pasiphaeoida . .
International Nuclear Information System (INIS)
Posselt, K.; Haedrich, W.
1986-01-01
In practice the cross-linking of irradiated polyethylene is mostly characterized by solubility and thermomechanical data. The irradiation of samples of a LDPE and a HDPE yields very different gel-dose curves. But for a quantitative comparison the complicated connection between the gel values and the corresponding densities of cross-links, especially the dependence on the initial molecular size distribution, has to take into consideration. The analysis of the solubility data according to the statistical theory of cross-linking developed by Inokuti and Saito shows that at equal doses in both investigated PE types in spite of the different gel values nearly the same densities of cross-links are present. That result is confirmed by the densities of cross-links determined from stress-strain measurements at 423 K. (author)
Linking GHG Emission Trading Systems and Markets
Energy Technology Data Exchange (ETDEWEB)
NONE
2006-07-01
Several different types of links are possible between different GHG-mitigation systems. These include: Linking two or more emission trading schemes so that emissions trading can occur both within and between different schemes ('direct links'); and Linking emission trading systems to registries/mechanisms and systems that generate offsets from project based mechanisms or from direct purchases/transfers of AAUs ('indirect links').
Attachment and the metabolic syndrome in midlife: the role of interview-based discourse patterns.
Davis, Cynthia R; Usher, Nicole; Dearing, Eric; Barkai, Ayelet R; Crowell-Doom, Cynthia; Neupert, Shevaun D; Mantzoros, Christos S; Crowell, Judith A
2014-10-01
Adult attachment discourse patterns and current family relationship quality were examined as correlates of health behaviors and number of metabolic syndrome (MetS) criteria met, and as mediators of the link between childhood adversity and these health outcomes. A sample of 215 white/European American and black/African American adults aged 35 to 55 years were examined using a cross-sectional study design. Discourse was assessed with the Adult Attachment Interview, using coherence (a marker of attachment security), unresolved trauma/loss (a marker of disorganized cognitions related to trauma or loss), and idealization (minimizing stressful experiences and their impact) scores. Relationship quality, adverse childhood experiences, and current depressive symptoms were assessed, as were health behaviors of diet, exercise, and smoking. MetS includes obesity, elevated blood pressure, elevated fasting glucose, high triglycerides, and low high-density lipoprotein cholesterol. Using path analysis and including childhood adversity severity and depressive symptoms in the model, both Adult Attachment Interview coherence and unresolved trauma/loss were directly linked to the number of MetS criteria (r = 0.186 and r = 0.170, respectively). Idealization was indirectly linked to MetS through poor diet (r = 0.183). The final model explained 21% of the variance in scores for the number of MetS criteria met. Insecure adult attachment is associated with increased risk of MetS.
The Versatile Link Demo Board (VLDB)
International Nuclear Information System (INIS)
Lesma, R. Martín; Alessio, F.; Barbosa, J.; Baron, S.; Caplan, C.; Leitao, P.; Porret, D.; Wyllie, K.; Pecoraro, C.
2017-01-01
The Versatile Link Demonstrator Board (VLDB) is the evaluation kit for the radiation-hard Optical Link ecosystem, which provides a 4.8 Gbps data transfer link for communication between front-end (FE) and back-end (BE) of the High Energy Physics experiments. It gathers the Versatile link main radiation-hard custom Application-Specific Integrated Circuits (ASICs) and modules: GBTx, GBT-SCA and VTRx/VTTx plus the FeastMP, a radiation-hard in-house designed DC-DC converter. This board is the first design allowing system-level tests of the Link with a complete interconnection of the constitutive components, allowing data acquisition, control and monitoring of FE devices with the GBT-SCA pair.
Restricted linking of emissions trading systems
Schneider, Lambert; Lazarus, Michael; Lee, Carrie; Asselt, van Harro
2017-01-01
With over 17 emissions trading systems (ETSs) now in place across four continents, interest in linking ETSs is growing. Linking ETSs offers economic, political, and administrative benefits. It also faces major challenges. Linking can affect overall ambition, financial flows, and the location and
Radiation-induced linking reactions in polyethylene
International Nuclear Information System (INIS)
Zoepfl, F.J.
1983-01-01
Three types of measurements are reported relating to chemical reactions in polyethylene induced by ionizing radiation: 1) viscometric and low-angle laser light scattering measurements to determine the effect of a radical scavenger on the yield of links; 2) calorimetric measurements to determine the effect of radiation-induced linking on the melting behavior of polyethylene; and 3) high-resolution solution carbon 13 nuclear magnetic resonance (NMR) spectrometry measurements to determine the nature of the links and the method of their formation. The NMR results present the first direct detection of radiation-induced long-chain branching (Y links) in polyethylene, and place an apparent upper limit on the yield of H-shaped crosslinks that are formed when polyethylene is irradiated to low absorbed doses. The effect of radiation-induced linking on the melting behavior of polyethylene was examined using differential scanning calorimetry (DSC). It was found that radiation-induced links do not change the heat of fusion of polythylene crystals, but decrease the melt entropy and increase the fold surface free energy per unit area of the crystals. The carbon 13 NMR results demonstrate that long-chain branches (Y links) are formed much more frequently than H-shaped crosslinks at low absorbed doses. The Y links are produced by reactions of alkyl free radicals with terminal vinyl groups in polyethylene
Linked data meets ontology matching: enhancing data linking through ontology alignments
Scharffe , François; Euzenat , Jérôme
2011-01-01
scharffe2011b; International audience; The Web of data consists of publishing data on the Web in such a way that they can be connected together and interpreted. It is thus critical to establish links between these data, both for the Web of data and for the Semantic Web that it contributes to feed. We consider here the various techniques which have been developed for that purpose and analyze their commonalities and differences. This provides a general framework that the diverse data linking sy...
2012-01-01
Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA) and a nuclear (histone H3) and mitochondrial (cytochrome oxidase subunit I) protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in which they maintain filter
Directory of Open Access Journals (Sweden)
Goto Ryutaro
2012-09-01
Full Text Available Abstract Background Galeommatoidea is a superfamily of bivalves that exhibits remarkably diverse lifestyles. Many members of this group live attached to the body surface or inside the burrows of other marine invertebrates, including crustaceans, holothurians, echinoids, cnidarians, sipunculans and echiurans. These symbiotic species exhibit high host specificity, commensal interactions with hosts, and extreme morphological and behavioral adaptations to symbiotic life. Host specialization to various animal groups has likely played an important role in the evolution and diversification of this bivalve group. However, the evolutionary pathway that led to their ecological diversity is not well understood, in part because of their reduced and/or highly modified morphologies that have confounded traditional taxonomy. This study elucidates the taxonomy of the Galeommatoidea and their evolutionary history of symbiotic lifestyle based on a molecular phylogenic analysis of 33 galeommatoidean and five putative galeommatoidean species belonging to 27 genera and three families using two nuclear ribosomal genes (18S and 28S ribosomal DNA and a nuclear (histone H3 and mitochondrial (cytochrome oxidase subunit I protein-coding genes. Results Molecular phylogeny recovered six well-supported major clades within Galeommatoidea. Symbiotic species were found in all major clades, whereas free-living species were grouped into two major clades. Species symbiotic with crustaceans, holothurians, sipunculans, and echiurans were each found in multiple major clades, suggesting that host specialization to these animal groups occurred repeatedly in Galeommatoidea. Conclusions Our results suggest that the evolutionary history of host association in Galeommatoidea has been remarkably dynamic, involving frequent host switches between different animal phyla. Such an unusual pattern of dynamic host switching is considered to have resulted from their commensalistic lifestyle, in
Optimisation of the link volume for weakest link failure prediction in NBG-18 nuclear graphite
International Nuclear Information System (INIS)
Hindley, Michael P.; Groenwold, Albert A.; Blaine, Deborah C.; Becker, Thorsten H.
2014-01-01
This paper describes the process for approximating the optimal size of a link volume required for weakest link failure calculation in nuclear graphite, with NBG-18 used as an example. As part of the failure methodology, the link volume is defined in terms of two grouping criteria. The first criterion is a factor of the maximum grain size and the second criterion is a function of an equivalent stress limit. A methodology for approximating these grouping criteria is presented. The failure methodology employs finite element analysis (FEA) in order to predict the failure load, at 50% probability of failure. The average experimental failure load, as determined for 26 test geometries, is used to evaluate the accuracy of the weakest link failure calculations. The influence of the two grouping criteria on the failure load prediction is evaluated by defining an error in prediction across all test cases. Mathematical optimisation is used to find the minimum error across a range of test case failure predictions. This minimum error is shown to deliver the most accurate failure prediction across a whole range of components, although some test cases in the range predict conservative failure load. The mathematical optimisation objective function is penalised to account for non-conservative prediction of the failure load for any test case. The optimisation is repeated and a link volume found for conservative failure prediction. The failure prediction for each test case is evaluated, in detail, for the proposed link volumes. Based on the analysis, link design volumes for NBG-18 are recommended for either accurate or conservative failure prediction
REDEN: Named Entity Linking in Digital Literary Editions Using Linked Data Sets
Directory of Open Access Journals (Sweden)
Carmen Brando
2016-07-01
Full Text Available This paper proposes a graph-based Named Entity Linking (NEL algorithm named REDEN for the disambiguation of authors’ names in French literary criticism texts and scientific essays from the 19th and early 20th centuries. The algorithm is described and evaluated according to the two phases of NEL as reported in current state of the art, namely, candidate retrieval and candidate selection. REDEN leverages knowledge from different Linked Data sources in order to select candidates for each author mention, subsequently crawls data from other Linked Data sets using equivalence links (e.g., owl:sameAs, and, finally, fuses graphs of homologous individuals into a non-redundant graph well-suited for graph centrality calculation; the resulting graph is used for choosing the best referent. The REDEN algorithm is distributed in open-source and follows current standards in digital editions (TEI and semantic Web (RDF. Its integration into an editorial workflow of digital editions in Digital humanities and cultural heritage projects is entirely plausible. Experiments are conducted along with the corresponding error analysis in order to test our approach and to help us to study the weaknesses and strengths of our algorithm, thereby to further improvements of REDEN.
Energy Technology Data Exchange (ETDEWEB)
Bjarnadottir, H.; Hilding-Rydevik, T. [Nordregio, Stockholm (Sweden)
2001-06-01
The aim of the study is to highlight some unresolved and challenging issues in the forthcoming approximately six year long Environmental Impact Assessment (EIA) and planning process of the long-term disposal of spent nuclear fuel in Sweden. Different international and Nordic experiences of the processes for final disposal as well as from other development of similar scope, where experiences assumed to be of importance for final disposal of nuclear waste, have been described. Furthermore, issues relating to 'good EIA practice' as well as certain aspects of planning theory have also been presented. The current Swedish situation for the planning and EIA process of the final disposal of spent nuclear fuel was also been summarized. These different 'knowledge areas' have been compared and measured against our perception of the expectations towards the forthcoming process, put forward by different Swedish actors in the field. The result is a presentation of a number of questions and identification issues that the authors consider need special attention in the design and conduction of the planning and EIA process. The study has been realized through a literature survey and followed by reading and analysis of the written material. The main focus of the literature search was on material describing planning processes, actor perspectives and EIA. Material and literature on the technical and scientific aspects of spent nuclear fuel disposal was however deliberately avoided. There is a wealth of international and Swedish literature concerning final disposal of spent nuclear fuel - concerning both technical issues and issues concerning for example public participation and risk perception. But material of a more systematic and comparative nature (relating to both empirical and theoretical issues, and to practical experiences) in relation to EIA processes and communicative planning for final disposal of spent nuclear fuel seems to be more sparsely represented
Blázquez Sevilla, Alegría; Borrás Gené, Oriol
2016-01-01
Manual básico sobre la red profesional LinkedIn, donde se analiza la red y se explica a fondo cómo crear un perfil y gestionarlo. Incluye información sobre las diferentes secciones características de la red LinkedIn y ofrece consejos para la correcta gestión de un perfil, buscando su mejor rendimiento.
The HANDSS-55 Linking Equipment
International Nuclear Information System (INIS)
Crosby, S.
2001-01-01
The Bucket Translation Unit (BTU) and the Drum Handler are two of the HANDSS-55 subsystems identified as linking components. Both subsystems link other modules together by moving material to or from another module
Fast Link Adaptation for MIMO-OFDM
DEFF Research Database (Denmark)
Jensen, Tobias Lindstrøm; Kant, Shashi; Wehinger, Joachim
2010-01-01
We investigate link-quality metrics (LQMs) based on raw bit-error-rate, effective signal-to-interference-plus-noise ratio, and mutual information (MI) for the purpose of fast link adaptation (LA) in communication systems employing orthogonal frequency-division multiplexing and multiple-input–mult......We investigate link-quality metrics (LQMs) based on raw bit-error-rate, effective signal-to-interference-plus-noise ratio, and mutual information (MI) for the purpose of fast link adaptation (LA) in communication systems employing orthogonal frequency-division multiplexing and multiple...
The importance of link evidence in Wikipedia
Kamps, J.; Koolen, M.
2008-01-01
Wikipedia is one of the most popular information sources on the Web. The free encyclopedia is densely linked. The link structure in Wikipedia differs from the Web at large: internal links in Wikipedia are typically based on words naturally occurring in a page, and link to another semantically
Shuttle/TDRSS modelling and link simulation study
Braun, W. R.; Mckenzie, T. M.; Biederman, L.; Lindsey, W. C.
1979-01-01
A Shuttle/TDRSS S-band and Ku-band link simulation package called LinCsim was developed for the evaluation of link performance for specific Shuttle signal designs. The link models were described in detail and the transmitter distortion parameters or user constraints were carefully defined. The overall link degradation (excluding hardware degradations) relative to an ideal BPSK channel were given for various sets of user constraint values. The performance sensitivity to each individual user constraint was then illustrated. The effect of excessive Spacelab clock jitter on the return link BER performance was also investigated as was the problem of subcarrier recovery for the K-band Shuttle return link signal.
Helically linked mirror arrangement
International Nuclear Information System (INIS)
Ranjan, P.
1986-08-01
A scheme is described for helical linking of mirror sections, which endeavors to combine the better features of toroidal and mirror devices by eliminating the longitudinal loss of mirror machines, having moderately high average β and steady state operation. This scheme is aimed at a device, with closed magnetic surfaces having rotational transform for equilibrium, one or more axisymmetric straight sections for reduced radial loss, a simple geometrical axis for the links and an overall positive magnetic well depth for stability. We start by describing several other attempts at linking of mirror sections, made both in the past and the present. Then a description of our helically linked mirror scheme is given. This example has three identical straight sections connected by three sections having helical geometric axes. A theoretical analysis of the magnetic field and single-particle orbits in them leads to the conclusion that most of the passing particles would be confined in the device and they would have orbits independent of pitch angle under certain conditions. Numerical results are presented, which agree well with the theoretical results as far as passing particle orbits are concerned
Cross-link guided molecular modeling with ROSETTA.
Directory of Open Access Journals (Sweden)
Abdullah Kahraman
Full Text Available Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.
Full Text Available ... the link between drug misuse and HIV infection. It contains information for young people, parents and teachers, ... present time. The virus (HIV) and the disease it causes (AIDS) are often linked and referred to ...
International Nuclear Information System (INIS)
Bieser, F.; Jones, R.; McParland, C.
1991-01-01
This paper reports on the design and performance of high speed data links and slower configuration control links used between the EOS TPC detector and the data processing electronics. Data rates of 5 MBytes/link are maintained over 30m with optical isolation. Pedestal subtraction, hit detection, and data reordering are performed online
Laird, Mhairi; Thomson, Kacie; Fenwick, Mark; Mora, Jocelyn; Franks, Stephen; Hardy, Kate
2017-04-01
Androgens are essential for the normal function of mature antral follicles but also have a role in the early stages of follicle development. Polycystic ovary syndrome (PCOS), the most common cause of anovulatory infertility, is characterized by androgen excess and aberrant follicle development that includes accelerated early follicle growth. We have examined the effects of testosterone and dihydrotestosterone (DHT) on development of isolated mouse preantral follicles in culture with the specific aim of investigating interaction with follicle-stimulating hormone (FSH), the steroidogenic pathway, and growth factors of the TGFβ superfamily that are known to have a role in early follicle development. Both testosterone and DHT stimulated follicle growth and augmented FSH-induced growth and increased the incidence of antrum formation among the granulosa cell layers of these preantral follicles after 72 hours in culture. Effects of both androgens were reversed by the androgen receptor antagonist flutamide. FSH receptor expression was increased in response to both testosterone and DHT, as was that of Star, whereas Cyp11a1 was down-regulated. The key androgen-induced changes in the TGFβ signaling pathway were down-regulation of Amh, Bmp15, and their receptors. Inhibition of Alk6 (Bmpr1b), a putative partner for Amhr2 and Bmpr2, by dorsomorphin resulted in augmentation of androgen-stimulated growth and modification of androgen-induced gene expression. Our findings point to varied effects of androgen on preantral follicle growth and function, including interaction with FSH-activated growth and steroidogenesis, and, importantly, implicate the intrafollicular TGFβ system as a key mediator of androgen action. These findings provide insight into abnormal early follicle development in PCOS.
Mapping the x-linked lymphoproliferative syndrome
International Nuclear Information System (INIS)
Skare, J.C.; Milunsky, A.; Byron, K.S.; Sullivan, J.L.
1987-01-01
The X-linked lymphoproliferative syndrome is triggered by Epstein-Barr virus infection and results in fatal mononucleosis, immunodeficiency, and lymphoproliferative disorders. This study shows that the mutation responsible for X-linked lymphoproliferative syndrome is genetically linked to a restriction fragment length polymorphism detected with the DXS42 probe (from Xq24-q27). The most likely recombination frequency between the loci is 4%, and the associated logarithm of the odds is 5.26. Haplotype analysis using flanking restriction fragment length polymorphism markers indicates that the locus for X-linked lymphoproliferative syndrome is distal to probe DXS42 but proximal to probe DXS99 (from Xq26-q27). It is now possible to predict which members of a family with X-linked lymphoproliferative syndrome are carrier females and to diagnose the syndrome prenatally
Mapping the x-linked lymphoproliferative syndrome
Energy Technology Data Exchange (ETDEWEB)
Skare, J.C.; Milunsky, A.; Byron, K.S.; Sullivan, J.L.
1987-04-01
The X-linked lymphoproliferative syndrome is triggered by Epstein-Barr virus infection and results in fatal mononucleosis, immunodeficiency, and lymphoproliferative disorders. This study shows that the mutation responsible for X-linked lymphoproliferative syndrome is genetically linked to a restriction fragment length polymorphism detected with the DXS42 probe (from Xq24-q27). The most likely recombination frequency between the loci is 4%, and the associated logarithm of the odds is 5.26. Haplotype analysis using flanking restriction fragment length polymorphism markers indicates that the locus for X-linked lymphoproliferative syndrome is distal to probe DXS42 but proximal to probe DXS99 (from Xq26-q27). It is now possible to predict which members of a family with X-linked lymphoproliferative syndrome are carrier females and to diagnose the syndrome prenatally.
Full Text Available ... the Link - Drugs and HIV Learn the Link - Drugs and HIV Email Facebook Twitter 2005 –Ongoing Behaviors ... GA: CDC, DHHS. Retrieved November 2017. How are Drug Misuse and HIV Related? Drug misuse and addiction ...
Full Text Available ... Link Need ideas for posts? We’ve provided sample Facebook status updates that you can easily copy ... LearntheLink. Need ideas for tweets? We’ve provided sample tweets that you can easily copy and paste ...
Full Text Available ... HIV. Post on Facebook About Learn the Link Need ideas for posts? We’ve provided sample Facebook ... HIV, be sure to use the hashtag #LearntheLink. Need ideas for tweets? We’ve provided sample tweets ...
Full Text Available ... teens and young adults have never known a world without it. NIDA’s "Learn the Link" campaign continues ... for HIV infection through risky sexual behaviors. NIDA researchers have studied and continue to study the links ...
International Nuclear Information System (INIS)
Wallace, J.J.
1988-01-01
It is possible to expand the data acquisition capabilities of an existing process computer to include other dedicated computer based systems, provided each system has at least minimal data link capabilities. The following paper discusses the addition of three computer based acquisition systems to a Honeywell 4500C (also designated the 45000) running the SEER system. Only one data link port was required to support the link. Each of the three specialized systems implemented data link protocols used by their suppliers in previous projects: none of the three were compatible with Honeywell's protocol. Part one of the following provides a generic overview of the project and would be relevent to the operator of any process system interested in expansion. Part two provides specific details of this project and may serve to provide performance benchmarks to those who wish to consider a similar project
Narock, T.; Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Finin, T.; Hitzler, P.; Krisnadhi, A.; Raymond, L. M.; Shepherd, A.; Wiebe, P. H.
2014-12-01
A wide spectrum of maturing methods and tools, collectively characterized as the Semantic Web, is helping to vastly improve the dissemination of scientific research. Creating semantic integration requires input from both domain and cyberinfrastructure scientists. OceanLink, an NSF EarthCube Building Block, is demonstrating semantic technologies through the integration of geoscience data repositories, library holdings, conference abstracts, and funded research awards. Meeting project objectives involves applying semantic technologies to support data representation, discovery, sharing and integration. Our semantic cyberinfrastructure components include ontology design patterns, Linked Data collections, semantic provenance, and associated services to enhance data and knowledge discovery, interoperation, and integration. We discuss how these components are integrated, the continued automated and semi-automated creation of semantic metadata, and techniques we have developed to integrate ontologies, link resources, and preserve provenance and attribution.
Use of Modular Approach to Obtain Molecular Glasses for Photonics: Triphenyl Moieties
Traskovskis, K; Kokars, V; Tokmakovs, A; Mihailovs, I; Rutkis, M
2012-01-01
Small molecular weight amorphous phase forming materials is a new emerging class of electro optical materials. While general principles linking molecular structure and material thermal and amorphous phase stability characteristics remain unresolved, molecular glasses have several considerable advantages such as relatively simple synthesis and purification, increased chromophore density and well defined structure. A wide spread strategy for obtaining molecular compounds capable of forming stab...
Propensity to Click on Suspicious Links
DEFF Research Database (Denmark)
Sudzina, Frantisek; Pavlicek, Antonin
2017-01-01
such behavior. Big Five Inventory traits (extraversion, agreeableness, conscientiousness, neuroticism, openness to experience) and narcissism were used. Impact of openness to experience was significant at 0.05 level, and of narcissism 0.1 level. Significance of remaining independent variables was above 0.......1. Openness to experience was linked positively linked to responsible behavior, narcissism was negatively linked....
International Nuclear Information System (INIS)
Bieser, F.; Jones, R.; McParland, C.
1990-10-01
We report on the design and performance of high speed data links and slower configuration control links used between the EOS TPC detector and the data processing electronics. Data rates of 5MBytes/s/link are maintained over 30m with optical isolation. Pedestal subtraction, hit detection, and data reordering are performed online. 3 refs., 1 fig
Full Text Available ... Children & Teens Search Connect with NIDA : Facebook LinkedIn Twitter YouTube Flickr RSS Menu Home Drugs of Abuse ... Learn the Link - Drugs and HIV Email Facebook Twitter 2005 –Ongoing Behaviors associated with drug misuse are ...
Full Text Available ... Parents & Educators Children & Teens Search Connect with NIDA : Facebook LinkedIn Twitter YouTube Flickr RSS Menu Home Drugs ... HIV Learn the Link - Drugs and HIV Email Facebook Twitter 2005 –Ongoing Behaviors associated with drug misuse ...
Track with overlapping links for dry coal extrusion pumps
Saunders, Timothy; Brady, John D
2014-01-21
A chain for a particulate material extrusion pump includes a plurality of links, each of the plurality of links having a link body and a link ledge, wherein each link ledge of the plurality of links at least partially overlaps the link body of an adjacent one of the plurality of links.
Energy Technology Data Exchange (ETDEWEB)
Cummings, J.; Fedorov, A; Xu, C; Brown, S; Fedorov, E; Babbitt, P; Almo, S; Raushel, F
2009-01-01
The catalytic activities of three members of the amidohydrolase superfamily were discovered using amino acid substrate libraries. Bb3285 from Bordetella bronchiseptica, Gox1177 from Gluconobacter oxidans, and Sco4986 from Streptomyces coelicolor are currently annotated as d-aminoacylases or N-acetyl-d-glutamate deacetylases. These three enzymes are 22-34% identical to one another in amino acid sequence. Substrate libraries containing nearly all combinations of N-formyl-d-Xaa, N-acetyl-d-Xaa, N-succinyl-d-Xaa, and l-Xaa-d-Xaa were used to establish the substrate profiles for these enzymes. It was demonstrated that Bb3285 is restricted to the hydrolysis of N-acyl-substituted derivatives of d-glutamate. The best substrates for this enzyme are N-formyl-d-glutamate (k{sub cat}/K{sub m} = 5.8 x 10{sup 6} M{sup -1} s{sup -1}), N-acetyl-d-glutamate (k{sub cat}/K{sub m} = 5.2 x 10{sup 6} M{sup -1} s{sup -1}), and l-methionine-d-glutamate (k{sub cat}/K{sub m} = 3.4 x 10{sup 5} M{sup -1} s{sup -1}). Gox1177 and Sco4986 preferentially hydrolyze N-acyl-substituted derivatives of hydrophobic d-amino acids. The best substrates for Gox1177 are N-acetyl-d-leucine (k{sub cat}/K{sub m} = 3.2 x 104 M{sup -1} s-1), N-acetyl-d-tryptophan (kcat/Km = 4.1 x 104 M-1 s-1), and l-tyrosine-d-leucine (kcat/Km = 1.5 x 104 M-1 s-1). A fourth protein, Bb2785 from B. bronchiseptica, did not have d-aminoacylase activity. The best substrates for Sco4986 are N-acetyl-d-phenylalanine and N-acetyl-d-tryptophan. The three-dimensional structures of Bb3285 in the presence of the product acetate or a potent mimic of the tetrahedral intermediate were determined by X-ray diffraction methods. The side chain of the d-glutamate moiety of the inhibitor is ion-paired to Arg-295, while the {alpha}-carboxylate is ion-paired with Lys-250 and Arg-376. These results have revealed the chemical and structural determinants for substrate specificity in this protein. Bioinformatic analyses of an additional {approx}250
Full Text Available ... Learn the Link campaign uses TV, print, and Web public service announcements (PSAs), as well as posters, e-cards, ... to misuse drugs. The Learn the Link public service campaign is just one ... site. Sincerely, Nora D. Volkow, M.D. Director ...
Full Text Available ... projects/learn-link-drugs-hiv . 120x90 460x80 486x60 Social Media Send the message to young people and ... HIV/AIDS and the discovery of promising treatment interventions for breaking the harmful links between them, we ...
Full Text Available ... NIDA : Facebook LinkedIn Twitter YouTube Flickr RSS Menu Home Drugs of Abuse Commonly Abused Drugs Charts Emerging ... Badges Other Resources Strategic Plan Search Share Print Home » News & Events » Public Education Projects » Learn the Link - ...
Australia's unresolved nuclear problems
International Nuclear Information System (INIS)
Kemeny, L.G.
1987-01-01
This paper examines three acts of monumental incompetence which have all but destroyed Australia's once great potential to play a leading role in nuclear technology in South East Asia. Political chicanery and monumental technological and economic foresight, professional weakness and vacillation in the engineering community and the vicious pseudo scientific propaganda of most branches of the media, the teaching profession and sadly, even the politicisation of our churches, has all but destroyed a potential Australian ''sunrise industry''. Over the next forty years the population of planet Earth will approximately double. Unless Australians realise that their children and grand-children, and future generations of our neighbouring third world countries will require nuclear technology for an equitable and acceptable shared life-style, they will continue to allow taxpayers' money to be wasted on costly, technically unacceptable and environmentally undesirable attempts to develop ''alternative'' or ''renewable'' energy sources. These are neither alternative nor renewable but politically trendy. The tragedy of such projects is that their limited applicability and suitability for small scale energy production by wealthy users in limited geographical locations will only increase the need for base load energy supplies of the conventional type. Unless this is nuclear, planet Earth faces environmental despolation of monumental proportions. (J.P.N.)
Full Text Available ... link between drug misuse and HIV. http://1.usa.gov/1z20ww6 How many of us think about ... can’t ignore. Learn the Link: http://1.usa.gov/1uSUAI3 Think you’re not at risk? ...
Full Text Available ... site. Please link these banners back to this site at: http://www.drugabuse.gov/news-events/public-education-projects/learn-link-drugs-hiv . 120x90 460x80 486x60 Social Media Send the message to young people and to ...
Interactions of cross-linked and uncross-linked chitosan hydrogels ...
African Journals Online (AJOL)
The swelling equilibrium of Chitosan and sodium tripolyphosphate (NaTPP) cross-linked chitosan hydrogels in aqueous solutions of surfactants differing in structure and hydrophobicity at 250C is reported. Anionic surfactant sodium dodecylsulfate (SDS), the cationic surfactant hexadecyltrimethylammonium bromide (HTAB) ...
International Nuclear Information System (INIS)
1988-09-01
This report presents the results of the NRC integrated program for the resolution of Unresolved Safety Issues (USIs) A-3, A-4, and A-5 regarding steam generator tube integrity. A generic risk assessment is provided and indicates that risk from steam generator tube rupture (SGTR) events is not a significant contributor to total risk at a given site, nor to the total risk to which the general public is routinely exposed. This finding is considered to be indicative of the effectiveness of licensee programs and regulatory requirements for ensuring steam generator tube integrity in accordance with 10 CFR 50, Appendices A and B. This report also identifies a number of staff-recommended actions that the staff finds can further improve the effectiveness of licensee programs in ensuring the integrity of steam generator tubes and in mitigating the consequences of an SGTR. As part of the integrated program, the staff issued Generic Letter 85-02 encouraging licensees of pressurized water reactors (PWRs) to upgrade their programs, as necessary, to meet the intent of the staff-recommended actions; however, such actions do not constitute NRC requirements. In addition, this report describes a number of ongoing staff actions and studies involving steam generator issues which are being pursued to provide added assurance that risk from SGTR events will continue to be small. 146 refs., 5 figs., 11 tabs
Uncovering missing links with cold ends
Zhu, Yu-Xiao; Lü, Linyuan; Zhang, Qian-Ming; Zhou, Tao
2012-11-01
To evaluate the performance of prediction of missing links, the known data are randomly divided into two parts, the training set and the probe set. We argue that this straightforward and standard method may lead to terrible bias, since in real biological and information networks, missing links are more likely to be links connecting low-degree nodes. We therefore study how to uncover missing links with low-degree nodes, namely links in the probe set are of lower degree products than a random sampling. Experimental analysis on ten local similarity indices and four disparate real networks reveals a surprising result that the Leicht-Holme-Newman index [E.A. Leicht, P. Holme, M.E.J. Newman, Vertex similarity in networks, Phys. Rev. E 73 (2006) 026120] performs the best, although it was known to be one of the worst indices if the probe set is a random sampling of all links. We further propose an parameter-dependent index, which considerably improves the prediction accuracy. Finally, we show the relevance of the proposed index to three real sampling methods: acquaintance sampling, random-walk sampling and path-based sampling.
Propagation engineering in radio links design
Ghasemi, Abdollah; Ghasemi, Farshid
2013-01-01
Propagation Engineering in Radio Link Design covers the basic principles of radiowaves propagation in a practical manner. This fundamental understanding enables the readers to design radio links efficiently. This book elaborates on new achievements as well as recently developed propagation models. This is in addition to a comprehensive overview of fundamentals of propagation in various scenarios. It examines theoretical calculations, approaches and applied procedures needed for radio links design. The authors study and analysis of the main propagation phenomena and its mechanisms based on the recommendations of International Telecommunications Union, (ITU). The book has been organized in 9 chapters and examines the role of antennas and passive reflectors in radio services, propagation mechanisms related to radar, satellite, short distance, broadcasting and trans-horizon radio links, with two chapters devoted to radio noise and main parameters of radio link design. The book presents some 278 illustration...
Genetics Home Reference: X-linked creatine deficiency
... Health Conditions X-linked creatine deficiency X-linked creatine deficiency Printable PDF Open All Close All Enable ... view the expand/collapse boxes. Description X-linked creatine deficiency is an inherited disorder that primarily affects ...
Genetics Home Reference: X-linked sideroblastic anemia
... Conditions X-linked sideroblastic anemia X-linked sideroblastic anemia Printable PDF Open All Close All Enable Javascript ... the expand/collapse boxes. Description X-linked sideroblastic anemia is an inherited disorder that prevents developing red ...
Energy Technology Data Exchange (ETDEWEB)
Rivas-Ubach, Albert [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99354 USA; CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; Hódar, José A. [Grupo de Ecología Terrestre, Departamento de Biología Animal y Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada Spain; Sardans, Jordi [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain; Kyle, Jennifer E. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Kim, Young-Mo [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Oravec, Michal [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Urban, Otmar [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Guenther, Alex [Department of Earth System Science, University of California, Irvine California 92697 USA; Peñuelas, Josep [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain
2016-06-02
The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but the entire metabolome (the set of molecular metabolites), including defensive compounds. Metabolomes are the final products of genotypes and are directly affected by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from Pinus pinaster, P. nigra and P. sylvestris to determine if these closely related Pinus species with different coevolutionary histories with the caterpillars of the processionary moth respond similarly to attacks by this lepidopteran. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the pine species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of phenolic metabolites were generally not higher in the attacked trees, which had lower concentrations of terpenes, suggesting that herbivores avoid individuals with high concentrations of terpenes. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.
Vasileiadou, E.; Besselaar, van den P.
2006-01-01
In this paper we explore the possibility of using Web links to study collaborations between organisations, combining the results of qualitative analysis of interviews and quantitative analysis of linking patterns. We use case studies of scientific intermediaries, that is, organisations that mediate
Blind links, a big challenge in the linked data idea: Analysis of Persian Subject Headings
Directory of Open Access Journals (Sweden)
Atefeh Sharif
2014-12-01
Full Text Available In this survey, Linked data concept as exposing, sharing, and connecting pieces of data, information, and knowledge on the Semantic Web and some potential problems in converting Persian subject headings (PSHs Records into linked data were discussed. A data set (11233 records of PSHs was searched in three information retrieval systems including National Library of Iran (NLI online catalog, Library of Congress (LC online catalog and NOSA books. Correct links between Persian and English subject headings in the 9519 common records of two catalogs were recorded. The results indicate that the links between Persian and English subjects in 20% of records were failed. The maximum error was associated with the anonymous databases (6/7 % in NLI online catalog. It is recommended to preprocess the PSHs records before any conversion projects. It seems that, during the preprocessing, the potential errors could be identified and corrected.
Full Text Available ... at: http://www.drugabuse.gov/news-events/public-education-projects/learn-link-drugs-hiv . 120x90 460x80 486x60 Social Media Send the message to young people and to parents, teachers, and the media about the link between drug ...
International Nuclear Information System (INIS)
Rehan, Aisyah M.; Bashiri, Ghader; Paterson, Neil G.; Baker, Edward N.; Squire, Christopher J.
2011-01-01
The C-terminal domain of FbiB, a bifunctional protein that is essential for the biosynthesis of cofactor F 420 in M. tuberculosis, has been expressed, purified and crystallized. The crystals diffracted to 2.0 Å resolution and were suitable for structure determination. During cofactor F 420 biosynthesis, the enzyme F 420 -γ-glutamyl ligase (FbiB) catalyzes the addition of γ-linked l-glutamate residues to form polyglutamylated F 420 derivatives. In Mycobacterium tuberculosis, Rv3262 (FbiB) consists of two domains: an N-terminal domain from the F 420 ligase superfamily and a C-terminal domain with sequence similarity to nitro-FMN reductase superfamily proteins. To characterize the role of the C-terminal domain of FbiB in polyglutamyl ligation, it has been purified and crystallized in an apo form. The crystals diffracted to 2.0 Å resolution using a synchrotron source and belonged to the tetragonal space group P4 1 2 1 2 (or P4 3 2 1 2), with unit-cell parameters a = b = 136.6, c = 101.7 Å, α = β = γ = 90°