Frequency of inhibitors of daphnid trypsin in the widely distributed cyanobacterial genus Planktothrix

DEFF Research Database (Denmark)

Rohrlack, T.; Christoffersen, K.; Friberg-Jensen, U.

2005-01-01

on the frequency of such compounds in the widely distributed cyanobacterial genus Planktothrix. Of the 89 Planktothrix strains analysed, about 70% produced inhibitors of daphnid trypsin. The strains tested positive represented three common Planktothrix species and were isolated from diverse localities...

Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions

Directory of Open Access Journals (Sweden)

Marin de Mas Igor

2011-10-01

Full Text Available Abstract Background Stable isotope tracers are used to assess metabolic flux profiles in living cells. The existing methods of measurement average out the isotopic isomer distribution in metabolites throughout the cell, whereas the knowledge of compartmental organization of analyzed pathways is crucial for the evaluation of true fluxes. That is why we accepted a challenge to create a software tool that allows deciphering the compartmentation of metabolites based on the analysis of average isotopic isomer distribution. Results The software Isodyn, which simulates the dynamics of isotopic isomer distribution in central metabolic pathways, was supplemented by algorithms facilitating the transition between various analyzed metabolic schemes, and by the tools for model discrimination. It simulated 13C isotope distributions in glucose, lactate, glutamate and glycogen, measured by mass spectrometry after incubation of hepatocytes in the presence of only labeled glucose or glucose and lactate together (with label either in glucose or lactate. The simulations assumed either a single intracellular hexose phosphate pool, or also channeling of hexose phosphates resulting in a different isotopic composition of glycogen. Model discrimination test was applied to check the consistency of both models with experimental data. Metabolic flux profiles, evaluated with the accepted model that assumes channeling, revealed the range of changes in metabolic fluxes in liver cells. Conclusions The analysis of compartmentation of metabolic networks based on the measured 13C distribution was included in Isodyn as a routine procedure. The advantage of this implementation is that, being a part of evaluation of metabolic fluxes, it does not require additional experiments to study metabolic compartmentation. The analysis of experimental data revealed that the distribution of measured 13C-labeled glucose metabolites is inconsistent with the idea of perfect mixing of hexose

The mechanical behavior of metal alloys with grain size distribution in a wide range of strain rates

Science.gov (United States)

Skripnyak, V. A.; Skripnyak, V. V.; Skripnyak, E. G.

2017-12-01

The paper discusses a multiscale simulation approach for the construction of grain structure of metals and alloys, providing high tensile strength with ductility. This work compares the mechanical behavior of light alloys and the influence of the grain size distribution in a wide range of strain rates. The influence of the grain size distribution on the inelastic deformation and fracture of aluminium and magnesium alloys is investigated by computer simulations in a wide range of strain rates. It is shown that the yield stress depends on the logarithm of the normalized strain rate for light alloys with a bimodal grain distribution and coarse-grained structure.

Freshwater Biogeography and Limnological Evolution of the Tibetan Plateau - Insights from a Plateau-Wide Distributed Gastropod Taxon (Radix spp.)

Science.gov (United States)

von Oheimb, Parm Viktor; Albrecht, Christian; Riedel, Frank; Du, Lina; Yang, Junxing; Aldridge, David C.; Bößneck, Ulrich; Zhang, Hucai; Wilke, Thomas

2011-01-01

Background The Tibetan Plateau is not only the highest and largest plateau on earth; it is also home to numerous freshwater lakes potentially harbouring endemic faunal elements. As it remains largely unknown whether these lakes have continuously existed during the Last Glacial Maximum (LGM), questions arise as to whether taxa have been able to exist on the plateau since before the latest Pleistocene, from where and how often the plateau was colonized, and by which mechanisms organisms conquered remote high altitude lentic freshwater systems. In this study, species of the plateau-wide distributed freshwater gastropod genus Radix are used to answer these biogeographical questions. Methodology/Principal Findings Based on a broad spatial sampling of Radix spp. on the Tibetan Plateau, and phylogenetic analyses of mtDNA sequence data, three probably endemic and one widespread major Radix clade could be identified on the plateau. Two of the endemic clades show a remarkably high genetic diversity, indicating a relatively great phylogenetic age. Phylogeographical analyses of individuals belonging to the most widely distributed clade indicate that intra-plateau distribution cannot be explained by drainage-related dispersal alone. Conclusions/Significance Our study reveals that Radix spp. persisted throughout the LGM on the Tibetan Plateau. Therefore, we assume the continuous existence of suitable water bodies during that time. The extant Radix diversity on the plateau might have been caused by multiple colonization events combined with a relatively long intra-plateau evolution. At least one colonization event has a Palaearctic origin. In contrast to freshwater fishes, passive dispersal, probably by water birds, might be an important mechanism for conquering remote areas on the plateau. Patterns found in Radix spp. are shared with some terrestrial plateau taxa, indicating that Radix may be a suitable model taxon for inferring general patterns of biotic origin, dispersal and

Genome-wide association scan meta-analysis identifies three loci influencing adiposity and fat distribution

NARCIS (Netherlands)

C.M. Lindgren (Cecilia); I.M. Heid (Iris); J.C. Randall (Joshua); C. Lamina (Claudia); V. Steinthorsdottir (Valgerdur); L. Qi (Lu); E.K. Speliotes (Elizabeth); G. Thorleifsson (Gudmar); C.J. Willer (Cristen); B.M. Herrera (Blanca); A.U. Jackson (Anne); N. Lim (Noha); P. Scheet (Paul); N. Soranzo (Nicole); N. Amin (Najaf); Y.S. Aulchenko (Yurii); J.C. Chambers (John); A. Drong (Alexander); J. Luan; H.N. Lyon (Helen); F. Rivadeneira Ramirez (Fernando); S. Sanna (Serena); N.J. Timpson (Nicholas); M.C. Zillikens (Carola); H.Z. Jing; P. Almgren (Peter); S. Bandinelli (Stefania); A.J. Bennett (Amanda); R.N. Bergman (Richard); L.L. Bonnycastle (Lori); S. Bumpstead (Suzannah); S.J. Chanock (Stephen); L. Cherkas (Lynn); P.S. Chines (Peter); L. Coin (Lachlan); C. Cooper (Charles); G. Crawford (Gabe); A. Doering (Angela); A. Dominiczak (Anna); A.S.F. Doney (Alex); S. Ebrahim (Shanil); P. Elliott (Paul); M.R. Erdos (Michael); K. Estrada Gil (Karol); L. Ferrucci (Luigi); G. Fischer (Guido); N.G. Forouhi (Nita); C. Gieger (Christian); H. Grallert (Harald); C.J. Groves (Christopher); S.M. Grundy (Scott); C. Guiducci (Candace); D. Hadley (David); A. Hamsten (Anders); A.S. Havulinna (Aki); A. Hofman (Albert); R. Holle (Rolf); J.W. Holloway (John); T. Illig (Thomas); B. Isomaa (Bo); L.C. Jacobs (Leonie); K. Jameson (Karen); P. Jousilahti (Pekka); F. Karpe (Fredrik); J. Kuusisto (Johanna); J. Laitinen (Jaana); G.M. Lathrop (Mark); D.A. Lawlor (Debbie); M. Mangino (Massimo); W.L. McArdle (Wendy); T. Meitinger (Thomas); M.A. Morken (Mario); A.P. Morris (Andrew); P. Munroe (Patricia); N. Narisu (Narisu); A. Nordström (Anna); B.A. Oostra (Ben); C.N.A. Palmer (Colin); F. Payne (Felicity); J. Peden (John); I. Prokopenko (Inga); F. Renström (Frida); A. Ruokonen (Aimo); V. Salomaa (Veikko); M.S. Sandhu (Manjinder); L.J. Scott (Laura); A. Scuteri (Angelo); K. Silander (Kaisa); K. Song (Kijoung); X. Yuan (Xin); H.M. Stringham (Heather); A.J. Swift (Amy); T. Tuomi (Tiinamaija); M. Uda (Manuela); P. Vollenweider (Peter); G. Waeber (Gérard); C. Wallace (Chris); G.B. Walters (Bragi); M.N. Weedon (Michael); J.C.M. Witteman (Jacqueline); C. Zhang (Cuilin); M. Caulfield (Mark); F.S. Collins (Francis); G.D. Smith; I.N.M. Day (Ian); P.W. Franks (Paul); A.T. Hattersley (Andrew); F.B. Hu (Frank); M.-R. Jarvelin (Marjo-Riitta); A. Kong (Augustine); J.S. Kooner (Jaspal); M. Laakso (Markku); E. Lakatta (Edward); V. Mooser (Vincent); L. Peltonen (Leena Johanna); N.J. Samani (Nilesh); T.D. Spector (Timothy); D.P. Strachan (David); T. Tanaka (Toshiko); J. Tuomilehto (Jaakko); A.G. Uitterlinden (André); P. Tikka-Kleemola (Päivi); N.J. Wareham (Nick); H. Watkins (Hugh); D. Waterworth (Dawn); M. Boehnke (Michael); P. Deloukas (Panagiotis); L. Groop (Leif); D.J. Hunter (David); U. Thorsteinsdottir (Unnur); D. Schlessinger (David); H.E. Wichmann (Erich); T.M. Frayling (Timothy); G.R. Abecasis (Gonçalo); J.N. Hirschhorn (Joel); R.J.F. Loos (Ruth); J-A. Zwart (John-Anker); K.L. Mohlke (Karen); I.E. Barroso (Inês); M.I. McCarthy (Mark)

2009-01-01

textabstractTo identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580) informative for adult waist circumference (WC) and waist-hip ratio (WHR). We selected 26 SNPs for follow-up, for which the

UNUSUALLY WIDE BINARIES: ARE THEY WIDE OR UNUSUAL?

International Nuclear Information System (INIS)

Kraus, Adam L.; Hillenbrand, Lynne A.

2009-01-01

We describe an astrometric and spectroscopic campaign to confirm the youth and association of a complete sample of candidate wide companions in Taurus and Upper Sco. Our survey found 15 new binary systems (three in Taurus and 12 in Upper Sco) with separations of 3''-30'' (500-5000 AU) among all of the known members with masses of 2.5-0.012 M sun . The total sample of 49 wide systems in these two regions conforms to only some expectations from field multiplicity surveys. Higher mass stars have a higher frequency of wide binary companions, and there is a marked paucity of wide binary systems near the substellar regime. However, the separation distribution appears to be log-flat, rather than declining as in the field, and the mass ratio distribution is more biased toward similar-mass companions than the initial mass function or the field G-dwarf distribution. The maximum separation also shows no evidence of a limit at ∼ sun . We attribute this result to the post-natal dynamical sculpting that occurs for most field systems; our binary systems will escape to the field intact, but most field stars are formed in denser clusters and undergo significant dynamical evolution. In summary, only wide binary systems with total masses ∼ sun appear to be 'unusually wide'.

Genome-Wide RNAi Ionomics Screen Reveals New Genes and Regulation of Human Trace Element Metabolism

OpenAIRE

Malinouski, Mikalai; Hasan, Nesrin M.; Zhang, Yan; Seravalli, Javier; Lin, Jie; Avanesov, Andrei; Lutsenko, Svetlana; Gladyshev, Vadim N.

2017-01-01

Trace elements are essential for human metabolism and dysregulation of their homeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundam...

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features.

Science.gov (United States)

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C; Assmann, Sarah M

2014-01-30

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

Mitochondrial DNA Variation Reveals a Sharp Genetic Break within the Distribution of the Blue Land Crab Cardisoma guanhumi in the Western Central Atlantic

Directory of Open Access Journals (Sweden)

Maria Rosimere Xavier Amaral

2015-08-01

Full Text Available The blue land crab Cardisoma guanhumi is widely distributed throughout tropical and subtropical estuarine regions in the Western Central Atlantic (WCA. Patterns of population genetic structure and historical demographics of the species were assessed by mtDNA control region sequence analysis to examine the connectivity among five populations (n = 97 within the region for future conservation strategies and decision-making of fishery management. A total of 234 polymorphic nucleotides were revealed within the sequence region, which have defined 93 distinct haplotypes. No dominant mtDNA haplotypes were found but instead a distribution of a few low-frequency recurrent haplotypes with a large number of singletons. A NJ-tree and a median-joining haplotype network revealed two distinct clusters, corresponding to individuals from estuaries located along the Caribbean Sea and Brazilian waters, respectively. AMOVA and FST statistics supported the hypothesis that two main geographic regions exists. Phylogeographical discontinuity was further demonstrated by the Bayesian assignment analysis and a significant pattern of isolation-by-distance. Additionally, tests of neutral evolution and analysis of mismatch distribution indicate a complex demographic history in the WCA, which corresponds to bottleneck and subsequent population growth. Overall, a sharp genetic break between Caribbean and Brazilian populations raised concerns over the conservation status of the blue land crab.

An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies.

Directory of Open Access Journals (Sweden)

Wesley K Thompson

2015-12-01

Full Text Available Characterizing the distribution of effects from genome-wide genotyping data is crucial for understanding important aspects of the genetic architecture of complex traits, such as number or proportion of non-null loci, average proportion of phenotypic variance explained per non-null effect, power for discovery, and polygenic risk prediction. To this end, previous work has used effect-size models based on various distributions, including the normal and normal mixture distributions, among others. In this paper we propose a scale mixture of two normals model for effect size distributions of genome-wide association study (GWAS test statistics. Test statistics corresponding to null associations are modeled as random draws from a normal distribution with zero mean; test statistics corresponding to non-null associations are also modeled as normal with zero mean, but with larger variance. The model is fit via minimizing discrepancies between the parametric mixture model and resampling-based nonparametric estimates of replication effect sizes and variances. We describe in detail the implications of this model for estimation of the non-null proportion, the probability of replication in de novo samples, the local false discovery rate, and power for discovery of a specified proportion of phenotypic variance explained from additive effects of loci surpassing a given significance threshold. We also examine the crucial issue of the impact of linkage disequilibrium (LD on effect sizes and parameter estimates, both analytically and in simulations. We apply this approach to meta-analysis test statistics from two large GWAS, one for Crohn's disease (CD and the other for schizophrenia (SZ. A scale mixture of two normals distribution provides an excellent fit to the SZ nonparametric replication effect size estimates. While capturing the general behavior of the data, this mixture model underestimates the tails of the CD effect size distribution. We discuss the

An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies.

Science.gov (United States)

Thompson, Wesley K; Wang, Yunpeng; Schork, Andrew J; Witoelar, Aree; Zuber, Verena; Xu, Shujing; Werge, Thomas; Holland, Dominic; Andreassen, Ole A; Dale, Anders M

2015-12-01

Characterizing the distribution of effects from genome-wide genotyping data is crucial for understanding important aspects of the genetic architecture of complex traits, such as number or proportion of non-null loci, average proportion of phenotypic variance explained per non-null effect, power for discovery, and polygenic risk prediction. To this end, previous work has used effect-size models based on various distributions, including the normal and normal mixture distributions, among others. In this paper we propose a scale mixture of two normals model for effect size distributions of genome-wide association study (GWAS) test statistics. Test statistics corresponding to null associations are modeled as random draws from a normal distribution with zero mean; test statistics corresponding to non-null associations are also modeled as normal with zero mean, but with larger variance. The model is fit via minimizing discrepancies between the parametric mixture model and resampling-based nonparametric estimates of replication effect sizes and variances. We describe in detail the implications of this model for estimation of the non-null proportion, the probability of replication in de novo samples, the local false discovery rate, and power for discovery of a specified proportion of phenotypic variance explained from additive effects of loci surpassing a given significance threshold. We also examine the crucial issue of the impact of linkage disequilibrium (LD) on effect sizes and parameter estimates, both analytically and in simulations. We apply this approach to meta-analysis test statistics from two large GWAS, one for Crohn's disease (CD) and the other for schizophrenia (SZ). A scale mixture of two normals distribution provides an excellent fit to the SZ nonparametric replication effect size estimates. While capturing the general behavior of the data, this mixture model underestimates the tails of the CD effect size distribution. We discuss the implications of

Field and long-term demonstration of a wide area quantum key distribution network.

Science.gov (United States)

Wang, Shuang; Chen, Wei; Yin, Zhen-Qiang; Li, Hong-Wei; He, De-Yong; Li, Yu-Hu; Zhou, Zheng; Song, Xiao-Tian; Li, Fang-Yi; Wang, Dong; Chen, Hua; Han, Yun-Guang; Huang, Jing-Zheng; Guo, Jun-Fu; Hao, Peng-Lei; Li, Mo; Zhang, Chun-Mei; Liu, Dong; Liang, Wen-Ye; Miao, Chun-Hua; Wu, Ping; Guo, Guang-Can; Han, Zheng-Fu

2014-09-08

A wide area quantum key distribution (QKD) network deployed on communication infrastructures provided by China Mobile Ltd. is demonstrated. Three cities and two metropolitan area QKD networks were linked up to form the Hefei-Chaohu-Wuhu wide area QKD network with over 150 kilometers coverage area, in which Hefei metropolitan area QKD network was a typical full-mesh core network to offer all-to-all interconnections, and Wuhu metropolitan area QKD network was a representative quantum access network with point-to-multipoint configuration. The whole wide area QKD network ran for more than 5000 hours, from 21 December 2011 to 19 July 2012, and part of the network stopped until last December. To adapt to the complex and volatile field environment, the Faraday-Michelson QKD system with several stability measures was adopted when we designed QKD devices. Through standardized design of QKD devices, resolution of symmetry problem of QKD devices, and seamless switching in dynamic QKD network, we realized the effective integration between point-to-point QKD techniques and networking schemes.

Genome-wide analysis reveals the vacuolar pH-stat of Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Christopher L Brett

Full Text Available Protons, the smallest and most ubiquitous of ions, are central to physiological processes. Transmembrane proton gradients drive ATP synthesis, metabolite transport, receptor recycling and vesicle trafficking, while compartmental pH controls enzyme function. Despite this fundamental importance, the mechanisms underlying pH homeostasis are not entirely accounted for in any organelle or organism. We undertook a genome-wide survey of vacuole pH (pH(v in 4,606 single-gene deletion mutants of Saccharomyces cerevisiae under control, acid and alkali stress conditions to reveal the vacuolar pH-stat. Median pH(v (5.27±0.13 was resistant to acid stress (5.28±0.14 but shifted significantly in response to alkali stress (5.83±0.13. Of 107 mutants that displayed aberrant pH(v under more than one external pH condition, functional categories of transporters, membrane biogenesis and trafficking machinery were significantly enriched. Phospholipid flippases, encoded by the family of P4-type ATPases, emerged as pH regulators, as did the yeast ortholog of Niemann Pick Type C protein, implicated in sterol trafficking. An independent genetic screen revealed that correction of pH(v dysregulation in a neo1(ts mutant restored viability whereas cholesterol accumulation in human NPC1(-/- fibroblasts diminished upon treatment with a proton ionophore. Furthermore, while it is established that lumenal pH affects trafficking, this study revealed a reciprocal link with many mutants defective in anterograde pathways being hyperacidic and retrograde pathway mutants with alkaline vacuoles. In these and other examples, pH perturbations emerge as a hitherto unrecognized phenotype that may contribute to the cellular basis of disease and offer potential therapeutic intervention through pH modulation.

Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function

Science.gov (United States)

Fuchsberger, Christian; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Chouraki, Vincent; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank B.; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H.-Erich; Kolcic, Ivana; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Endlich, Karlhans; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Giulianini, Franco; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Metzger, Marie; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid; Kardia, Sharon L. R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline C. M.; Hayward, Caroline; Ridker, Paul; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Goessling, Wolfram; Chasman, Daniel I.; Kao, W. H. Linda; Fox, Caroline S.

2012-01-01

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD. PMID:22479191

Genome-wide association and functional follow-up reveals new loci for kidney function.

Science.gov (United States)

Pattaro, Cristian; Köttgen, Anna; Teumer, Alexander; Garnaas, Maija; Böger, Carsten A; Fuchsberger, Christian; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; O'Seaghdha, Conall M; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D; Gierman, Hinco J; Feitosa, Mary; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Chouraki, Vincent; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank B; Demirkan, Ayse; Oostra, Ben A; de Andrade, Mariza; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H-Erich; Kolcic, Ivana; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Endlich, Karlhans; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Giulianini, Franco; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Metzger, Marie; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S; van Duijn, Cornelia M; Borecki, Ingrid; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline C M; Hayward, Caroline; Ridker, Paul; Parsa, Afshin; Bochud, Murielle; Heid, Iris M; Goessling, Wolfram; Chasman, Daniel I; Kao, W H Linda; Fox, Caroline S

2012-01-01

Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.

Genome-wide association and functional follow-up reveals new loci for kidney function.

Directory of Open Access Journals (Sweden)

Cristian Pattaro

Full Text Available Chronic kidney disease (CKD is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR, the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD.

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

Energy Technology Data Exchange (ETDEWEB)

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMcahon, Katherine D.; Mamlstrom, Rex R.

2014-05-12

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

Energy Technology Data Exchange (ETDEWEB)

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie; Schwientek, Patrick; Tremblay, Julien; Schackwitz, Wendy; Martin, Joel; Pati, Amrita; Bushnell, Brian; Foster, Brian; Kang, Dongwan; Tringe, Susannah G.; Bertilsson, Stefan; Moran, Mary Ann; Shade, Ashley; Newton, Ryan J.; Stevens, Sarah; McMahon, Katherine D.; Malmstrom, Rex R.

2014-06-18

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.

Genome-wide identification of Bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling.

Directory of Open Access Journals (Sweden)

Bin Tang

Full Text Available B-cell leukemia/lymphoma 11B (Bcl11b is a transcription factor showing predominant expression in the striatum. To date, there are no known gene targets of Bcl11b in the nervous system. Here, we define targets for Bcl11b in striatal cells by performing chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq in combination with genome-wide expression profiling. Transcriptome-wide analysis revealed that 694 genes were significantly altered in striatal cells over-expressing Bcl11b, including genes showing striatal-enriched expression similar to Bcl11b. ChIP-seq analysis demonstrated that Bcl11b bound a mixture of coding and non-coding sequences that were within 10 kb of the transcription start site of an annotated gene. Integrating all ChIP-seq hits with the microarray expression data, 248 direct targets of Bcl11b were identified. Functional analysis on the integrated gene target list identified several zinc-finger encoding genes as Bcl11b targets, and further revealed a significant association of Bcl11b to brain-derived neurotrophic factor/neurotrophin signaling. Analysis of ChIP-seq binding regions revealed significant consensus DNA binding motifs for Bcl11b. These data implicate Bcl11b as a novel regulator of the BDNF signaling pathway, which is disrupted in many neurological disorders. Specific targeting of the Bcl11b-DNA interaction could represent a novel therapeutic approach to lowering BDNF signaling specifically in striatal cells.

Wide Distribution and Genetic Diversity of Babesia microti in Small Mammals from Yunnan Province, Southwestern China.

Science.gov (United States)

Gao, Zi-Hou; Huang, Tao-Hua; Jiang, Bao-Gui; Jia, Na; Liu, Zheng-Xiang; Shao, Zong-Ti; Jiang, Rui-Ruo; Liu, Hong-Bo; Wei, Ran; Li, Yu-Qiong; Yao, Hong-Wu; von Fricken, Michael E; Jiang, Jia-Fu; Du, Chun-Hong; Cao, Wu-Chun

2017-10-01

Babesia, usually found in wild and domestic mammals worldwide, have recently been responsible for emerging malaria-like zoonosis in infected patients. Human B. microti infection has been identified in China, primarily in the Southwest along the Myanmar border but little direct surveillance of B. microti infection in rodents has been carried out here (Yunnan province). In this region, a diverse topographic range combined with tropical moisture sustains a high biodiversity of small mammals, which might play important role on Babesia transmission. Small mammals were captured in 141 sample locations from 18 counties located Yunnan Province, and screened for B. microti-like parasites infection by a nested PCR to target 18S rRNA gene of Babesia, plus directly sequencing for positive samples. Univariate and multivariate forward stepwise logistic regression analysis was used to access the association between infections and some related risk factors. Infection with Babesia microti was confirmed in 2.4% (53/ 2204) of small mammals. Significant differences in prevalence rates of B. microti were observed based on variations in forest, agricultural, and residential landscapes. Furthermore, adult small mammals had higher prevalence rates than younger, pubertal mammals. The near full-length 18S rRNA gene revealed that there were two types of B. microti, Kobe and Otsu, which demonstrate the genetic diversity and regional distribution. There exists a wide distribution and genetic diversity of endemic B. microti in Southwestern China, warranting further investigations and monitoring of clinical disease in individuals presenting with Babesia like symptoms in these areas.

Landmark Study Reveals Antarctic Glacier's Long History of Retreat

OpenAIRE

Kuska, Dale M.

2016-01-01

Faculty Showcase Archive Article Approved for public release; distribution is unlimited. A major study, released in late November in the journal “Nature,” reveals the history of retreat of the massive Pine Island Glacier (PIG) in western Antarctica, widely considered one of the largest contributors to global sea-level rise.

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

Science.gov (United States)

Mao, Peng; Brown, Alexander J; Malc, Ewa P; Mieczkowski, Piotr A; Smerdon, Michael J; Roberts, Steven A; Wyrick, John J

2017-10-01

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers. © 2017 Mao et al.; Published by Cold Spring Harbor Laboratory Press.

Distributed nuclear medicine applications using World Wide Web and Java technology

International Nuclear Information System (INIS)

Knoll, P.; Hoell, K.; Koriska, K.; Mirzaei, S.; Koehn, H.

2000-01-01

At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT). (orig.)

A Novel Wide-Area Backup Protection Based on Fault Component Current Distribution and Improved Evidence Theory

Directory of Open Access Journals (Sweden)

Zhe Zhang

2014-01-01

Full Text Available In order to solve the problems of the existing wide-area backup protection (WABP algorithms, the paper proposes a novel WABP algorithm based on the distribution characteristics of fault component current and improved Dempster/Shafer (D-S evidence theory. When a fault occurs, slave substations transmit to master station the amplitudes of fault component currents of transmission lines which are the closest to fault element. Then master substation identifies suspicious faulty lines according to the distribution characteristics of fault component current. After that, the master substation will identify the actual faulty line with improved D-S evidence theory based on the action states of traditional protections and direction components of these suspicious faulty lines. The simulation examples based on IEEE 10-generator-39-bus system show that the proposed WABP algorithm has an excellent performance. The algorithm has low requirement of sampling synchronization, small wide-area communication flow, and high fault tolerance.

A Novel Wide-Area Backup Protection Based on Fault Component Current Distribution and Improved Evidence Theory

Science.gov (United States)

Zhang, Zhe; Kong, Xiangping; Yin, Xianggen; Yang, Zengli; Wang, Lijun

2014-01-01

In order to solve the problems of the existing wide-area backup protection (WABP) algorithms, the paper proposes a novel WABP algorithm based on the distribution characteristics of fault component current and improved Dempster/Shafer (D-S) evidence theory. When a fault occurs, slave substations transmit to master station the amplitudes of fault component currents of transmission lines which are the closest to fault element. Then master substation identifies suspicious faulty lines according to the distribution characteristics of fault component current. After that, the master substation will identify the actual faulty line with improved D-S evidence theory based on the action states of traditional protections and direction components of these suspicious faulty lines. The simulation examples based on IEEE 10-generator-39-bus system show that the proposed WABP algorithm has an excellent performance. The algorithm has low requirement of sampling synchronization, small wide-area communication flow, and high fault tolerance. PMID:25050399

Object Distribution Networks for World-wide Document Circulation

NARCIS (Netherlands)

Lijding, M.E.M.; Righetti, Claudio E.; Moldes, Leandro Navarro

1997-01-01

This paper presents an Object Distribution System (ODS), a distributed system inspired by the ultra-large scale distribution models used in everyday life (e.g. food or newspapers distribution chains). Beyond traditional mechanisms of approaching information to readers (e.g. caching and mirroring),

Genome-wide association of body fat distribution in African ancestry populations suggests new loci.

Directory of Open Access Journals (Sweden)

Ching-Ti Liu

Full Text Available Central obesity, measured by waist circumference (WC or waist-hip ratio (WHR, is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS of fat distribution among those of predominantly African ancestry (AA. We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1. Overall, 25 SNPs with single genomic control (GC-corrected p-values<5.0 × 10(-6 were followed-up (stage 2 in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8 for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8 for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8; RREB1: p = 5.7 × 10(-8. Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN. Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02. In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept

Wide distribution of virulence genes among Enterococcus faecium and Enterococcus faecalis clinical isolates.

Science.gov (United States)

Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasanthakumari; Sadeghifard, Nourkhoda; Ramli, Ramliza; Hamat, Rukman Awang

2014-01-01

Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%), and the extended temperatures between 5(°)C and 65(°)C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species.

Wide Distribution of Virulence Genes among Enterococcus faecium and Enterococcus faecalis Clinical Isolates

Directory of Open Access Journals (Sweden)

Sara Soheili

2014-01-01

Full Text Available Enterococcus, a Gram-positive facultative anaerobic cocci belonging to the lactic acid bacteria of the phylum Firmicutes, is known to be able to resist a wide range of hostile conditions such as different pH levels, high concentration of NaCl (6.5%, and the extended temperatures between 5°C and 65°C. Despite being the third most common nosocomial pathogen, our understanding on its virulence factors is still poorly understood. The current study was aimed to determine the prevalence of different virulence genes in Enterococcus faecalis and Enterococcus faecium. For this purpose, 79 clinical isolates of Malaysian enterococci were evaluated for the presence of virulence genes. pilB, fms8, efaAfm, and sgrA genes are prevalent in all clinical isolates. In conclusion, the pathogenicity of E. faecalis and E. faecium could be associated with different virulence factors and these genes are widely distributed among the enterococcal species.

Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

International Nuclear Information System (INIS)

Pillay, K.K.S.; Driscoll, D.C.; Jester, W.A.

1975-01-01

A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

CASTOR: Widely Distributed Scalable Infospaces

Science.gov (United States)

2008-11-01

Symposium on Networked System Design and Implementation (NSDI 08). San Francisco , CA. April 2008. Gossip-based Distribution Estimation in Peer-to...and S. Paul. RMTP: A reliable multicast transport protocol. In INFOCOM, pages 1414–1424, San Francisco , CA, Mar. 1996. [22] T. Montgomery, B. Whetten...Fast approx- imate reconciliation of set differences. Boston University Computer Science Technical Report 2002-019., 2002. [5] L. Camargos , F. Pedone

Asymmetric biotic interactions and abiotic niche differences revealed by a dynamic joint species distribution model.

Science.gov (United States)

Lany, Nina K; Zarnetske, Phoebe L; Schliep, Erin M; Schaeffer, Robert N; Orians, Colin M; Orwig, David A; Preisser, Evan L

2018-05-01

A species' distribution and abundance are determined by abiotic conditions and biotic interactions with other species in the community. Most species distribution models correlate the occurrence of a single species with environmental variables only, and leave out biotic interactions. To test the importance of biotic interactions on occurrence and abundance, we compared a multivariate spatiotemporal model of the joint abundance of two invasive insects that share a host plant, hemlock woolly adelgid (HWA; Adelges tsugae) and elongate hemlock scale (EHS; Fiorina externa), to independent models that do not account for dependence among co-occurring species. The joint model revealed that HWA responded more strongly to abiotic conditions than EHS. Additionally, HWA appeared to predispose stands to subsequent increase of EHS, but HWA abundance was not strongly dependent on EHS abundance. This study demonstrates how incorporating spatial and temporal dependence into a species distribution model can reveal the dependence of a species' abundance on other species in the community. Accounting for dependence among co-occurring species with a joint distribution model can also improve estimation of the abiotic niche for species affected by interspecific interactions. © 2018 by the Ecological Society of America.

Optogenetic activation of CA1 pyramidal neurons at the dorsal and ventral hippocampus evokes distinct brain-wide responses revealed by mouse fMRI.

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Norio Takata

Full Text Available The dorsal and ventral hippocampal regions (dHP and vHP are proposed to have distinct functions. Electrophysiological studies have revealed intra-hippocampal variances along the dorsoventral axis. Nevertheless, the extra-hippocampal influences of dHP and vHP activities remain unclear. In this study, we compared the spatial distribution of brain-wide responses upon dHP or vHP activation and further estimate connection strengths between the dHP and the vHP with corresponding extra-hippocampal areas. To achieve this, we first investigated responses of local field potential (LFP and multi unit activities (MUA upon light stimulation in the hippocampus of an anesthetized transgenic mouse, whose CA1 pyramidal neurons expressed a step-function opsin variant of channelrhodopsin-2 (ChR2. Optogenetic stimulation increased hippocampal LFP power at theta, gamma, and ultra-fast frequency bands, and augmented MUA, indicating light-induced activation of CA1 pyramidal neurons. Brain-wide responses examined using fMRI revealed that optogenetic activation at the dHP or vHP caused blood oxygenation level-dependent (BOLD fMRI signals in situ. Although activation at the dHP induced BOLD responses at the vHP, the opposite was not observed. Outside the hippocampal formation, activation at the dHP, but not the vHP, evoked BOLD responses at the retrosplenial cortex (RSP, which is in line with anatomical evidence. In contrast, BOLD responses at the lateral septum (LS were induced only upon vHP activation, even though both dHP and vHP send axonal fibers to the LS. Our findings suggest that the primary targets of dHP and vHP activation are distinct, which concurs with attributed functions of the dHP and RSP in spatial memory, as well as of the vHP and LS in emotional responses.

Suggested Grid Code Modifications to Ensure Wide-Scale Adoption of Photovoltaic Energy in Distributed Power Generation Systems

DEFF Research Database (Denmark)

Yang, Yongheng; Enjeti, Prasad; Blaabjerg, Frede

2013-01-01

Current grid standards seem to largely require low power (e.g. several kilowatts) single-phase photovoltaic (PV) systems to operate at unity power factor with maximum power point tracking, and disconnect from the grid under grid faults. However, in case of a wide-scale penetration of single......-phase PV systems in the distributed grid, the disconnection under grid faults can contribute to: a) voltage flickers, b) power outages, and c) system instability. In this paper, grid code modifications are explored for wide-scale adoption of PV systems in the distribution grid. More recently, Italy...... and Japan, have undertaken a major review of standards for PV power conversion systems connected to low voltage networks. In view of this, the importance of low voltage ride-through for single-phase PV power systems under grid faults along with reactive power injection is studied in this paper. Three...

Radiation distribution measurement using plastic scintillating optical fibers for survey of radioactive contamination in wide area

International Nuclear Information System (INIS)

Ito, Chikara; Ito, Keisuke; Ishikawa, Takashi; Yoshida, Akihiro; Sanada, Yukihisa; Torii, Tatsuo; Nohtomi, Akihiro; Wakabayashi, Genichiro; Miyazaki, Nobuyuki

2013-01-01

It is important to examine distribution of environmental contamination due to the accident of Fukushima Daiichi Nuclear Power Station and to confirm the effect of decontamination works. We have applied radiation distribution measurement using plastic scintillating optical fibers (PSFs) in the survey of contamination in wide area including residential, farmland, forests, etc. In the measurements system, two scintillation lights that emitted at an incidence of a radiation transmit to photomultiplier tubes at the both end of PSFs. The position where scintillation light emitted is obtained from the detection time difference of each photomultiplier tube. The distribution of light emission quantity indicates the distribution of radiation incident in a PSF which is corresponds to the distribution of dose-rate. The radiation detection system using the PSFs has been applied to the radiation distribution measurement on grounds, trees, etc. The results show a good agreement with point data measured by survey meters using sodium iodide scintillators. As the PSFs which have water resistance, they have been successfully applied to the radiation distribution measurement in the river. We have also succeeded in measuring two-dimensional distribution of radiation by measuring the count rate while moving to the fiber at a constant speed. (author)

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).

Science.gov (United States)

Opik, M; Vanatoa, A; Vanatoa, E; Moora, M; Davison, J; Kalwij, J M; Reier, U; Zobel, M

2010-10-01

• Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.

Self-similar drop-size distributions produced by breakup in chaotic flows

International Nuclear Information System (INIS)

Muzzio, F.J.; Tjahjadi, M.; Ottino, J.M.; Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003; Department of Chemical Engineering, Northwestern University, Evanston, Illinois 60208)

1991-01-01

Deformation and breakup of immiscible fluids in deterministic chaotic flows is governed by self-similar distributions of stretching histories and stretching rates and produces populations of droplets of widely distributed sizes. Scaling reveals that distributions of drop sizes collapse into two self-similar families; each family exhibits a different shape, presumably due to changes in the breakup mechanism

An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies

DEFF Research Database (Denmark)

Thompson, Wesley K.; Wang, Yunpeng; Schork, Andrew J.

2015-01-01

-wide association study (GWAS) test statistics. Test statistics corresponding to null associations are modeled as random draws from a normal distribution with zero mean; test statistics corresponding to non-null associations are also modeled as normal with zero mean, but with larger variance. The model is fit via...... analytically and in simulations. We apply this approach to meta-analysis test statistics from two large GWAS, one for Crohn’s disease (CD) and the other for schizophrenia (SZ). A scale mixture of two normals distribution provides an excellent fit to the SZ nonparametric replication effect size estimates. While...... minimizing discrepancies between the parametric mixture model and resampling-based nonparametric estimates of replication effect sizes and variances. We describe in detail the implications of this model for estimation of the non-null proportion, the probability of replication in de novo samples, the local...

Genome-wide characterization of the WRKY gene family in radish (Raphanus sativus L.) reveals its critical functions under different abiotic stresses.

Science.gov (United States)

Karanja, Bernard Kinuthia; Fan, Lianxue; Xu, Liang; Wang, Yan; Zhu, Xianwen; Tang, Mingjia; Wang, Ronghua; Zhang, Fei; Muleke, Everlyne M'mbone; Liu, Liwang

2017-11-01

The radish WRKY gene family was genome-widely identified and played critical roles in response to multiple abiotic stresses. The WRKY is among the largest transcription factors (TFs) associated with multiple biological activities for plant survival, including control response mechanisms against abiotic stresses such as heat, salinity, and heavy metals. Radish is an important root vegetable crop and therefore characterization and expression pattern investigation of WRKY transcription factors in radish is imperative. In the present study, 126 putative WRKY genes were retrieved from radish genome database. Protein sequence and annotation scrutiny confirmed that RsWRKY proteins possessed highly conserved domains and zinc finger motif. Based on phylogenetic analysis results, RsWRKYs candidate genes were divided into three groups (Group I, II and III) with the number 31, 74, and 20, respectively. Additionally, gene structure analysis revealed that intron-exon patterns of the WRKY genes are highly conserved in radish. Linkage map analysis indicated that RsWRKY genes were distributed with varying densities over nine linkage groups. Further, RT-qPCR analysis illustrated the significant variation of 36 RsWRKY genes under one or more abiotic stress treatments, implicating that they might be stress-responsive genes. In total, 126 WRKY TFs were identified from the R. sativus genome wherein, 35 of them showed abiotic stress-induced expression patterns. These results provide a genome-wide characterization of RsWRKY TFs and baseline for further functional dissection and molecular evolution investigation, specifically for improving abiotic stress resistances with an ultimate goal of increasing yield and quality of radish.

Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids

Directory of Open Access Journals (Sweden)

Ogata Hiroyuki

2011-09-01

Full Text Available Abstract Background The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes. Results Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (Deferribacter desulfuricans and the plasmid of Clostridium kluyveri. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms. Conclusions The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.

Waiting time distribution revealing the internal spin dynamics in a double quantum dot

Science.gov (United States)

Ptaszyński, Krzysztof

2017-07-01

Waiting time distribution and the zero-frequency full counting statistics of unidirectional electron transport through a double quantum dot molecule attached to spin-polarized leads are analyzed using the quantum master equation. The waiting time distribution exhibits a nontrivial dependence on the value of the exchange coupling between the dots and the gradient of the applied magnetic field, which reveals the oscillations between the spin states of the molecule. The zero-frequency full counting statistics, on the other hand, is independent of the aforementioned quantities, thus giving no insight into the internal dynamics. The fact that the waiting time distribution and the zero-frequency full counting statistics give a nonequivalent information is associated with two factors. Firstly, it can be explained by the sensitivity to different timescales of the dynamics of the system. Secondly, it is associated with the presence of the correlation between subsequent waiting times, which makes the renewal theory, relating the full counting statistics and the waiting time distribution, no longer applicable. The study highlights the particular usefulness of the waiting time distribution for the analysis of the internal dynamics of mesoscopic systems.

Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior.

Science.gov (United States)

Portugues, Ruben; Feierstein, Claudia E; Engert, Florian; Orger, Michael B

2014-03-19

Most behaviors, even simple innate reflexes, are mediated by circuits of neurons spanning areas throughout the brain. However, in most cases, the distribution and dynamics of firing patterns of these neurons during behavior are not known. We imaged activity, with cellular resolution, throughout the whole brains of zebrafish performing the optokinetic response. We found a sparse, broadly distributed network that has an elaborate but ordered pattern, with a bilaterally symmetrical organization. Activity patterns fell into distinct clusters reflecting sensory and motor processing. By correlating neuronal responses with an array of sensory and motor variables, we find that the network can be clearly divided into distinct functional modules. Comparing aligned data from multiple fish, we find that the spatiotemporal activity dynamics and functional organization are highly stereotyped across individuals. These experiments systematically reveal the functional architecture of neural circuits underlying a sensorimotor behavior in a vertebrate brain. Copyright © 2014 Elsevier Inc. All rights reserved.

Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

Directory of Open Access Journals (Sweden)

Cecilia M Lindgren

2009-06-01

Full Text Available To identify genetic loci influencing central obesity and fat distribution, we performed a meta-analysis of 16 genome-wide association studies (GWAS, N = 38,580 informative for adult waist circumference (WC and waist-hip ratio (WHR. We selected 26 SNPs for follow-up, for which the evidence of association with measures of central adiposity (WC and/or WHR was strong and disproportionate to that for overall adiposity or height. Follow-up studies in a maximum of 70,689 individuals identified two loci strongly associated with measures of central adiposity; these map near TFAP2B (WC, P = 1.9x10(-11 and MSRA (WC, P = 8.9x10(-9. A third locus, near LYPLAL1, was associated with WHR in women only (P = 2.6x10(-8. The variants near TFAP2B appear to influence central adiposity through an effect on overall obesity/fat-mass, whereas LYPLAL1 displays a strong female-only association with fat distribution. By focusing on anthropometric measures of central obesity and fat distribution, we have identified three loci implicated in the regulation of human adiposity.

Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling

DEFF Research Database (Denmark)

Almstrup, Kristian; Hoei-Hansen, Christina E; Wirkner, Ute

2004-01-01

in their stoichiometry on progression into embryonic carcinoma. We compared the CIS expression profile with patterns reported in embryonic stem cells (ESCs), which revealed a substantial overlap that may be as high as 50%. We also demonstrated an over-representation of expressed genes in regions of 17q and 12, reported......Carcinoma in situ (CIS) is the common precursor of histologically heterogeneous testicular germ cell tumors (TGCTs), which in recent decades have markedly increased and now are the most common malignancy of young men. Using genome-wide gene expression profiling, we identified >200 genes highly...

Distributed Large Data-Object Environments: End-to-End Performance Analysis of High Speed Distributed Storage Systems in Wide Area ATM Networks

Science.gov (United States)

Johnston, William; Tierney, Brian; Lee, Jason; Hoo, Gary; Thompson, Mary

1996-01-01

We have developed and deployed a distributed-parallel storage system (DPSS) in several high speed asynchronous transfer mode (ATM) wide area networks (WAN) testbeds to support several different types of data-intensive applications. Architecturally, the DPSS is a network striped disk array, but is fairly unique in that its implementation allows applications complete freedom to determine optimal data layout, replication and/or coding redundancy strategy, security policy, and dynamic reconfiguration. In conjunction with the DPSS, we have developed a 'top-to-bottom, end-to-end' performance monitoring and analysis methodology that has allowed us to characterize all aspects of the DPSS operating in high speed ATM networks. In particular, we have run a variety of performance monitoring experiments involving the DPSS in the MAGIC testbed, which is a large scale, high speed, ATM network and we describe our experience using the monitoring methodology to identify and correct problems that limit the performance of high speed distributed applications. Finally, the DPSS is part of an overall architecture for using high speed, WAN's for enabling the routine, location independent use of large data-objects. Since this is part of the motivation for a distributed storage system, we describe this architecture.

Genome-Wide Association Study Reveals Natural Variations Contributing to Drought Resistance in Crops

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Hongwei Wang

2017-06-01

Full Text Available Crops are often cultivated in regions where they will face environmental adversities; resulting in substantial yield loss which can ultimately lead to food and societal problems. Thus, significant efforts have been made to breed stress tolerant cultivars in an attempt to minimize these problems and to produce more stability with respect to crop yields across broad geographies. Since stress tolerance is a complex and multi-genic trait, advancements with classical breeding approaches have been challenging. On the other hand, molecular breeding, which is based on transgenics, marker-assisted selection and genome editing technologies; holds great promise to enable farmers to better cope with these challenges. However, identification of the key genetic components underlying the trait is critical and will serve as the foundation for future crop genetic improvement. Recently, genome-wide association studies have made significant contributions to facilitate the discovery of natural variation contributing to stress tolerance in crops. From these studies, the identified loci can serve as targets for genomic selection or editing to enable the molecular design of new cultivars. Here, we summarize research progress on this issue and focus on the genetic basis of drought tolerance as revealed by genome-wide association studies and quantitative trait loci mapping. Although many favorable loci have been identified, elucidation of their molecular mechanisms contributing to increased stress tolerance still remains a challenge. Thus, continuous efforts are still required to functionally dissect this complex trait through comprehensive approaches, such as system biological studies. It is expected that proper application of the acquired knowledge will enable the development of stress tolerant cultivars; allowing agricultural production to become more sustainable under dynamic environmental conditions.

Seismic Evidence of A Widely Distributed West Napa Fault Zone, Hendry Winery, Napa, California

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Goldman, M.; Catchings, R.; Chan, J. H.; Criley, C.

2015-12-01

Following the 24 August 2014 Mw 6.0 South Napa earthquake, surface rupture was mapped along the West Napa Fault Zone (WNFZ) for a distance of ~ 14 km and locally within zones up to ~ 2 km wide. Near the northern end of the surface rupture, however, several strands coalesced to form a narrow, ~100-m-wide zone of surface rupture. To determine the location, width, and shallow (upper few hundred meters) geometry of the fault zone, we acquired an active-source seismic survey across the northern surface rupture in February 2015. We acquired both P- and S-wave data, from which we developed reflection images and tomographic images of Vp, Vs, Vp/Vs, and Poisson's ratio of the upper 100 m. We also used small explosive charges within surface ruptures located ~600 m north of our seismic array to record fault-zone guided waves. Our data indicate that at the latitude of the Hendry Winery, the WNFZ is characterized by at least five fault traces that are spaced 60 to 200 m apart. Zones of low-Vs, low-Vp/Vs, and disrupted reflectors highlight the fault traces on the tomography and reflection images. On peak-ground-velocity (PGV) plots, the most pronounced high-amplitude guided-wave seismic energy coincides precisely with the mapped surface ruptures, and the guided waves also show discrete high PGV zones associated with unmapped fault traces east of the surface ruptures. Although the surface ruptures of the WNFZ were observed only over a 100-m-wide zone at the Hendry Winery, our data indicate that the fault zone is at least 400 m wide, which is probably a minimum width given the 400-m length of our seismic profile. Slip on the WNFZ is generally considered to be low relative to most other Bay Area faults, but we suggest that the West Napa Fault is a zone of widely distributed shear, and to fully account for the total slip on the WNFZ, slip on all traces of this wide fault zone must be considered.

Diversity of sharp-wave–ripple LFP signatures reveals differentiated brain-wide dynamical events

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Ramirez-Villegas, Juan F.; Logothetis, Nikos K.; Besserve, Michel

2015-01-01

Sharp-wave–ripple (SPW-R) complexes are believed to mediate memory reactivation, transfer, and consolidation. However, their underlying neuronal dynamics at multiple scales remains poorly understood. Using concurrent hippocampal local field potential (LFP) recordings and functional MRI (fMRI), we study local changes in neuronal activity during SPW-R episodes and their brain-wide correlates. Analysis of the temporal alignment between SPW and ripple components reveals well-differentiated SPW-R subtypes in the CA1 LFP. SPW-R–triggered fMRI maps show that ripples aligned to the positive peak of their SPWs have enhanced neocortical metabolic up-regulation. In contrast, ripples occurring at the trough of their SPWs relate to weaker neocortical up-regulation and absent subcortical down-regulation, indicating differentiated involvement of neuromodulatory pathways in the ripple phenomenon mediated by long-range interactions. To our knowledge, this study provides the first evidence for the existence of SPW-R subtypes with differentiated CA1 activity and metabolic correlates in related brain areas, possibly serving different memory functions. PMID:26540729

Diversity of sharp-wave-ripple LFP signatures reveals differentiated brain-wide dynamical events.

Science.gov (United States)

Ramirez-Villegas, Juan F; Logothetis, Nikos K; Besserve, Michel

2015-11-17

Sharp-wave-ripple (SPW-R) complexes are believed to mediate memory reactivation, transfer, and consolidation. However, their underlying neuronal dynamics at multiple scales remains poorly understood. Using concurrent hippocampal local field potential (LFP) recordings and functional MRI (fMRI), we study local changes in neuronal activity during SPW-R episodes and their brain-wide correlates. Analysis of the temporal alignment between SPW and ripple components reveals well-differentiated SPW-R subtypes in the CA1 LFP. SPW-R-triggered fMRI maps show that ripples aligned to the positive peak of their SPWs have enhanced neocortical metabolic up-regulation. In contrast, ripples occurring at the trough of their SPWs relate to weaker neocortical up-regulation and absent subcortical down-regulation, indicating differentiated involvement of neuromodulatory pathways in the ripple phenomenon mediated by long-range interactions. To our knowledge, this study provides the first evidence for the existence of SPW-R subtypes with differentiated CA1 activity and metabolic correlates in related brain areas, possibly serving different memory functions.

Wide-range high-resolution transmission electron microscopy reveals morphological and distributional changes of endomembrane compartments during log to stationary transition of growth phase in tobacco BY-2 cells.

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Toyooka, Kiminori; Sato, Mayuko; Kutsuna, Natsumaro; Higaki, Takumi; Sawaki, Fumie; Wakazaki, Mayumi; Goto, Yumi; Hasezawa, Seiichiro; Nagata, Noriko; Matsuoka, Ken

2014-09-01

Rapid growth of plant cells by cell division and expansion requires an endomembrane trafficking system. The endomembrane compartments, such as the Golgi stacks, endosome and vesicles, are important in the synthesis and trafficking of cell wall materials during cell elongation. However, changes in the morphology, distribution and number of these compartments during the different stages of cell proliferation and differentiation have not yet been clarified. In this study, we examined these changes at the ultrastructural level in tobacco Bright yellow 2 (BY-2) cells during the log and stationary phases of growth. We analyzed images of the BY-2 cells prepared by the high-pressure freezing/freeze substitution technique with the aid of an auto-acquisition transmission electron microscope system. We quantified the distribution of secretory and endosomal compartments in longitudinal sections of whole cells by using wide-range gigapixel-class images obtained by merging thousands of transmission electron micrographs. During the log phase, all Golgi stacks were composed of several thick cisternae. Approximately 20 vesicle clusters (VCs), including the trans-Golgi network and secretory vesicle cluster, were observed throughout the cell. In the stationary-phase cells, Golgi stacks were thin with small cisternae, and only a few VCs were observed. Nearly the same number of multivesicular body and small high-density vesicles were observed in both the stationary and log phases. Results from electron microscopy and live fluorescence imaging indicate that the morphology and distribution of secretory-related compartments dramatically change when cells transition from log to stationary phases of growth. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Genome-wide analyses reveal a role for peptide hormones in planarian germline development.

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James J Collins

Full Text Available Bioactive peptides (i.e., neuropeptides or peptide hormones represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation

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Shiraiwa, Manabu; Yee, Lindsay D.; Schilling, Katherine A.; Loza, Christine L.; Craven, Jill S.; Zuend, Andreas; Ziemann, Paul J.; Seinfeld, John H.

2013-01-01

Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process. PMID:23818634

Size distribution dynamics reveal particle-phase chemistry in organic aerosol formation.

Science.gov (United States)

Shiraiwa, Manabu; Yee, Lindsay D; Schilling, Katherine A; Loza, Christine L; Craven, Jill S; Zuend, Andreas; Ziemann, Paul J; Seinfeld, John H

2013-07-16

Organic aerosols are ubiquitous in the atmosphere and play a central role in climate, air quality, and public health. The aerosol size distribution is key in determining its optical properties and cloud condensation nucleus activity. The dominant portion of organic aerosol is formed through gas-phase oxidation of volatile organic compounds, so-called secondary organic aerosols (SOAs). Typical experimental measurements of SOA formation include total SOA mass and atomic oxygen-to-carbon ratio. These measurements, alone, are generally insufficient to reveal the extent to which condensed-phase reactions occur in conjunction with the multigeneration gas-phase photooxidation. Combining laboratory chamber experiments and kinetic gas-particle modeling for the dodecane SOA system, here we show that the presence of particle-phase chemistry is reflected in the evolution of the SOA size distribution as well as its mass concentration. Particle-phase reactions are predicted to occur mainly at the particle surface, and the reaction products contribute more than half of the SOA mass. Chamber photooxidation with a midexperiment aldehyde injection confirms that heterogeneous reaction of aldehydes with organic hydroperoxides forming peroxyhemiacetals can lead to a large increase in SOA mass. Although experiments need to be conducted with other SOA precursor hydrocarbons, current results demonstrate coupling between particle-phase chemistry and size distribution dynamics in the formation of SOAs, thereby opening up an avenue for analysis of the SOA formation process.

Glycogen distribution in the microwave-fixed mouse brain reveals heterogeneous astrocytic patterns.

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Oe, Yuki; Baba, Otto; Ashida, Hitoshi; Nakamura, Kouichi C; Hirase, Hajime

2016-09-01

In the brain, glycogen metabolism has been implied in synaptic plasticity and learning, yet the distribution of this molecule has not been fully described. We investigated cerebral glycogen of the mouse by immunohistochemistry (IHC) using two monoclonal antibodies that have different affinities depending on the glycogen size. The use of focused microwave irradiation yielded well-defined glycogen immunoreactive signals compared with the conventional periodic acid-Schiff method. The IHC signals displayed a punctate distribution localized predominantly in astrocytic processes. Glycogen immunoreactivity (IR) was high in the hippocampus, striatum, cortex, and cerebellar molecular layer, whereas it was low in the white matter and most of the subcortical structures. Additionally, glycogen distribution in the hippocampal CA3-CA1 and striatum had a 'patchy' appearance with glycogen-rich and glycogen-poor astrocytes appearing in alternation. The glycogen patches were more evident with large-molecule glycogen in young adult mice but they were hardly observable in aged mice (1-2 years old). Our results reveal brain region-dependent glycogen accumulation and possibly metabolic heterogeneity of astrocytes. GLIA 2016;64:1532-1545. © 2016 The Authors. Glia Published by Wiley Periodicals, Inc.

Glycogen distribution in the microwave‐fixed mouse brain reveals heterogeneous astrocytic patterns

Science.gov (United States)

Baba, Otto; Ashida, Hitoshi; Nakamura, Kouichi C.

2016-01-01

In the brain, glycogen metabolism has been implied in synaptic plasticity and learning, yet the distribution of this molecule has not been fully described. We investigated cerebral glycogen of the mouse by immunohistochemistry (IHC) using two monoclonal antibodies that have different affinities depending on the glycogen size. The use of focused microwave irradiation yielded well‐defined glycogen immunoreactive signals compared with the conventional periodic acid‐Schiff method. The IHC signals displayed a punctate distribution localized predominantly in astrocytic processes. Glycogen immunoreactivity (IR) was high in the hippocampus, striatum, cortex, and cerebellar molecular layer, whereas it was low in the white matter and most of the subcortical structures. Additionally, glycogen distribution in the hippocampal CA3‐CA1 and striatum had a ‘patchy’ appearance with glycogen‐rich and glycogen‐poor astrocytes appearing in alternation. The glycogen patches were more evident with large‐molecule glycogen in young adult mice but they were hardly observable in aged mice (1–2 years old). Our results reveal brain region‐dependent glycogen accumulation and possibly metabolic heterogeneity of astrocytes. GLIA 2016;64:1532–1545 PMID:27353480

Sea surface temperature data from a world wide distribution from 01 January 1971 to 31 December 2000 (NODC Accession 0000712)

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National Oceanic and Atmospheric Administration, Department of Commerce — Sea surface temperature data were collected in a world wide distribution from January 1, 1971 to December 31, 2000. Data were submitted by Japan Meteorological...

Genus-wide comparison of Pseudovibrio bacterial genomes reveal diverse adaptations to different marine invertebrate hosts.

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Alex, Anoop; Antunes, Agostinho

2018-01-01

Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater. The analyses revealed a certain degree of commonality among the majority of sponge- and coral-associated bacteria. Isolates from other marine invertebrate host, tunicates, exhibited a genetic repertoire for cold adaptation and specific metabolic abilities including mucin degradation in the Antarctic tunicate-associated bacterium Pseudovibrio sp. Tun.PHSC04_5.I4. Reductive genome evolution was simultaneously detected in the flatworm-associated bacteria and the sponge-associated bacterium P. axinellae AD2, through the loss of major secretion systems (type III/VI) and virulence/symbioses factors such as proteins involved in adhesion and attachment to the host. Our study also unraveled the presence of a CRISPR-Cas system in P. stylochi UST20140214-052 a flatworm-associated bacterium possibly suggesting the role of CRISPR-based adaptive immune system against the invading virus particles. Detection of mobile elements and genomic islands (GIs) in all bacterial members highlighted the role of horizontal gene transfer for the acquisition of novel genetic features, likely enhancing the bacterial ecological fitness. These findings are insightful to understand the role of genome diversity in Pseudovibrio as an evolutionary strategy to increase their colonizing success across a wide range of marine eukaryotic hosts.

Mammalian RNA polymerase II core promoters: insights from genome-wide studies

DEFF Research Database (Denmark)

Sandelin, Albin; Carninci, Piero; Lenhard, Boris

2007-01-01

The identification and characterization of mammalian core promoters and transcription start sites is a prerequisite to understanding how RNA polymerase II transcription is controlled. New experimental technologies have enabled genome-wide discovery and characterization of core promoters, revealing...... in the mammalian transcriptome and proteome. Promoters can be described by their start site usage distribution, which is coupled to the occurrence of cis-regulatory elements, gene function and evolutionary constraints. A comprehensive survey of mammalian promoters is a major step towards describing...

Revealing the influence of water-cement ratio on the pore size distribution in hydrated cement paste by using cyclohexane

Science.gov (United States)

Bede, Andrea; Ardelean, Ioan

2017-12-01

Varying the amount of water in a concrete mix will influence its final properties considerably due to the changes in the capillary porosity. That is why a non-destructive technique is necessary for revealing the capillary pore distribution inside hydrated cement based materials and linking the capillary porosity with the macroscopic properties of these materials. In the present work, we demonstrate a simple approach for revealing the differences in capillary pore size distributions introduced by the preparation of cement paste with different water-to-cement ratios. The approach relies on monitoring the nuclear magnetic resonance transverse relaxation distribution of cyclohexane molecules confined inside the cement paste pores. The technique reveals the whole spectrum of pores inside the hydrated cement pastes, allowing a qualitative and quantitative analysis of different pore sizes. The cement pastes with higher water-to-cement ratios show an increase in capillary porosity, while for all the samples the intra-C-S-H and inter-C-S-H pores (also known as gel pores) remain unchanged. The technique can be applied to various porous materials with internal mineral surfaces.

Biogeography and ecology of Cetraria aculeata, a widely distributed lichen with a bipolar distribution

Directory of Open Access Journals (Sweden)

Christian Printzen

2013-04-01

Full Text Available Ecological and historical biogeography of lichens have rarely been studied in a concerted effort, but both aspects have to be taken into consideration when explaining the distributional patterns of species. This review summarizes, partly preliminary, results from a series of studies on phylogeography, ecophysiology and symbiotic interactions of the lichen Cetraria aculeata. This species is not only widespread but also occupies a very wide ecological niche. Evidence suggests that Cetraria aculeata has evolved and diversified in the Northern Hemisphere and colonised the Southern Hemisphere from there. Genetic isolation of populations indicates the absence of ongoing long range dispersal and genetic exchange between geographically isolated populations. We observe a hitherto unrecognized genetic diversity that may indicate ecotypic differentiation and speciation processes. Mediterranean and Polar populations differ not only genetically, but also in ecophysiological properties. Ongoing common garden experiments will have to show whether genetically fixed adaptation or acclimation is responsible for these differences. The genetic structure of the photobiont is best explained by climatic differences between localities, but co-dispersal with the mycobiont plays an important role as well. Taken together, these results indicate that a photobiont switch in the past enabled C. aculeata to widen its ecological niche, with subsequent genetic isolation of populations. Photobiont switches may play a crucial role in speciation processes of lichens. A combination of ecophysiological and phylogeographic studies with experimental approaches is necessary to better understand the reaction of lichens to changing environmental conditions.

Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

OpenAIRE

Zheng, Xiaoying; Hoffmann, Ary; Xi, Zhiyong; Zhang, Dongjing; Rasic, Gordana; Schmidt, Thomas

2017-01-01

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found ...

Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

Directory of Open Access Journals (Sweden)

Pierre Lefeuvre

Full Text Available Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.

Temperature profile data from XBT casts from a World-Wide Distribution 31 March 1985 to 24 November 1990 (NODC Accession 9700191)

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National Oceanic and Atmospheric Administration, Department of Commerce — Physical data were collected from XBT casts from from a World-Wide Distribution from 31 March 1985 to 24 November 1990. Physical parameters include temperature...

Feature-Based Visual Short-Term Memory Is Widely Distributed and Hierarchically Organized.

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Dotson, Nicholas M; Hoffman, Steven J; Goodell, Baldwin; Gray, Charles M

2018-06-15

Feature-based visual short-term memory is known to engage both sensory and association cortices. However, the extent of the participating circuit and the neural mechanisms underlying memory maintenance is still a matter of vigorous debate. To address these questions, we recorded neuronal activity from 42 cortical areas in monkeys performing a feature-based visual short-term memory task and an interleaved fixation task. We find that task-dependent differences in firing rates are widely distributed throughout the cortex, while stimulus-specific changes in firing rates are more restricted and hierarchically organized. We also show that microsaccades during the memory delay encode the stimuli held in memory and that units modulated by microsaccades are more likely to exhibit stimulus specificity, suggesting that eye movements contribute to visual short-term memory processes. These results support a framework in which most cortical areas, within a modality, contribute to mnemonic representations at timescales that increase along the cortical hierarchy. Copyright © 2018 Elsevier Inc. All rights reserved.

Genome-Wide Association Analysis Reveals Genetic Heterogeneity of Sjögren's Syndrome According to Ancestry

DEFF Research Database (Denmark)

Taylor, Kimberly E; Wong, Quenna; Levine, David M

2017-01-01

common protocol-directed methods. The aim of this study was to examine the genetic etiology of Sjögren's syndrome (SS) across ancestry and disease subsets. METHODS: We performed genome-wide association study analyses using SICCA subjects and external controls obtained from dbGaP data sets, one using all......OBJECTIVE: The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study of participants in whom genotyping was performed on the Omni2.5M platform and who had undergone deep phenotyping using...... subphenotype distributions differ by ethnicity, and whether this contributes to the heterogeneity of genetic associations. RESULTS: We observed significant associations in established regions of the major histocompatibility complex (MHC), IRF5, and STAT4 (P = 3 × 10(-42) , P = 3 × 10(-14) , and P = 9 × 10...

Kinome-wide transcriptional profiling of uveal melanoma reveals new vulnerabilities to targeted therapeutics.

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Bailey, Fiona P; Clarke, Kim; Kalirai, Helen; Kenyani, Jenna; Shahidipour, Haleh; Falciani, Francesco; Coulson, Judy M; Sacco, Joseph J; Coupland, Sarah E; Eyers, Patrick A

2018-03-01

Metastatic uveal melanoma (UM) is invariably fatal, usually within a year of diagnosis. There are currently no effective therapies, and clinical studies employing kinase inhibitors have so far demonstrated limited success. This is despite common activating mutations in GNAQ/11 genes, which trigger signalling pathways that might predispose tumours to a variety of targeted drugs. In this study, we have profiled kinome expression network dynamics in various human ocular melanomas. We uncovered a shared transcriptional profile in human primary UM samples and across a variety of experimental cell-based models. The poor overall response of UM cells to FDA-approved kinase inhibitors contrasted with much higher sensitivity to the bromodomain inhibitor JQ1, a broad transcriptional repressor. Mechanistically, we identified a repressed FOXM1-dependent kinase subnetwork in JQ1-exposed cells that contained multiple cell cycle-regulated protein kinases. Consistently, we demonstrated vulnerability of UM cells to inhibitors of mitotic protein kinases within this network, including the investigational PLK1 inhibitor BI6727. We conclude that analysis of kinome-wide signalling network dynamics has the potential to reveal actionable drug targets and inhibitors of potential therapeutic benefit for UM patients. © 2017 The Authors. Pigment Cell & Melanoma Research Published by John Wiley & Sons.

Genome-Wide RNAi Ionomics Screen Reveals New Genes and Regulation of Human Trace Element Metabolism

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Malinouski, Mikalai; Hasan, Nesrin M.; Zhang, Yan; Seravalli, Javier; Lin, Jie; Avanesov, Andrei; Lutsenko, Svetlana; Gladyshev, Vadim N.

2017-01-01

Trace elements are essential for human metabolism and dysregulation of their homeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundamental differences in the regulation of different trace elements. Specifically, selenium levels are controlled through the selenocysteine machinery and expression of abundant selenoproteins; copper balance is affected by lipid metabolism and requires machinery involved in protein trafficking and posttranslational modifications; and the iron levels are influenced by iron import and expression of the iron/heme-containing enzymes. Our approach can be applied to a variety of disease models and/or nutritional conditions, and the generated dataset opens new directions for studies of human trace element metabolism. PMID:24522796

Foundations of data-intensive science: Technology and practice for high throughput, widely distributed, data management and analysis systems

Science.gov (United States)

Johnston, William; Ernst, M.; Dart, E.; Tierney, B.

2014-04-01

Today's large-scale science projects involve world-wide collaborations depend on moving massive amounts of data from an instrument to potentially thousands of computing and storage systems at hundreds of collaborating institutions to accomplish their science. This is true for ATLAS and CMS at the LHC, and it is true for the climate sciences, Belle-II at the KEK collider, genome sciences, the SKA radio telescope, and ITER, the international fusion energy experiment. DOE's Office of Science has been collecting science discipline and instrument requirements for network based data management and analysis for more than a decade. As a result of this certain key issues are seen across essentially all science disciplines that rely on the network for significant data transfer, even if the data quantities are modest compared to projects like the LHC experiments. These issues are what this talk will address; to wit: 1. Optical signal transport advances enabling 100 Gb/s circuits that span the globe on optical fiber with each carrying 100 such channels; 2. Network router and switch requirements to support high-speed international data transfer; 3. Data transport (TCP is still the norm) requirements to support high-speed international data transfer (e.g. error-free transmission); 4. Network monitoring and testing techniques and infrastructure to maintain the required error-free operation of the many R&E networks involved in international collaborations; 5. Operating system evolution to support very high-speed network I/O; 6. New network architectures and services in the LAN (campus) and WAN networks to support data-intensive science; 7. Data movement and management techniques and software that can maximize the throughput on the network connections between distributed data handling systems, and; 8. New approaches to widely distributed workflow systems that can support the data movement and analysis required by the science. All of these areas must be addressed to enable large

Continent-wide survey reveals massive decline in African savannah elephants.

Science.gov (United States)

Chase, Michael J; Schlossberg, Scott; Griffin, Curtice R; Bouché, Philippe J C; Djene, Sintayehu W; Elkan, Paul W; Ferreira, Sam; Grossman, Falk; Kohi, Edward Mtarima; Landen, Kelly; Omondi, Patrick; Peltier, Alexis; Selier, S A Jeanetta; Sutcliffe, Robert

2016-01-01

African elephants (Loxodonta africana) are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC), the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants' downward trajectory by preventing poaching and protecting habitat.

Continent-wide survey reveals massive decline in African savannah elephants

Directory of Open Access Journals (Sweden)

Michael J. Chase

2016-08-01

Full Text Available African elephants (Loxodonta africana are imperiled by poaching and habitat loss. Despite global attention to the plight of elephants, their population sizes and trends are uncertain or unknown over much of Africa. To conserve this iconic species, conservationists need timely, accurate data on elephant populations. Here, we report the results of the Great Elephant Census (GEC, the first continent-wide, standardized survey of African savannah elephants. We also provide the first quantitative model of elephant population trends across Africa. We estimated a population of 352,271 savannah elephants on study sites in 18 countries, representing approximately 93% of all savannah elephants in those countries. Elephant populations in survey areas with historical data decreased by an estimated 144,000 from 2007 to 2014, and populations are currently shrinking by 8% per year continent-wide, primarily due to poaching. Though 84% of elephants occurred in protected areas, many protected areas had carcass ratios that indicated high levels of elephant mortality. Results of the GEC show the necessity of action to end the African elephants’ downward trajectory by preventing poaching and protecting habitat.

Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant.

Science.gov (United States)

Rabeling, Christian; Gonzales, Omar; Schultz, Ted R; Bacci, Maurício; Garcia, Marcos V B; Verhaagh, Manfred; Ishak, Heather D; Mueller, Ulrich G

2011-07-26

Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species Mycocepurus smithii was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless, M. smithii is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that M. smithii actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in M. smithii. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that M. smithii is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that M. smithii evolved 0.5-1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.

Temperature profile data from MBT casts in a world-wide distribution from 23 December 1964 to 19 December 1991 (NODC Accession 0000216)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using MBT casts from multiple platforms in a world-wide distribution from December 23, 1964 to December 19, 1991. Additonal...

Temperature profile data from XBT casts in a world wide distribution from 1996-06-01 to 1997-08-10 (NODC Accession 9700224)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected from XBT casts from several research vessels in a world wide distribution. Data were collected from June 1, 1996 to August...

Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

Science.gov (United States)

Statham, Mark J; Murdoch, James; Janecka, Jan; Aubry, Keith B; Edwards, Ceiridwen J; Soulsbury, Carl D; Berry, Oliver; Wang, Zhenghuan; Harrison, David; Pearch, Malcolm; Tomsett, Louise; Chupasko, Judith; Sacks, Benjamin N

2014-10-01

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva. © 2014 John Wiley & Sons Ltd.

Wide-band operation of quasi-optical distributed superconductor/insulator/superconductor mixers with epitaxial NbN/AlN/NbN junctions

International Nuclear Information System (INIS)

Kohjiro, S; Shitov, S V; Wang, Z; Uzawa, Y; Miki, S; Kawakami, A; Shoji, A

2004-01-01

For the optimum design of integrated receivers operating above the gap frequency of Nb, we have designed, fabricated and tested NbN-based quasi-optical superconductor/insulator/superconductor (SIS) mixers. The mixer chip incorporates a resonant half-wavelength epitaxial NbN/AlN/NbN junction, a twin-slot antenna and their coupling circuits. We adopted two kinds of coupling circuit between the antenna and the SIS junction: one is an in-phase feed with a length of 95 μm and the other is an anti-phase feed of 30 μm length. It was found that the anti-phase mixer reveals a 3 dB bandwidth of 43% of the centre frequency; the uncorrected double-sideband receiver noise temperature T RX = 691 K at 0.91 THz and T RX = 844 K at 0.80 THz, while 17% and T RX = 1250 K at 0.79 THz for the in-phase version. Possible reasons for this difference are discussed, which could be transmission loss and its robustness with respect to the variation of junction parameters. These experimental results suggest the NbN-based distributed mixer with the anti-phase feed is a better candidate for wide-band integrated receivers operating above 0.7 THz

Beyond funding: What can acknowledgements reveal about credit distribution in science?

Energy Technology Data Exchange (ETDEWEB)

Paul-Hus, A.; DiazFaes, A.; Desrochers, N.; Costas, R.; Sainte-Marie, M.; Macaluso, B.; Lariviere, V.

2016-07-01

Funding acknowledgements found in scientific publications have been used for decades to study the role of funding in science production. However, beyond funding information, acknowledgements convey the indebtedness of authors to individuals, institutions and organizations that contributed, in some way, to the research that lead to publication. The objective of this paper is to explore the different types of contributions acknowledged in WoS funding acknowledgement (FA) texts. The Correspondence Analysis performed in this study reveals that FAs offer a unique window on research and collaborative practices, credit distribution, and how these vary across disciplines. FAs thus contribute to make the traditionally “invisible contributions” visible to the scientific community. Results presented in this study go further in demonstrating that acknowledgements are not confined to credit attribution, as they include disclosures of conflict of interest. (Author)

Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling.

Science.gov (United States)

Almstrup, Kristian; Hoei-Hansen, Christina E; Wirkner, Ute; Blake, Jonathon; Schwager, Christian; Ansorge, Wilhelm; Nielsen, John E; Skakkebaek, Niels E; Rajpert-De Meyts, Ewa; Leffers, Henrik

2004-07-15

Carcinoma in situ (CIS) is the common precursor of histologically heterogeneous testicular germ cell tumors (TGCTs), which in recent decades have markedly increased and now are the most common malignancy of young men. Using genome-wide gene expression profiling, we identified >200 genes highly expressed in testicular CIS, including many never reported in testicular neoplasms. Expression was further verified by semiquantitative reverse transcription-PCR and in situ hybridization. Among the highest expressed genes were NANOG and POU5F1, and reverse transcription-PCR revealed possible changes in their stoichiometry on progression into embryonic carcinoma. We compared the CIS expression profile with patterns reported in embryonic stem cells (ESCs), which revealed a substantial overlap that may be as high as 50%. We also demonstrated an over-representation of expressed genes in regions of 17q and 12, reported as unstable in cultured ESCs. The close similarity between CIS and ESCs explains the pluripotency of CIS. Moreover, the findings are consistent with an early prenatal origin of TGCTs and thus suggest that etiologic factors operating in utero are of primary importance for the incidence trends of TGCTs. Finally, some of the highly expressed genes identified in this study are promising candidates for new diagnostic markers for CIS and/or TGCTs.

HIGH-REDSHIFT DUST OBSCURED GALAXIES: A MORPHOLOGY-SPECTRAL ENERGY DISTRIBUTION CONNECTION REVEALED BY KECK ADAPTIVE OPTICS

International Nuclear Information System (INIS)

Melbourne, J.; Matthews, K.; Soifer, B. T.

2009-01-01

A simple optical to mid-IR color selection, R - [24]>14, i.e., f ν (24 μm)/f ν (R) ∼> 1000, identifies highly dust obscured galaxies (DOGs) with typical redshifts of z ∼ 2 ± 0.5. Extreme mid-IR luminosities (L IR > 10 12-14 ) suggest that DOGs are powered by a combination of active galactic nuclei (AGNs) and star formation, possibly driven by mergers. In an effort to compare their photometric properties with their rest-frame optical morphologies, we obtained high-spatial resolution (0.''05-0.''1) Keck Adaptive Optics K'-band images of 15 DOGs. The images reveal a wide range of morphologies, including small exponential disks (eight of 15), small ellipticals (four of 15), and unresolved sources (two of 15). One particularly diffuse source could not be classified because of low signal-to-noise ratio. We find a statistically significant correlation between galaxy concentration and mid-IR luminosity, with the most luminous DOGs exhibiting higher concentration and smaller physical size. DOGs with high concentration also tend to have spectral energy distributions (SEDs) suggestive of AGN activity. Thus, central AGN light may be biasing the morphologies of the more luminous DOGs to higher concentration. Conversely, more diffuse DOGs tend to show an SED shape suggestive of star formation. Two of 15 in the sample show multiple resolved components with separations of ∼1 kpc, circumstantial evidence for ongoing mergers.

A comparison of cancer burden and research spending reveals discrepancies in the distribution of research funding

Directory of Open Access Journals (Sweden)

Carter Ashley JR

2012-07-01

Full Text Available Abstract Background Ideally, the distribution of research funding for different types of cancer should be equitable with respect to the societal burden each type of cancer imposes. These burdens can be estimated in a variety of ways; “Years of Life Lost” (YLL measures the severity of death in regard to the age it occurs, "Disability-Adjusted Life-Years" (DALY estimates the effects of non-lethal disabilities incurred by disease and economic metrics focus on the losses to tax revenue, productivity or direct medical expenses. We compared research funding from the National Cancer Institute (NCI to a variety of burden metrics for the most common types of cancer to identify mismatches between spending and societal burden. Methods Research funding levels were obtained from the NCI website and information for societal health and economic burdens were collected from government databases and published reports. We calculated the funding levels per unit burden for a wide range of different cancers and burden metrics and compared these values to identify discrepancies. Results Our analysis reveals a considerable mismatch between funding levels and burden. Some cancers are funded at levels far higher than their relative burden suggests (breast cancer, prostate cancer, and leukemia while other cancers appear underfunded (bladder, esophageal, liver, oral, pancreatic, stomach, and uterine cancers. Conclusions These discrepancies indicate that an improved method of health care research funding allocation should be investigated to better match funding levels to societal burden.

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken.

Science.gov (United States)

Wragg, David; Mason, Andrew S; Yu, Le; Kuo, Richard; Lawal, Raman A; Desta, Takele Taye; Mwacharo, Joram M; Cho, Chang-Yeon; Kemp, Steve; Burt, David W; Hanotte, Olivier

2015-10-14

EAV-HP is an ancient retrovirus pre-dating Gallus speciation, which continues to circulate in modern chicken populations, and led to the emergence of avian leukosis virus subgroup J causing significant economic losses to the poultry industry. We mapped EAV-HP integration sites in Ethiopian village chickens, a Silkie, Taiwan Country chicken, red junglefowl Gallus gallus and several inbred experimental lines using whole-genome sequence data. An average of 75.22 ± 9.52 integration sites per bird were identified, which collectively group into 279 intervals of which 5 % are common to 90 % of the genomes analysed and are suggestive of pre-domestication integration events. More than a third of intervals are specific to individual genomes, supporting active circulation of EAV-HP in modern chickens. Interval density is correlated with chromosome length (P < 2.31(-6)), and 27 % of intervals are located within 5 kb of a transcript. Functional annotation clustering of genes reveals enrichment for immune-related functions (P < 0.05). Our results illustrate a non-random distribution of EAV-HP in the genome, emphasising the importance it may have played in the adaptation of the species, and provide a platform from which to extend investigations on the co-evolutionary significance of endogenous retroviral genera with their hosts.

AID/APOBEC cytosine deaminase induces genome-wide kataegis

Directory of Open Access Journals (Sweden)

Lada Artem G

2012-12-01

Full Text Available Abstract Clusters of localized hypermutation in human breast cancer genomes, named “kataegis” (from the Greek for thunderstorm, are hypothesized to result from multiple cytosine deaminations catalyzed by AID/APOBEC proteins. However, a direct link between APOBECs and kataegis is still lacking. We have sequenced the genomes of yeast mutants induced in diploids by expression of the gene for PmCDA1, a hypermutagenic deaminase from sea lamprey. Analysis of the distribution of 5,138 induced mutations revealed localized clusters very similar to those found in tumors. Our data provide evidence that unleashed cytosine deaminase activity is an evolutionary conserved, prominent source of genome-wide kataegis events. Reviewers This article was reviewed by: Professor Sandor Pongor, Professor Shamil R. Sunyaev, and Dr Vladimir Kuznetsov.

Multiple surveys employing a new sample-processing protocol reveal the genetic diversity of placozoans in Japan.

Science.gov (United States)

Miyazawa, Hideyuki; Nakano, Hiroaki

2018-03-01

Placozoans, flat free-living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest-branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S rRNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, "ethanol-treated substrate sampling," for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine-jima, Chichi-jima, and Haha-jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine-jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina) as a Case Study.

Science.gov (United States)

Vergara, María; Basto, Mafalda P; Madeira, María José; Gómez-Moliner, Benjamín J; Santos-Reis, Margarida; Fernandes, Carlos; Ruiz-González, Aritz

2015-01-01

The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP). However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA) sequencing (621 bp) and microsatellite genotyping (23 polymorphic markers) to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a) spatial and non-spatial Bayesian individual-based clustering (IBC) approaches (STRUCTURE, TESS, BAPS and GENELAND), and b) multivariate methods [discriminant analysis of principal components (DAPC) and spatial principal component analysis (sPCA)]. Additionally, because isolation by distance (IBD) is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence of the

Inferring Population Genetic Structure in Widely and Continuously Distributed Carnivores: The Stone Marten (Martes foina as a Case Study.

Directory of Open Access Journals (Sweden)

María Vergara

Full Text Available The stone marten is a widely distributed mustelid in the Palaearctic region that exhibits variable habitat preferences in different parts of its range. The species is a Holocene immigrant from southwest Asia which, according to fossil remains, followed the expansion of the Neolithic farming cultures into Europe and possibly colonized the Iberian Peninsula during the Early Neolithic (ca. 7,000 years BP. However, the population genetic structure and historical biogeography of this generalist carnivore remains essentially unknown. In this study we have combined mitochondrial DNA (mtDNA sequencing (621 bp and microsatellite genotyping (23 polymorphic markers to infer the population genetic structure of the stone marten within the Iberian Peninsula. The mtDNA data revealed low haplotype and nucleotide diversities and a lack of phylogeographic structure, most likely due to a recent colonization of the Iberian Peninsula by a few mtDNA lineages during the Early Neolithic. The microsatellite data set was analysed with a spatial and non-spatial Bayesian individual-based clustering (IBC approaches (STRUCTURE, TESS, BAPS and GENELAND, and b multivariate methods [discriminant analysis of principal components (DAPC and spatial principal component analysis (sPCA]. Additionally, because isolation by distance (IBD is a common spatial genetic pattern in mobile and continuously distributed species and it may represent a challenge to the performance of the above methods, the microsatellite data set was tested for its presence. Overall, the genetic structure of the stone marten in the Iberian Peninsula was characterized by a NE-SW spatial pattern of IBD, and this may explain the observed disagreement between clustering solutions obtained by the different IBC methods. However, there was significant indication for contemporary genetic structuring, albeit weak, into at least three different subpopulations. The detected subdivision could be attributed to the influence

Family-based Association Analyses of Imputed Genotypes Reveal Genome-Wide Significant Association of Alzheimer’s disease with OSBPL6, PTPRG and PDCL3

Science.gov (United States)

Herold, Christine; Hooli, Basavaraj V.; Mullin, Kristina; Liu, Tian; Roehr, Johannes T; Mattheisen, Manuel; Parrado, Antonio R.; Bertram, Lars; Lange, Christoph; Tanzi, Rudolph E.

2015-01-01

The genetic basis of Alzheimer's disease (AD) is complex and heterogeneous. Over 200 highly penetrant pathogenic variants in the genes APP, PSEN1 and PSEN2 cause a subset of early-onset familial Alzheimer's disease (EOFAD). On the other hand, susceptibility to late-onset forms of AD (LOAD) is indisputably associated to the ε4 allele in the gene APOE, and more recently to variants in more than two-dozen additional genes identified in the large-scale genome-wide association studies (GWAS) and meta-analyses reports. Taken together however, although the heritability in AD is estimated to be as high as 80%, a large proportion of the underlying genetic factors still remain to be elucidated. In this study we performed a systematic family-based genome-wide association and meta-analysis on close to 15 million imputed variants from three large collections of AD families (~3,500 subjects from 1,070 families). Using a multivariate phenotype combining affection status and onset age, meta-analysis of the association results revealed three single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with AD risk: rs7609954 in the gene PTPRG (P-value = 3.98·10−08), rs1347297 in the gene OSBPL6 (P-value = 4.53·10−08), and rs1513625 near PDCL3 (P-value = 4.28·10−08). In addition, rs72953347 in OSBPL6 (P-value = 6.36·10−07) and two SNPs in the gene CDKAL1 showed marginally significant association with LOAD (rs10456232, P-value: 4.76·10−07; rs62400067, P-value: 3.54·10−07). In summary, family-based GWAS meta-analysis of imputed SNPs revealed novel genomic variants in (or near) PTPRG, OSBPL6, and PDCL3 that influence risk for AD with genome-wide significance. PMID:26830138

Genome-wide assessment in Escherichia coli reveals time-dependent nanotoxicity paradigms.

Science.gov (United States)

Reyes, Vincent C; Li, Minghua; Hoek, Eric M V; Mahendra, Shaily; Damoiseaux, Robert

2012-11-27

The use of engineered nanomaterials (eNM) in consumer and industrial products is increasing exponentially. Our ability to rapidly assess their potential effects on human and environmental health is limited by our understanding of nanomediated toxicity. High-throughput screening (HTS) enables the investigation of nanomediated toxicity on a genome-wide level, thus uncovering their novel mechanisms and paradigms. Herein, we investigate the toxicity of zinc-containing nanomaterials (Zn-eNMs) using a time-resolved HTS methodology in an arrayed Escherichia coli genome-wide knockout (KO) library. The library was screened against nanoscale zerovalent zinc (nZn), nanoscale zinc oxide (nZnO), and zinc chloride (ZnCl(2)) salt as reference. Through sequential screening over 24 h, our method identified 173 sensitive clones from diverse biological pathways, which fell into two general groups: early and late responders. The overlap between these groups was small. Our results suggest that bacterial toxicity mechanisms change from pathways related to general metabolic function, transport, signaling, and metal ion homeostasis to membrane synthesis pathways over time. While all zinc sources shared pathways relating to membrane damage and metal ion homeostasis, Zn-eNMs and ZnCl(2) displayed differences in their sensitivity profiles. For example, ZnCl(2) and nZnO elicited unique responses in pathways related to two-component signaling and monosaccharide biosynthesis, respectively. Single isolated measurements, such as MIC or IC(50), are inadequate, and time-resolved approaches utilizing genome-wide assays are therefore needed to capture this crucial dimension and illuminate the dynamic interplay at the nano-bio interface.

Time Distribution Capabilities of the Wide Area Augmentation System (WAAS)

National Research Council Canada - National Science Library

Klepczynski, William J; Fenton, Pat; Powers, Ed

2001-01-01

...), the FAA has been interested in developing the use of the WAAS for time distribution. An economical, evolutionary approach to the development of the WAAS for time distribution has been pursued...

Temperature profile data collected in a world wide distribution using XBT casts from 01 January 1994 to 25 May 1994 (NODC Accession 9600159)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT casts from the ANGO and other platforms in a world wide distribution. Data were collected from 01 January 1994 to...

State Electricity Regulatory Policy and Distributed Resources: Distributed Resource Distribution Credit Pilot Programs--Revealing the Value to Consumers and Vendors

Energy Technology Data Exchange (ETDEWEB)

Moskovitz, D.; Harrington, C.; Shirley, W.; Cowart, R.; Sedano, R.; Weston, F.

2002-10-01

Designing and implementing credit-based pilot programs for distributed resources distribution is a low-cost, low-risk opportunity to find out how these resources can help defer or avoid costly electric power system (utility grid) distribution upgrades. This report describes implementation options for deaveraged distribution credits and distributed resource development zones. Developing workable programs implementing these policies can dramatically increase the deployment of distributed resources in ways that benefit distributed resource vendors, users, and distribution utilities. This report is one in the State Electricity Regulatory Policy and Distributed Resources series developed under contract to NREL (see Annual Technical Status Report of the Regulatory Assistance Project: September 2000-September 2001, NREL/SR-560-32733). Other titles in this series are: (1) Accommodating Distributed Resources in Wholesale Markets, NREL/SR-560-32497; (2) Distributed Resources and Electric System Re liability, NREL/SR-560-32498; (3) Distribution System Cost Methodologies for Distributed Generation, NREL/SR-560-32500; (4) Distribution System Cost Methodologies for Distributed Generation Appendices, NREL/SR-560-32501.

Wireless sensor networks distributed consensus estimation

CERN Document Server

Chen, Cailian; Guan, Xinping

2014-01-01

This SpringerBrief evaluates the cooperative effort of sensor nodes to accomplish high-level tasks with sensing, data processing and communication. The metrics of network-wide convergence, unbiasedness, consistency and optimality are discussed through network topology, distributed estimation algorithms and consensus strategy. Systematic analysis reveals that proper deployment of sensor nodes and a small number of low-cost relays (without sensing function) can speed up the information fusion and thus improve the estimation capability of wireless sensor networks (WSNs). This brief also investiga

An RT distribution analysis of relatedness proportion effects in lexical decision and semantic categorization reveals different mechanisms.

Science.gov (United States)

de Wit, Bianca; Kinoshita, Sachiko

2015-01-01

The magnitude of the semantic priming effect is known to increase as the proportion of related prime-target pairs in an experiment increases. This relatedness proportion (RP) effect was studied in a lexical decision task at a short prime-target stimulus onset asynchrony (240 ms), which is widely assumed to preclude strategic prospective usage of the prime. The analysis of the reaction time (RT) distribution suggested that the observed RP effect reflected a modulation of a retrospective semantic matching process. The pattern of the RP effect on the RT distribution found here is contrasted to that reported in De Wit and Kinoshita's (2014) semantic categorization study, and it is concluded that the RP effect is driven by different underlying mechanisms in lexical decision and semantic categorization.

Genome-wide analysis of gene expression in primate taste buds reveals links to diverse processes.

Directory of Open Access Journals (Sweden)

Peter Hevezi

Full Text Available Efforts to unravel the mechanisms underlying taste sensation (gustation have largely focused on rodents. Here we present the first comprehensive characterization of gene expression in primate taste buds. Our findings reveal unique new insights into the biology of taste buds. We generated a taste bud gene expression database using laser capture microdissection (LCM procured fungiform (FG and circumvallate (CV taste buds from primates. We also used LCM to collect the top and bottom portions of CV taste buds. Affymetrix genome wide arrays were used to analyze gene expression in all samples. Known taste receptors are preferentially expressed in the top portion of taste buds. Genes associated with the cell cycle and stem cells are preferentially expressed in the bottom portion of taste buds, suggesting that precursor cells are located there. Several chemokines including CXCL14 and CXCL8 are among the highest expressed genes in taste buds, indicating that immune system related processes are active in taste buds. Several genes expressed specifically in endocrine glands including growth hormone releasing hormone and its receptor are also strongly expressed in taste buds, suggesting a link between metabolism and taste. Cell type-specific expression of transcription factors and signaling molecules involved in cell fate, including KIT, reveals the taste bud as an active site of cell regeneration, differentiation, and development. IKBKAP, a gene mutated in familial dysautonomia, a disease that results in loss of taste buds, is expressed in taste cells that communicate with afferent nerve fibers via synaptic transmission. This database highlights the power of LCM coupled with transcriptional profiling to dissect the molecular composition of normal tissues, represents the most comprehensive molecular analysis of primate taste buds to date, and provides a foundation for further studies in diverse aspects of taste biology.

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions

Science.gov (United States)

2014-01-01

Background The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Results Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT

Genome-wide transcriptome study in wheat identified candidate genes related to processing quality, majority of them showing interaction (quality x development) and having temporal and spatial distributions.

Science.gov (United States)

Singh, Anuradha; Mantri, Shrikant; Sharma, Monica; Chaudhury, Ashok; Tuli, Rakesh; Roy, Joy

2014-01-16

The cultivated bread wheat (Triticum aestivum L.) possesses unique flour quality, which can be processed into many end-use food products such as bread, pasta, chapatti (unleavened flat bread), biscuit, etc. The present wheat varieties require improvement in processing quality to meet the increasing demand of better quality food products. However, processing quality is very complex and controlled by many genes, which have not been completely explored. To identify the candidate genes whose expressions changed due to variation in processing quality and interaction (quality x development), genome-wide transcriptome studies were performed in two sets of diverse Indian wheat varieties differing for chapatti quality. It is also important to understand the temporal and spatial distributions of their expressions for designing tissue and growth specific functional genomics experiments. Gene-specific two-way ANOVA analysis of expression of about 55 K transcripts in two diverse sets of Indian wheat varieties for chapatti quality at three seed developmental stages identified 236 differentially expressed probe sets (10-fold). Out of 236, 110 probe sets were identified for chapatti quality. Many processing quality related key genes such as glutenin and gliadins, puroindolines, grain softness protein, alpha and beta amylases, proteases, were identified, and many other candidate genes related to cellular and molecular functions were also identified. The ANOVA analysis revealed that the expression of 56 of 110 probe sets was involved in interaction (quality x development). Majority of the probe sets showed differential expression at early stage of seed development i.e. temporal expression. Meta-analysis revealed that the majority of the genes expressed in one or a few growth stages indicating spatial distribution of their expressions. The differential expressions of a few candidate genes such as pre-alpha/beta-gliadin and gamma gliadin were validated by RT-PCR. Therefore, this study

Distributed neural system for emotional intelligence revealed by lesion mapping.

Science.gov (United States)

Barbey, Aron K; Colom, Roberto; Grafman, Jordan

2014-03-01

Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease.

Distributed neural system for emotional intelligence revealed by lesion mapping

Science.gov (United States)

Colom, Roberto; Grafman, Jordan

2014-01-01

Cognitive neuroscience has made considerable progress in understanding the neural architecture of human intelligence, identifying a broadly distributed network of frontal and parietal regions that support goal-directed, intelligent behavior. However, the contributions of this network to social and emotional aspects of intellectual function remain to be well characterized. Here we investigated the neural basis of emotional intelligence in 152 patients with focal brain injuries using voxel-based lesion-symptom mapping. Latent variable modeling was applied to obtain measures of emotional intelligence, general intelligence and personality from the Mayer, Salovey, Caruso Emotional Intelligence Test (MSCEIT), the Wechsler Adult Intelligence Scale and the Neuroticism-Extroversion-Openness Inventory, respectively. Regression analyses revealed that latent scores for measures of general intelligence and personality reliably predicted latent scores for emotional intelligence. Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal and parietal brain regions. The results support an integrative framework for understanding the architecture of executive, social and emotional processes and make specific recommendations for the interpretation and application of the MSCEIT to the study of emotional intelligence in health and disease. PMID:23171618

Distribution of suspended particulate matter in the waters of eastern continental margin of India

Digital Repository Service at National Institute of Oceanography (India)

Rao, Ch.M.

Distribution of total suspended matter (TSM) in surface and near bottom (approximately 5 m above sea bed) waters reveals a wide variation in concentration and composition. TSM varies from 0.05 to 122 mg.l/1 in surface waters, and from 0.25 top 231...

Chlorophyll, temperature, depth, and irradiance data from bottle in a world-wide distribution from 28 February 1964 to 02 April 1994 (NODC Accession 0000268)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Chlorophyll, temperature, depth, and irradiance data were collected using bottle from multiple vessels in a world-wide distribution from 28 February 1964 to 02 April...

Anomalously-dense firn in an ice-shelf channel revealed by wide-angle radar

Science.gov (United States)

Drews, R.; Brown, J.; Matsuoka, K.; Witrant, E.; Philippe, M.; Hubbard, B.; Pattyn, F.

2015-10-01

The thickness of ice shelves, a basic parameter for mass balance estimates, is typically inferred using hydrostatic equilibrium for which knowledge of the depth-averaged density is essential. The densification from snow to ice depends on a number of local factors (e.g. temperature and surface mass balance) causing spatial and temporal variations in density-depth profiles. However, direct measurements of firn density are sparse, requiring substantial logistical effort. Here, we infer density from radio-wave propagation speed using ground-based wide-angle radar datasets (10 MHz) collected at five sites on Roi Baudouin Ice Shelf (RBIS), Dronning Maud Land, Antarctica. Using a novel algorithm including traveltime inversion and raytracing with a prescribed shape of the depth-density relationship, we show that the depth to internal reflectors, the local ice thickness and depth-averaged densities can reliably be reconstructed. For the particular case of an ice-shelf channel, where ice thickness and surface slope change substantially over a few kilometers, the radar data suggests that firn inside the channel is about 5 % denser than outside the channel. Although this density difference is at the detection limit of the radar, it is consistent with a similar density anomaly reconstructed from optical televiewing, which reveals 10 % denser firn inside compared to outside the channel. The denser firn in the ice-shelf channel should be accounted for when using the hydrostatic ice thickness for determining basal melt rates. The radar method presented here is robust and can easily be adapted to different radar frequencies and data-acquisition geometries.

Phylogeographic analysis reveals significant spatial genetic structure of Incarvillea sinensis as a product of mountain building

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Chen Shaotian

2012-04-01

Full Text Available Abstract Background Incarvillea sinensis is widely distributed from Southwest China to Northeast China and in the Russian Far East. The distribution of this species was thought to be influenced by the uplift of the Qinghai-Tibet Plateau and Quaternary glaciation. To reveal the imprints of geological events on the spatial genetic structure of Incarvillea sinensis, we examined two cpDNA segments ( trnH- psbA and trnS- trnfM in 705 individuals from 47 localities. Results A total of 16 haplotypes was identified, and significant genetic differentiation was revealed (GST =0.843, NST = 0.975, P  Conclusions The results revealed that the uplift of the Qinghai-Tibet Plateau likely resulted in the significant divergence between the lineage in the eastern Qinghai-Tibet Plateau and the other one outside this area. The diverse niches in the eastern Qinghai-Tibet Plateau created a wide spectrum of habitats to accumulate and accommodate new mutations. The features of genetic diversity of populations outside the eastern Qinghai-Tibet Plateau seemed to reveal the imprints of extinction during the Glacial and the interglacial and postglacial recolonization. Our study is a typical case of the significance of the uplift of the Qinghai-Tibet Plateau and the Quaternary Glacial in spatial genetic structure of eastern Asian plants, and sheds new light on the evolution of biodiversity in the Qinghai-Tibet Plateau at the intraspecies level.

Temperature profiles from MBT casts from a World-Wide distribution from MULTIPLE PLATFORMS from 1948-04-08 to 1968-12-14 (NODC Accession 9300131)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected from MBT casts from a World-Wide distribution. Data were collected from MULTIPLE PLATFORMS from 08 April 1948 to 14 Decmeber...

Chemical, temperature, and other data from bottle casts in a world-wide distribution from 04 October 1961 to 24 August 1990 (NODC Accession 0000231)

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National Oceanic and Atmospheric Administration, Department of Commerce — Chemical, temperature, and other data were collected using bottle casts in a world-wide distribution from multiple ships from October 4, 1961 to August 24, 1990....

A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes.

Science.gov (United States)

Dimkpa, Stanley O N; Lahari, Zobaida; Shrestha, Roshi; Douglas, Alex; Gheysen, Godelieve; Price, Adam H

2016-02-01

The root-knot nematode Meloidogyne graminicola is one of the most serious nematode pests worldwide and represents a major constraint on rice production. While variation in the susceptibility of Asian rice (Oryza sativa) exists, so far no strong and reliable resistance has been reported. Quantitative trait loci for partial resistance have been reported but no underlying genes have been tagged or cloned. Here, 332 accessions of the Rice Diversity Panel 1 were assessed for gall formation, revealing large variation across all subpopulations of rice and higher susceptibility in temperate japonica accessions. Accessions Khao Pahk Maw and LD 24 appeared to be resistant, which was confirmed in large pot experiments where no galls were observed. Detailed observations on these two accessions revealed no nematodes inside the roots 2 days after inoculation and very few females after 17 days (5 in Khao Pahk Maw and 100 in the susceptible controls). These two cultivars appear ideal donors for breeding root-knot nematode resistance. A genome-wide association study revealed 11 quantitative trait loci, two of which are close to epistatic loci detected in the Bala x Azucena population. The discussion highlights a small number of candidate genes worth exploring further, in particular many genes with lectin domains and genes on chromosome 11 with homology to the Hordeum Mla locus. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Temperature profiles from XBT casts from a World-Wide distribution from MULTIPLE PLATFORMS from 1979-06-03 to 1988-05-27 (NODC Accession 8800182)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profiles were collected from XBT casts from a World-Wide distribution. Data were collected from MULTIPLE PLATFORMS from 03 June 1979 to 27 May 1988. Data...

Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility.

Science.gov (United States)

Vrljicak, Pavle; Tao, Shijie; Varshney, Gaurav K; Quach, Helen Ngoc Bao; Joshi, Adita; LaFave, Matthew C; Burgess, Shawn M; Sampath, Karuna

2016-04-07

DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germ-line transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence the integration of heterologous DNA in genomes, and have implications for targeted genome engineering. Copyright © 2016 Vrljicak et al.

Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivum, L.

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Simerjeet Kaur

2017-11-01

Full Text Available Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful. We present results on the analysis of the stem cellulose content of 288 diverse wheat accessions and its genome-wide association study (GWAS. Cellulose concentration ranged from 35 to 52% (w/w. Cellulose content was normally distributed in the accessions around a mean and median of 45% (w/w. Genome-wide marker-trait association study using 21,073 SNPs helped identify nine SNPs that were associated (p < 1E-05 with cellulose content. Four strongly associated (p < 8.17E-05 SNP markers were linked to wheat unigenes, which included β-tubulin, Auxin-induced protein 5NG4, and a putative transmembrane protein of unknown function. These genes may be directly or indirectly involved in the formation of cellulose in wheat culms. GWAS results from this study have the potential for genetic manipulation of cellulose content in bread wheat and other small grain cereals to enhance culm strength and improve biofuel production.

Melatonin Distribution Reveals Clues to Its Biological Significance in Basal Metazoans

Science.gov (United States)

Roopin, Modi; Levy, Oren

2012-01-01

Although nearly ubiquitous in nature, the precise biological significance of endogenous melatonin is poorly understood in phylogenetically basal taxa. In the present work, we describe insights into the functional role of melatonin at the most “basal” level of metazoan evolution. Hitherto unknown morphological determinants of melatonin distribution were evaluated in Nematostella vectensis by detecting melatonin immunoreactivity and examining the spatial gene expression patterns of putative melatonin biosynthetic and receptor elements that are located at opposing ends of the melatonin signaling pathway. Immuno-melatonin profiling indicated an elaborate interaction with reproductive tissues, reinforcing previous conjectures of a melatonin-responsive component in anthozoan reproduction. In situ hybridization (ISH) to putative melatonin receptor elements highlighted the possibility that the bioregulatory effects of melatonin in anthozoan reproduction may be mediated by interactions with membrane receptors, as in higher vertebrates. Another intriguing finding of the present study pertains to the prevalence of melatonin in centralized nervous structures. This pattern may be of great significance given that it 1) identifies an ancestral association between melatonin and key neuronal components and 2) potentially implies that certain effects of melatonin in basal species may be spread widely by regionalized nerve centers. PMID:23300630

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.

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Stephen R Doyle

2017-07-01

Full Text Available Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread.Pooled next generation sequencing (Pool-seq was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR and sub-optimal responder (SOR parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs, with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure had a significantly greater role in shaping genetic diversity than the evolution of SOR.This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different parasite populations. Furthermore, we propose that genetic

Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity

Science.gov (United States)

Nana-Djeunga, Hugues C.; Kengne-Ouafo, Jonas A.; Pion, Sébastien D. S.; Bopda, Jean; Kamgno, Joseph; Wanji, Samuel; Che, Hua; Kuesel, Annette C.; Walker, Martin; Basáñez, Maria-Gloria; Boakye, Daniel A.; Osei-Atweneboana, Mike Y.; Boussinesq, Michel; Prichard, Roger K.; Grant, Warwick N.

2017-01-01

Background Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana—exposed to more than a decade of regular ivermectin treatment—have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread. Methodology/Principal findings Pooled next generation sequencing (Pool-seq) was used to characterise genetic diversity within and between 108 adult female worms differing in ivermectin treatment history and response. Genome-wide analyses revealed genetic variation that significantly differentiated good responder (GR) and sub-optimal responder (SOR) parasites. These variants were not randomly distributed but clustered in ~31 quantitative trait loci (QTLs), with little overlap in putative QTL position and gene content between the two countries. Published candidate ivermectin SOR genes were largely absent in these regions; QTLs differentiating GR and SOR worms were enriched for genes in molecular pathways associated with neurotransmission, development, and stress responses. Finally, single worm genotyping demonstrated that geographic isolation and genetic change over time (in the presence of drug exposure) had a significantly greater role in shaping genetic diversity than the evolution of SOR. Conclusions/Significance This study is one of the first genome-wide association analyses in a parasitic nematode, and provides insight into the genomics of ivermectin response and population structure of O. volvulus. We argue that ivermectin response is a polygenically-determined quantitative trait (QT) whereby identical or related molecular pathways but not necessarily individual genes are likely to determine the extent of ivermectin response in different

Genome-wide SNPs reveal the drivers of gene flow in an urban population of the Asian Tiger Mosquito, Aedes albopictus.

Science.gov (United States)

Schmidt, Thomas L; Rašić, Gordana; Zhang, Dongjing; Zheng, Xiaoying; Xi, Zhiyong; Hoffmann, Ary A

2017-10-01

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Aedes albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.

Genome-wide Comparative Analyses Reveal the Dynamic Evolution of Nucleotide-Binding Leucine-Rich Repeat Gene Family among Solanaceae Plants

Directory of Open Access Journals (Sweden)

Eunyoung Seo

2016-08-01

Full Text Available Plants have evolved an elaborate innate immune system against invading pathogens. Within this system, intracellular nucleotide-binding leucine-rich repeat (NLR immune receptors are known play critical roles in effector-triggered immunity (ETI plant defense. We performed genome-wide identification and classification of NLR-coding sequences from the genomes of pepper, tomato, and potato using fixed criteria. We then compared genomic duplication and evolution features. We identified intact 267, 443, and 755 NLR-encoding genes in tomato, potato, and pepper genomes, respectively. Phylogenetic analyses and classification of Solanaceae NLRs revealed that the majority of NLR super family members fell into 14 subgroups, including a TIR-NLR (TNL subgroup and 13 non-TNL subgroups. Specific subgroups have expanded in each genome, with the expansion in pepper showing subgroup-specific physical clusters. Comparative analysis of duplications showed distinct duplication patterns within pepper and among Solanaceae plants suggesting subgroup- or species-specific gene duplication events after speciation, resulting in divergent evolution. Taken together, genome-wide analyses of NLR family members provide insights into their evolutionary history in Solanaceae. These findings also provide important foundational knowledge for understanding NLR evolution and will empower broader characterization of disease resistance genes to be used for crop breeding.

Genome-wide analysis reveals novel regulators of growth in Drosophila melanogaster

OpenAIRE

Vonesch, Sibylle; Mackay, Trudy; Lamparter, David; Hafen, Ernst; Bergmann, Sven

2015-01-01

Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. We performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequen...

Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae).

Science.gov (United States)

Morse, Peter; Kjeldsen, Shannon R; Meekan, Mark G; Mccormick, Mark I; Finn, Julian K; Huffard, Christine L; Zenger, Kyall R

2018-02-01

The southern blue-ringed octopus, Hapalochlaena maculosa (Hoyle, 1883) lacks a planktonic dispersal phase, yet ranges across Australia's southern coastline. This species' brief and holobenthic life history suggests gene flow might be limited, leaving distant populations prone to strong genetic divergence. This study used 17,523 genome-wide SNP loci to investigate genetic structuring and local adaptation patterns of H. maculosa among eight sampling sites along its reported range. Within sites, interrelatedness was very high, consistent with the limited dispersal of this taxon. However, inbreeding coefficients were proportionally lower among sites where substructuring was not detected, suggesting H. maculosa might possess a mechanism for inbreeding avoidance. Genetic divergence was extremely high among all sites, with the greatest divergence observed between both ends of the distribution, Fremantle, WA, and Stanley, TAS. Genetic distances closely followed an isolation by geographic distance pattern. Outlier analyses revealed distinct selection signatures at all sites, with the strongest divergence reported between Fremantle and the other Western Australian sites. Phylogenetic reconstructions using the described sister taxon H. fasciata (Hoyle, 1886) further supported that the genetic divergence between distal H. maculosa sites in this study was equivalent to that of between established heterospecifics within this genus. However, it is advocated that taxonomic delineations within this species should be made with caution. These data indicate that H. maculosa forms a clinal species pattern across its geographic range, with gene flow present through allele sharing between adjacent populations. Morphological investigations are recommended for a robust resolution of the taxonomic identity and ecotype boundaries of this species.

Word-wide meta-analysis of Quercus forests ectomycorrhizal fungal diversity reveals southwestern Mexico as a hotspot.

Science.gov (United States)

García-Guzmán, Olimpia Mariana; Garibay-Orijel, Roberto; Hernández, Edith; Arellano-Torres, Elsa; Oyama, Ken

2017-11-01

Quercus is the most diverse genus of ectomycorrhizal (ECM) host plants; it is distributed in the Northern and Southern Hemispheres, from temperate to tropical regions. However, their ECM communities have been scarcely studied in comparison to those of conifers. The objectives of this study were to determine the richness of ECM fungi associated with oak forests in the Cuitzeo basin in southwestern Mexico; and to determine the level of richness, potential endemism and species similarity among ECM fungal communities associated with natural oak forests worldwide through a meta-analysis. The ITS DNA sequences of ECM root tips from 14 studies were included in the meta-analysis. In total, 1065 species of ECM fungi have been documented worldwide; however, 812 species have been only found at one site. Oak forests in Europe contain 416 species, Mexico 307, USA 285, and China 151. Species with wider distributions are Sebacinaceae sp. SH197130, Amanita subjunquillea, Cenococcum geophilum, Cortinarius decipiens, Russula hortensis, R. risigallina, R. subrubescens, Sebacinaceae sp. SH214607, Tomentella ferruginea, and T. lapida. The meta-analysis revealed (1) that Mexico is not only a hotspot for oak species but also for their ECM mycobionts. (2) There is a particularly high diversity of ECM Pezizales in oak seasonal forests from western USA to southwestern Mexico. (3) The oak forests in southwestern Mexico have the largest number of potential endemic species. (4) Globally, there is a high turnover of ECM fungal species associated with oaks, which indicates high levels of alpha and beta diversity in these communities.

Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters.

Science.gov (United States)

Michael, Victoria; Frank, Oliver; Bartling, Pascal; Scheuner, Carmen; Göker, Markus; Brinkmann, Henner; Petersen, Jörn

2016-10-01

Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic 'swim-or-stick' lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.

Temperature profile data from XBT casts in a world wide distribution from multiple platforms from 04 September 2002 to 18 November 2002 (NODC Accession 0000831)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD casts from LYKES COMMANDER and other platforms in a world wide distribution from 04 September 2002 to 18 November...

Strong trans-Pacific break and local conservation units in the Galapagos shark (Carcharhinus galapagensis) revealed by genome-wide cytonuclear markers.

Science.gov (United States)

Pazmiño, Diana A; Maes, Gregory E; Green, Madeline E; Simpfendorfer, Colin A; Hoyos-Padilla, E Mauricio; Duffy, Clinton J A; Meyer, Carl G; Kerwath, Sven E; Salinas-de-León, Pelayo; van Herwerden, Lynne

2018-05-01

The application of genome-wide cytonuclear molecular data to identify management and adaptive units at various spatio-temporal levels is particularly important for overharvested large predatory organisms, often characterized by smaller, localized populations. Despite being "near threatened", current understanding of habitat use and population structure of Carcharhinus galapagensis is limited to specific areas within its distribution. We evaluated population structure and connectivity across the Pacific Ocean using genome-wide single-nucleotide polymorphisms (~7200 SNPs) and mitochondrial control region sequences (945 bp) for 229 individuals. Neutral SNPs defined at least two genetically discrete geographic groups: an East Tropical Pacific (Mexico, east and west Galapagos Islands), and another central-west Pacific (Lord Howe Island, Middleton Reef, Norfolk Island, Elizabeth Reef, Kermadec, Hawaii and Southern Africa). More fine-grade population structure was suggested using outlier SNPs: west Pacific, Hawaii, Mexico, and Galapagos. Consistently, mtDNA pairwise Φ ST defined three regional stocks: east, central and west Pacific. Compared to neutral SNPs (F ST  = 0.023-0.035), mtDNA exhibited more divergence (Φ ST  = 0.258-0.539) and high overall genetic diversity (h = 0.794 ± 0.014; π = 0.004 ± 0.000), consistent with the longstanding eastern Pacific barrier between the east and central-west Pacific. Hawaiian and Southern African populations group within the west Pacific cluster. Effective population sizes were moderate/high for east/west populations (738 and 3421, respectively). Insights into the biology, connectivity, genetic diversity, and population demographics informs for improved conservation of this species, by delineating three to four conservation units across their Pacific distribution. Implementing such conservation management may be challenging, but is necessary to achieve long-term population resilience at basin and

Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus MYB Transcription Factor Families in Sweet Orange

Science.gov (United States)

Hou, Xiao-Jin; Li, Si-Bei; Liu, Sheng-Rui; Hu, Chun-Gen; Zhang, Jin-Zhi

2014-01-01

MYB family genes are widely distributed in plants and comprise one of the largest transcription factors involved in various developmental processes and defense responses of plants. To date, few MYB genes and little expression profiling have been reported for citrus. Here, we describe and classify 177 members of the sweet orange MYB gene (CsMYB) family in terms of their genomic gene structures and similarity to their putative Arabidopsis orthologs. According to these analyses, these CsMYBs were categorized into four groups (4R-MYB, 3R-MYB, 2R-MYB and 1R-MYB). Gene structure analysis revealed that 1R-MYB genes possess relatively more introns as compared with 2R-MYB genes. Investigation of their chromosomal localizations revealed that these CsMYBs are distributed across nine chromosomes. Sweet orange includes a relatively small number of MYB genes compared with the 198 members in Arabidopsis, presumably due to a paralog reduction related to repetitive sequence insertion into promoter and non-coding transcribed region of the genes. Comparative studies of CsMYBs and Arabidopsis showed that CsMYBs had fewer gene duplication events. Expression analysis revealed that the MYB gene family has a wide expression profile in sweet orange development and plays important roles in development and stress responses. In addition, 337 new putative microsatellites with flanking sequences sufficient for primer design were also identified from the 177 CsMYBs. These results provide a useful reference for the selection of candidate MYB genes for cloning and further functional analysis forcitrus. PMID:25375352

Temperature profile data from XBT casts in a world wide distribution from multiple platforms from 20 February 2003 to 24 April 200 (NODC Accession 0001019)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using CTD casts from LYKES RAIDER and other platforms in a world wide distribution from 20 February 2003 to 24 April 2003....

Temperature profile data from XBT casts from MULTIPLE PLATFORMS from a World-Wide distribution from 02 January 1990 to 31 December 1995 (NODC Accession 0001268)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — XBT data were collected from MULTIPLE PLATFORMS from a World-Wide distribution from 02 January 1990 to 31 December 1995. Data were submitted by the UK Hydrographic...

Characterization of replication and conjugation of plasmid pWTY27 from a widely distributed Streptomyces species

Directory of Open Access Journals (Sweden)

Wang Tao

2012-11-01

Full Text Available Abstract Background Streptomyces species are widely distributed in natural habitats, such as soils, lakes, plants and some extreme environments. Replication loci of several Streptomyces theta-type plasmids have been reported, but are not characterized in details. Conjugation loci of some Streptomyces rolling-circle-type plasmids are identified and mechanism of conjugal transferring are described. Results We report the detection of a widely distributed Streptomyces strain Y27 and its indigenous plasmid pWTY27 from fourteen plants and four soil samples cross China by both culturing and nonculturing methods. The complete nucleotide sequence of pWTY27 consisted of 14,288 bp. A basic locus for plasmid replication comprised repAB genes and an adjacent iteron sequence, to a long inverted-repeat (ca. 105 bp of which the RepA protein bound specifically in vitro, suggesting that RepA may recognize a second structure (e.g. a long stem-loop of the iteron DNA. A plasmid containing the locus propagated in linear mode when the telomeres of a linear plasmid were attached, indicating a bi-directional replication mode for pWTY27. As for rolling-circle plasmids, a single traA gene and a clt sequence (covering 16 bp within traA and its adjacent 159 bp on pWTY27 were required for plasmid transfer. TraA recognized and bound specifically to the two regions of the clt sequence, one containing all the four DC1 of 7 bp (TGACACC and one DC2 (CCCGCCC and most of IC1, and another covering two DC2 and part of IC1, suggesting formation of a high-ordered DNA-protein complex. Conclusions This work (i isolates a widespread Streptomyces strain Y27 and sequences its indigenous theta-type plasmid pWTY27; (ii identifies the replication and conjugation loci of pWTY27 and; (iii characterizes the binding sequences of the RepA and TraA proteins.

Characterization of replication and conjugation of plasmid pWTY27 from a widely distributed Streptomyces species

Science.gov (United States)

2012-01-01

Background Streptomyces species are widely distributed in natural habitats, such as soils, lakes, plants and some extreme environments. Replication loci of several Streptomyces theta-type plasmids have been reported, but are not characterized in details. Conjugation loci of some Streptomyces rolling-circle-type plasmids are identified and mechanism of conjugal transferring are described. Results We report the detection of a widely distributed Streptomyces strain Y27 and its indigenous plasmid pWTY27 from fourteen plants and four soil samples cross China by both culturing and nonculturing methods. The complete nucleotide sequence of pWTY27 consisted of 14,288 bp. A basic locus for plasmid replication comprised repAB genes and an adjacent iteron sequence, to a long inverted-repeat (ca. 105 bp) of which the RepA protein bound specifically in vitro, suggesting that RepA may recognize a second structure (e.g. a long stem-loop) of the iteron DNA. A plasmid containing the locus propagated in linear mode when the telomeres of a linear plasmid were attached, indicating a bi-directional replication mode for pWTY27. As for rolling-circle plasmids, a single traA gene and a clt sequence (covering 16 bp within traA and its adjacent 159 bp) on pWTY27 were required for plasmid transfer. TraA recognized and bound specifically to the two regions of the clt sequence, one containing all the four DC1 of 7 bp (TGACACC) and one DC2 (CCCGCCC) and most of IC1, and another covering two DC2 and part of IC1, suggesting formation of a high-ordered DNA-protein complex. Conclusions This work (i) isolates a widespread Streptomyces strain Y27 and sequences its indigenous theta-type plasmid pWTY27; (ii) identifies the replication and conjugation loci of pWTY27 and; (iii) characterizes the binding sequences of the RepA and TraA proteins. PMID:23134842

Genome-wide comparison and taxonomic relatedness of multiple Xylella fastidiosa strains reveal the occurrence of three subspecies and a new Xylella species.

Science.gov (United States)

Marcelletti, Simone; Scortichini, Marco

2016-10-01

A total of 21 Xylella fastidiosa strains were assessed by comparing their genomes to infer their taxonomic relationships. The whole-genome-based average nucleotide identity and tetranucleotide frequency correlation coefficient analyses were performed. In addition, a consensus tree based on comparisons of 956 core gene families, and a genome-wide phylogenetic tree and a Neighbor-net network were constructed with 820,088 nucleotides (i.e., approximately 30-33 % of the entire X. fastidiosa genome). All approaches revealed the occurrence of three well-demarcated genetic clusters that represent X. fastidiosa subspecies fastidiosa, multiplex and pauca, with the latter appeared to diverge. We suggest that the proposed but never formally described subspecies 'sandyi' and 'morus' are instead members of the subspecies fastidiosa. These analyses support the view that the Xylella strain isolated from Pyrus pyrifolia in Taiwan is likely to be a new species. A widely used multilocus sequence typing analysis yielded conflicting results.

Genome-wide investigation reveals high evolutionary rates in annual model plants.

Science.gov (United States)

Yue, Jia-Xing; Li, Jinpeng; Wang, Dan; Araki, Hitoshi; Tian, Dacheng; Yang, Sihai

2010-11-09

Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials. According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those

Temperature profile data from XBT casts in a world wide distribution from multiple platforms from 02 April 2003 to 21 May 2003 (NODC Accession 0001042)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT casts from SEA-LAND DEFENDER and other platforms in a world wide distribution from 02 April 2003 to 21 May 2003....

Temperature and other data from XBT and MBT casts in a world-wide distribution from 06 March 1958 to 01 April 1958 (NODC Accession 0000336)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and other data were collected using XBT and MBT casts in a world-wide distribution from March 6, 1958 to April 1, 1958. Data were submitted by Duetsches...

Charged-particle multiplicity distributions over a wide pseudorapidity range in proton-proton collisions at root s=0.9, 7, and 8 TeV

NARCIS (Netherlands)

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W.; Harton, A.; Hasan, H.; Hatzifotiadou, D.; Hayashi, S.; Heckel, S. T.; Hellbaer, E.; Helstrup, H.; Herghelegiu, A.; HerreraCorral, G.; Herrmann, F.; Hess, B. A.; Hetland, K. F.; Hillemanns, H.; Hills, C.; Hippolyte, B.; Hladky, J.; Hohlweger, B.; Horak, D.; Sorkine-Hornung, Olga; Hosokawa, R.; Hristov, P.; Hughes, C.W.; Humanic, T. J.; Hussain, N.; Hussain, T.; Hutter, D.; Hwang, D. S.; Iga Buitron, S. A.; Ilkaev, R.; Inaba, M.; Ippolitov, M.; Irfan, M.; Isakov, V.; Ivanov, M.; Ivanov, V.; Izucheev, V.; Jacak, B.; Jacazio, N.; Jacholkowski, A.; Jacobs, P. M.; Jadhav, M. B.; Jadlovska, S.; Jadlovsky, J.; Jaelani, S.; Jahnke, C.; Jakubowska, M. J.; Janik, M. A.; Jayarathna, P. H S Y; Jena, C.; Jena, S.; Jeric, M.; Bustamante, R. T Jimenez; Jones, P. G.; Jusko, A.; Kalinak, P.; Kalweit, A.; Kang, J. H.; Kaplin, V.; Kar, S.; Uysal, A. Karasu; Karavichev, O.; Karavicheva, T.; Karayan, L.; Karpechev, E.; Kebschull, U.; Keidel, R.; Keijdener, D. L. D.; Keil, M.; Ketzer, B.; Khan, P.M.; Khan, Shfaqat A.; Khanzadeev, A.; Kharlov, Y.; Khatun, A.; Khuntia, A.; Kielbowicz, M. M.; Kileng, B.; Kim, D.-S.; Kim, D. W.; Kim, D. J.; Kim, H.; Kim, J. S.; Kim, J.; Kim, M.; Kim, M.; Kim, S.; Kim, T.; Kirsch, S.; Kisel, I.; Kiselev, S.; Kisiel, A.; Kiss, G.; Klay, J. L.; Klein, C; Klein, J.; Klein-Boeing, C.; Klewin, S.; Kluge, A.; Knichel, M. L.; Knospe, A. G.; Kobdaj, C.; Kofarago, M.; Kollegger, T.; Kolojvari, A.; Kondratiev, V.; Kondratyeva, N.; Kondratyuk, E.; Konevskikh, A.; Konyushikhin, M.; Kopcik, M.; Kour, M.; Kouzinopoulos, C.; Kovalenko, O.; Kovalenko, V.; Kowalski, M.L.; Meethaleveedu, G. Koyithatta; Kralik, I.; Kravcakova, A.; Krivda, M.; Krizek, F.; Kryshen, E.; Krzewicki, M.; Kubera, A. M.; Kucera, V.; Kuhn, C.; Kuijer, P. G.; Kumar, A.; Kumar, J.; Kumar, L.; Kumar, S.; Kundu, Seema; Kurashvili, P.; Kurepin, A.; Kurepin, A. B.; Kuryakin, A.; Kushpil, S.; Kweon, M. J.; Kwon, Y.; La Pointe, S. L.; La Rocca, P.; Lagana Fernandes, C.; Lai, Y. S.; Lakomov, I.; Langoy, R.; Lapidus, K.; Lara, C.; Lardeux, A.; Lattuca, A.; Laudi, E.; Lavicka, R.; Lazaridis, L.; Lea, R.; Leardini, L.; Lee, S.; Lehas, F.; Strunz-Lehner, Christine; Lehrbach, J.; Lemmon, R. C.; Lenti, V.; Leogrande, E.; Leon Monzon, I.; Levai, P.; Li, S.; Li, X.; Lien, J.; Lietava, R.; Lim, B.; Lindal, S.; Lindenstruth, V.; Lindsay, S. W.; Lippmann, C.; Lisa, M. A.; Litichevskyi, V.; Ljunggren, H. M.; Llope, W. J.; Lodato, D. F.; Loenne, P. I.; Loginov, V.; Loizides, C.; Loncar, P.; Lopez, X.; Lopez Torres, E.; Lowe, A.; Luettig, P.; Lunardon, M.; Luparello, G.; Lupi, M.; Lutz, T. H.; Maevskaya, A.; Mager, M.; Mahajan, S.; Mahmood, S. M.; Maire, A.; Majka, R. D.; Malaev, M.; Malinina, L.; Mal'kevich, D.; Malzacher, P.; Mamonov, A.; Manko, V.; Manso, F.; Manzari, V.; Mao, Y.; Marchisone, M.; Mares, J.; Margagliotti, G. V.; Margotti, A.; Margutti, J.; Marin, A.; Markert, C.; Marquard, M.; Martin, N. 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E.; Sekiguchi, Y.; Sekihata, D.; Selyuzhenkov, I.; Senosi, K.; Senyukov, S.; Serradilla, E.; Sett, P.; Sevcenco, A.; Shabanov, A.; Shabetai, A.; Shahoyan, R.; Shaikh, W.; Shangaraev, A.; Sharma, A.; Sharma, A.; Sharma, M.; Sharma, M.; Sharma, N.; Sheikh, A. I.; Shigaki, K.; Shou, Q. Y.; Shtejer, K.; Sibiriak, Y.; Siddhanta, S.; Sielewicz, K. M.; Siemiarczuk, T.; Silvermyr, D.; Silvestre, C.; Simatovic, G.; Simonetti, G.; Singaraju, R.; Singh, R; Singhal, V.; Sinha, T.; Sitar, B.; Sitta, M.; Skaali, T. B.; Slupecki, M.; Smirnov, N.; Snellings, R. J. M.; Snellman, T. W.; Song, J.; Song, M.; Soramel, F.; Sorensen, S.; Sozzi, F.; Spiriti, E.; Sputowska, I.; Srivastava, B. K.; Stachel, J.; Stan, I.; Stankus, P.; Stenlund, E.; Stocco, D.; Strmen, P.; Suaide, A. A P; Sugitate, T.; Suire, C.; Suleymanov, M.; Suljic, M.; Sultanov, R.; Sumbera, M.; Sumowidagdo, S.; Suzuki, K.; Swain, S.; Szabo, A.; Szarka, I.; Szczepankiewicz, A.; Tabassam, U.; Takahashi, J.; Tambave, G. J.; Tanaka, N.; Tarhini, M.; Tariq, M.; Tarzila, M. G.; Tauro, A.; Tejeda Munoz, G.; Telesca, A.; Terasaki, K.; Terrevoli, C.; Teyssier, B.; Thakur, D.; Thakur, J. S.; Thomas, D.; Tieulent, R.; Tikhonov, A.; Timmins, A. R.; Toia, A.; tripathy, S.; Trogolo, S.; Trombetta, G.; Tropp, Linda; Trubnikov, V.; Trzaska, W. H.; Trzeciak, B. A.; Tsuji, T.; Tumkin, A.; Turrisi, R.; Tveter, T. S.; Ullaland, K.; Umaka, E. N.; Uras, A.; Usai, G. L.; Utrobicic, A.; Vala, M.; Van der Maarel, J.; Van Hoorne, J. W.; van Leeuwen, M.; Vanat, T.; Vyvre, P. Vande; Varga, D.; Vargas, A.; Vargyas, M.; Varma, R.; Vasileiou, M.; Vasiliev, A.; Vauthier, A.; Doce, O. Vazquez; Vechernin, V.; Veen, A. M.; Velure, A.; Vercellin, E.; Vergara Limon, S.; Vernet, R.; Vertesi, R.; Vickovic, L.; Vigolo, S.; Viinikainen, J.; Vilakazi, Z.; Baillie, O. Villalobos; Villatoro Tello, A.; Vinogradov, A.; Vinogradov, L.; Virgili, T.; Vislavicius, V.; Vodopyanov, A.; Voelkl, M. A.; Voloshin, K.; Voloshin, S. A.; Volpe, G.; Haller, B.; Vorobyev, I.; Voscek, D.; Vranic, D.; Vrlakova, J.; Wagner, B.; Wagner, J.; Wang, H.; Wang, M.; Watanabe, D.; Watanabe, Y.; Weber, M.; Weber, S. G.; Weiser, D. F.; Wenzel, S. C.; Wessels, J. P.; Westerhoff, U.; Whitehead, A. M.; Wiechula, J.; Wikne, J.; Wilk, G.; Wilkinson, J.; Willems, G. A.; Williams, M. C S; Willsher, E.; Windelband, B.; Witt, W. E.; Yalcin, S.; Yamakawa, K.; Yang, P.; Yano, S.; Yin, Z.; Yokoyama, H.; Yoo, I. K.; Yoon, J. H.; Yurchenko, V.; Zaccolo, V.; Zaman, A.; Zampolli, C.; Zanoli, H. J. C.; Zardoshti, N.; Zarochentsev, A.; Zavada, P.; Zaviyalov, N.; Zbroszczyk, H.; Zhalov, M.; Zhang, H.; Zhang, X.; Zhang, Y.; Zhang, C.; Zhang, Z.; Zhao, C.; Zhigareva, N.; Zhou, D.; Zhou, Y.; Zhou, Z.; Zhu, H.; Zhu, J.; Zhu, X.; Zichichi, A.; Zimmermann, A.; Zimmermann, M. B.; Zinovjev, G.; Zmeskal, J.; Zou, Shui

2017-01-01

We present the charged-particle multiplicity distributions over a wide pseudorapidity range ( −3.4<η<5.0 ) for pp collisions at s√=0.9,7 , and 8 TeV at the LHC. Results are based on information from the Silicon Pixel Detector and the Forward Multiplicity Detector of ALICE, extending the

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

NARCIS (Netherlands)

I.M. Heid (Iris); A.U. Jackson (Anne); J.C. Randall (Joshua); T.W. Winkler (Thomas); L. Qi (Lu); V. Ssteinthorsdottir (Valgerdur); G. Tthorleifsson (Ggudmar); M.C. Zillikens (Carola); E.K. Sspeliotes (Eelizabeth); R. Mägi (Reedik); T. Workalemahu (Tsegaselassie); C.C. White (Charles); N. Bouatia-Naji (Nabila); T.B. Harris (Tamara); S.I. Berndt (Sonja); E. Ingelsson (Erik); C.J. Willer (Cristen); J. Luan; S. Vedantam (Sailaja); T. Eesko (Tõnu); T.O. Kilpeläinen (Tuomas); Z. Kutalik (Zoltán); S. Li (Shengxu); K.L. Monda (Keri); A.L. Dixon (Anna); C. Holmes (Christopher); R.C. Kaplan (Robert); L. Liang (Liming); J. Min (Josine); M.F. Moffatt (Miriam); C. Molony (Cliona); G. Nicholson (Ggeorge); E.E. Sschadt (Eeric); K.T. Zondervan (Krina); M.F. Feitosa (Mary Furlan); T. Ferreira (Teresa); H.L. Allen; R.J. Weyant (Robert); E. Wheeler (Eleanor); A.R. Wood (Andrew); K. Eestrada (Karol); M.E. Goddard (Michael); G. Lettre (Guillaume); M. Mangino (Massimo); D.R. Nyholt (Dale); S. Purcell (Shaun); A.V. Ssmith; P.M. Visscher (Peter); J. Yang (Joanna); S.A. McCcarroll (Ssteven); J. Nemesh (James); B.F. Voight (Benjamin); D. Absher (Devin); N. Amin (Najaf); T. Aspelund (Thor); L. Coin (Lachlan); N.L. Glazer (Nicole); C. Hayward (Caroline); N. Heard-Ccosta (Nancy); J.J. Hottenga (Jouke Jan); A. Johansson (Åsa); T. Johnson (Toby); M. Kaakinen (Marika); K. Kapur (Karen); S. Ketkar (Shamika); J.W. Knowles (Joshua); P. Kraft (Peter); A. Kraja (Aldi); C. Lamina (Claudia); M.F. Leitzmann (Michael); B. McKknight (Barbara); A.D. Morris (Andrew); K. Oong (Ken); J.R.B. Perry (John); M.J. Peters (Marjolein); O. Polasek (Ozren); I. Prokopenko (Inga); N.W. Rayner (Nigel William); S. Ripatti (Samuli); F. Rivadeneira Ramirez (Fernando); N.R. Robertson (Neil); S. Sanna (Serena); U. Sovio (Ulla); I. Surakka (Ida); A. Teumer (Alexander); S. van Wingerden (Sophie); V. Vitart (Veronique); J.H. Zhao (Jing Hua); C. Cavalcanti-Proença (Christine); P.S. Chines (Peter); E. Fisher (Eeva); J.R. Kulzer (Jennifer); C. Lecoeur (Cécile); N. Narisu (Narisu); C. Sandholt (Camilla); L.J. Scott (Laura); K. Silander (Kaisa); K. Stark (Klaus); M.L. Tammesoo; T.M. Teslovich (Tanya); N.J. Timpson (Nicholas); R.P. Welch (Ryan); D.I. Chasman (Daniel); M.N. Cooper (Matthew); J.O. Jansson; J. Kettunen (Johannes); R. Wlawrence (Robert); N. Pellikka (Niina); M. Perola (Markus); L. Vandenput (Liesbeth); H. Alavere (Helene); P. Almgren (Peter); L.D. Atwood (Larry); A.J. Bennett (Amanda); R. Biffar (Reiner); L.L. Bonnycastle (Lori); S.R. Bornstein (Stefan); T.A. Buchanan (Thomas); H. Campbell (Harry); I.N.M. Day (Ian); M. Dei (Mariano); M. Dörr (Marcus); P. Eelliott (Paul); M.R. Eerdos (Micheal); J.G. Eeriksson (Johan); N.B. Freimer (Nelson); M. Fu (Mao); S. Gaget (Stefan); E.J.C. de Geus (Eco); A.P. Gjesing (Anette); H. Grallert (Harald); J. Gräßler (Jürgen); C.J. Groves (Christopher); C. Guiducci (Candace); A.L. Hartikainen; N. Hassanali (Neelam); A.S. Havulinna (Aki); K.H. Herzig; A.A. Hicks (Andrew); J. Hui (Jennie); W. Igl (Wilmar); P. Jousilahti (Pekka); A. Jula (Antti); E. Kajantie (Eero); L. Kinnunen (Leena); I. Kolcic (Ivana); S. Koskinen (Seppo); P. Kovacs (Peter); H.K. Kroemer (Heyo); V. Krzelj (Vjekoslav); J. Kuusisto (Johanna); K. Kvaløy (Kirsti); J. Laitinen (Jaana); O. Lantieri (Olivier); G.M. Lathrop (Mark); M.L. Lokki; R.N. Luben (Robert); B. Ludwig (Barbara); W.L. McArdle (Wendy); A. McCcarthy (Anne); M.A. Morken (Mario); M. Nelis (Mari); M.J. Neville (Matthew); G. Paré (Guillaume); A.N. Parker (Alex); J. Peden (John); I. Pichler (Irene); K.H. Pietilainen (Kirsi Hannele); C.P. Platou (Carl); A. Pouta (Anneli); M. Ridderstråle (Martin); N.J. Samani (Nilesh); J. Saramies (Jouko); J. Sinisalo (Juha); J.H. Smit (Jan); R.J. Strawbridge (Rona); H.M. Stringham (Heather); A.J. Swift (Amy); M. Teder-Llaving (Maris); B. Thomson (Brian); G. Usala; J.B.J. van Meurs (Joyce); G.J. van Ommen (Gert); V. Vatin (Vincent); C.B. Volpato; H. Wallaschofski (Henri); G.B. Walters (Bragi); E. Widen (Elisabeth); S.H. Wild (Sarah); G.A.H.M. Willemsen (Gonneke); D.R. Witte (Deniel); L. Zgaga (Lina); P. Zitting (Paavo); J.P. Beilby (John); A. James (Alan); M. Kähönen (Mika); T. Lehtimäki (Terho); M.S. Nieminen (Markku); C. Ohlsson (Claes); C. Palmer (Cameron); O. Raitakari (Olli); P.M. Ridker (Paul); M. Stumvoll (Michael); A. Tönjes (Anke); J. Viikari (Jorma); B. Balkau (Beverley); Y. Ben-Shlomo; R.N. Bergman (Richard); H. Boeing (Heiner); A.V. Smith (Albert Vernon); S. Eebrahim (Shah); P. Froguel (Philippe); T. Hansen (Torben); C. Hengstenberg (Christian); K. Hveem (Kristian); B. Isomaa (Bo); T. Jørgensen (Torben); F. Karpe (Fredrik); K-T. Khaw (Kay-Tee); M. Laakso (Markku); D.A. Lawlor (Debbie); M. Marre (Michel); T. Meitinger (Thomas); A. Metspalu (Andres); K. Midthjell (Kristian); O. Pedersen (Oluf); V. Salomaa (Veikko); P.E.H. Schwarz (Peter); T. Tuomi (Tiinamaija); J. Tuomilehto (Jaakko); T.T. Valle (Timo); N.J. Wareham (Nick); A.M. Arnold (Alice); J.S. Beckmann (Jacques); S.M. Bergmann (Sven); E.A. Boerwinkle (Eric); D.I. Boomsma (Dorret); M. Caulfield (Mark); F.S. Collins (Francis); G. Eeiriksdottir (Gudny); V. Gudnason (Vilmundur); U. Gyllensten (Ulf); A. Hamsten (Anders); A.T. Hattersley (Andrew); A. Hofman (Albert); F.B. Hu (Frank); T. Illig (Thomas); C. Iribarren (Carlos); M.R. Järvelin; W.H.L. Kao (Wen); J. Kaprio (Jaakko); L.J. Launer (Lenore); P. Munroe (Patricia); B.A. Oostra (Ben); B.W.J.H. Penninx (Brenda); P.P. Pramstaller (Peter Paul); B.M. Psaty (Bruce); T. Quertermous (Thomas); A. Rissanen (Aila); I. Rudan (Igor); A.R. Shuldiner (Alan); N. Soranzo (Nicole); T.D. Spector (Timothy); A.C. Syvanen; M. Uda (Manuela); A.G. Uitterlinden (André); H. Völzke (Henry); P. Vollenweider (Peter); J.F. Wilson (James); J.C.M. Witteman (Jacqueline); A.F. Wright (Alan); G.R. Abecasis (Gonçalo); M. Boehnke (Michael); I.B. Borecki (Ingrid); P. Deloukas (Panagiotis); T.M. Frayling (Timothy); L. Groop (Leif); T. Haritunians (Talin); D.J. Hunter (David); K.E. North (Kari); J.R. O'Cconnell (Jeffrey); L. Peltonen (Leena Johanna); D. Schlessinger; D.P. Strachan (David); J.N. Hirschhorn (Joel); T.L. Assimes (Themistocles); H.E. Wichmann (Heinz Erich); U. Thorsteinsdottir (Unnur); C.M. van Duijn (Cornelia); K. Stefansson (Kari); L.A. Cupples (Adrienne); R.J.F. Loos (Ruth); I.E. Barroso (Inês); C.S. Fox (Caroline); K.L. Mohlke (Karen); C.M. Lindgren (Cecilia); R.M. Watanabe (Richard); M.N. Weedon (Michael)

2010-01-01

textabstractWaist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association

Temperature profile data collected using XBT casts from multiple platforms in a world wide distribution from 07 November 2001 to 24 July 2002 (NODC Accession 0000762)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT casts from OLEANDER, TAI HE, SEA-LAND ENTERPRISE, and other platforms in a world wide distribution. Data were...

Integrated wide-band low-background amplifiers

International Nuclear Information System (INIS)

Il'yushchenko, I.I.

1980-01-01

Ways of increasing stability and reproduction of characteristics of wide-band integral amplifiers that would to the least extent increase their background noises, are discussed. Considered are some certain flowsheets of integral wide-band amplifiers with low background noise of foreign production which differ from one another by construction of inlet cascades as well as by the applied feedback type. The principal flowsheets of the amplifiers and their main performances are presented. The analysis of the data obtained has revealed that microcircuits made of cascades with a common emitter and local combined feedback are most wide-band among all the considered microcircuits [ru

Temperature profile data collected using XBT casts from multiple platforms in a world wide distribution from 01 March 2002 to 26 August 2002 (NODC Accession 0000777)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT casts from MELBOURNE STAR and other platforms in a world wide distribution. Data were collected from 01 March 2002...

Capataz: a framework for distributing algorithms via the World Wide Web

Directory of Open Access Journals (Sweden)

Gonzalo J. Martínez

2015-08-01

Full Text Available In recent years, some scientists have embraced the distributed computing paradigm. As experiments and simulations demand ever more computing power, coordinating the efforts of many different processors is often the only reasonable resort. We developed an open-source distributed computing framework based on web technologies, and named it Capataz. Acting as an HTTP server, web browsers running on many different devices can connect to it to contribute in the execution of distributed algorithms written in Javascript. Capataz takes advantage of architectures with many cores using web workers. This paper presents an improvement in Capataz´ usability and why it was needed. In previous experiments the total time of distributed algorithms proved to be susceptible to changes in the execution time of the jobs. The system now adapts by bundling jobs together if they are too simple. The computational experiment to test the solution is a brute force estimation of pi. The benchmark results show that by bundling jobs, the overall perfomance is greatly increased.

Estimating System-wide Impacts of Smart Grid Demonstrations

Energy Technology Data Exchange (ETDEWEB)

Schneider, Kevin P.; Lightner, Eric M.; Fuller, Jason C.

2015-03-01

Quantifying the impact of a new technology on a single specific distribution feeder is relatively easy, but it does not provide insight into the complexities and variations of a system-wide deployment. It is the inability to extrapolate system-wide impacts that hinders the deployment of many promising new technologies. This paper presents a method of extrapolating technology impacts, either simulated or from a field demonstration, from a limited number of distribution feeders to a system-wide impact. The size of the system can vary from the service territory of a single utility, to a region, or to an entire country. The paper will include an example analysis using the United States Department of Energy (DOE) funded Smart Grid Investment Grant (SGIG) projects, extrapolating their benefits to a national level.

World Wide Web voted most wonderful wonder by web-wide world

CERN Multimedia

2007-01-01

The results are in, and the winner is...the World Wide Web! An online survey conducted by the CNN news group ranks the World Wide Web-invented at CERN--as the most wonderful of the seven modern wonders of the world. (See Bulletin No. 49/2006.) There is currently no speculation about whether they would have had the same results had they distributed the survey by post. The World Wide Web won with a whopping 50 per cent of the votes (3,665 votes). The runner up was CERN again, with 16 per cent of voters (1130 votes) casting the ballot in favour of the CERN particle accelerator. Stepping into place behind CERN and CERN is 'None of the Above' with 8 per cent of the votes (611 votes), followed by the development of Dubai (7%), the bionic arm (7%), China's Three Gorges Damn (5%), The Channel Tunnel (4%), and France's Millau viaduct (3%). Thanks to everyone from CERN who voted. You can view the results on http://edition.cnn.com/SPECIALS/2006/modern.wonders/

A genome-wide analysis of putative functional and exonic variation associated with extremely high intelligence.

Science.gov (United States)

Spain, S L; Pedroso, I; Kadeva, N; Miller, M B; Iacono, W G; McGue, M; Stergiakouli, E; Davey Smith, G; Putallaz, M; Lubinski, D; Meaburn, E L; Plomin, R; Simpson, M A

2016-08-01

Although individual differences in intelligence (general cognitive ability) are highly heritable, molecular genetic analyses to date have had limited success in identifying specific loci responsible for its heritability. This study is the first to investigate exome variation in individuals of extremely high intelligence. Under the quantitative genetic model, sampling from the high extreme of the distribution should provide increased power to detect associations. We therefore performed a case-control association analysis with 1409 individuals drawn from the top 0.0003 (IQ >170) of the population distribution of intelligence and 3253 unselected population-based controls. Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadChip. We did not observe any individual protein-altering variants that are reproducibly associated with extremely high intelligence and within the entire distribution of intelligence. Moreover, no significant associations were found for multiple rare alleles within individual genes. However, analyses using genome-wide similarity between unrelated individuals (genome-wide complex trait analysis) indicate that the genotyped functional protein-altering variation yields a heritability estimate of 17.4% (s.e. 1.7%) based on a liability model. In addition, investigation of nominally significant associations revealed fewer rare alleles associated with extremely high intelligence than would be expected under the null hypothesis. This observation is consistent with the hypothesis that rare functional alleles are more frequently detrimental than beneficial to intelligence.

Indigenous knowledge and science unite to reveal spatial and temporal dimensions of distributional shift in wildlife of conservation concern.

Directory of Open Access Journals (Sweden)

Christina N Service

Full Text Available Range shifts among wildlife can occur rapidly and impose cascading ecological, economic, and cultural consequences. However, occurrence data used to define distributional limits derived from scientific approaches are often outdated for wide ranging and elusive species, especially in remote environments. Accordingly, our aim was to amalgamate indigenous and western scientific evidence of grizzly bear (Ursus arctos horribilis records and detail a potential range shift on the central coast of British Columbia, Canada. In addition, we test the hypothesis that data from each method yield similar results, as well as illustrate the complementary nature of this coupled approach. Combining information from traditional and local ecological knowledge (TEK/LEK interviews with remote camera, genetic, and hunting data revealed that grizzly bears are now present on 10 islands outside their current management boundary. LEK interview data suggested this expansion has accelerated over the last 10 years. Both approaches provided complementary details and primarily affirmed one another: all islands with scientific evidence for occupation had consistent TEK/LEK evidence. Moreover, our complementary methods approach enabled a more spatially and temporally detailed account than either method would have afforded alone. In many cases, knowledge already held by local indigenous people could provide timely and inexpensive data about changing ecological processes. However, verifying the accuracy of scientific and experiential knowledge by pairing sources at the same spatial scale allows for increased confidence and detail. A similarly coupled approach may be useful across taxa in many regions.

Proteome-wide analysis of arginine monomethylation reveals widespread occurrence in human cells

DEFF Research Database (Denmark)

Larsen, Sara C; Sylvestersen, Kathrine B; Mund, Andreas

2016-01-01

to the frequency of somatic mutations at arginine methylation sites throughout the proteome, we observed that somatic mutations were common at arginine methylation sites in proteins involved in mRNA splicing. Furthermore, in HeLa and U2OS cells, we found that distinct arginine methyltransferases differentially...... kidney 293 cells, indicating that the occurrence of this modification is comparable to phosphorylation and ubiquitylation. A site-level conservation analysis revealed that arginine methylation sites are less evolutionarily conserved compared to arginines that were not identified as modified...... as coactivator-associated arginine methyltransferase 1 (CARM1)] or PRMT1 increased the RNA binding function of HNRNPUL1. High-content single-cell imaging additionally revealed that knocking down CARM1 promoted the nuclear accumulation of SRSF2, independent of cell cycle phase. Collectively, the presented human...

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1995-02-24 to 1996-06-23 (NODC Accession 9700060)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts from several vessels in a world wide distribution from February 24,...

Temperature profile data from MBT casts from AELITA and other platforms in a World wide distribution from 30 January 1970 to 26 July 1990 (NODC Accession 0000227)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using MBT casts in a world wide distribution from AELITA, ESTAFETA OKTYABRYA, MARLIN, ORHEVI, POLYAKOV, and ZVEZDA AZOVA from...

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1996-09-30 to 1997-05-27 (NODC Accession 9700161)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts from several vessels in a world wide distribution from September 30,...

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1996-09-19 to 1997-03-25 (NODC Accession 9700061)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts from several vessels in a world wide distribution from September 19,...

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

Science.gov (United States)

Singh, Sangeeta; Chand, Suresh; Singh, N. K.; Sharma, Tilak Raj

2015-01-01

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species. PMID:25902056

Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast.

Directory of Open Access Journals (Sweden)

Elke Ericson

2008-08-01

Full Text Available To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac interfered with establishment of cell polarity, cyproheptadine (Periactin targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol and pimozide (Orap. Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.

Temperature profile data from bucket, surface seawater intake, and XBT casts in a world wide distribution from 07 December 1995 to 18 October 1996 (NODC Accession 9600167)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using bucket, surface seawater intake, and XBT casts from several vessels in a world wide distribution from December 07, 1995...

Dissolved organic carbon and dissolved organic nitrogen data collected using bottle in a world wide distribution from 02 September 1998 to 02 November 2003 (NODC Accession 0002403)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) data were collected using bottle casts in a world wide distribution. Data were collected from 02...

Design and analysis of the location of an online resale business distribution centre in Japan

Directory of Open Access Journals (Sweden)

K. Suzuki

2016-01-01

Full Text Available The location of distribution centres for online retailers has become an important issue for many companies. The operation of the distribution centre for e-commerce seems to be different from the traditional concept of distribution centres. This study considers how the location of distribution centres are designed and operated for online retailing using a computer simulation with actual data. This paper analyses current issues in order to propose an effective location for e-commerce distribution centres. An effective location for a multi-distribution system over a wide geographical area is required. This paper clearly points out the importance of locating e-commerce distribution centres over a wide geographical area by performing a computer simulation using actual data on the assumption that online resale business customers live in a metropolitan area. The study created a business model in which a buffer warehouse, which primarily handled commodities with high-frequency shipments, was located near a large consumption area and was used in addition to a large-scale distribution centre. The validity of the created business model was verified by performing a simulation based on actual data. The result revealed that these recommended improvement measures for the location of e-commerce distribution centres can function effectively.

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1994-06-29 to 1996-06-08 (NODC Accession 9600120)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts from multiple vessels in a world wide distribution from June 29, 1994 to...

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1996-03-01 to 1997-01-03 (NODC Accession 9700036)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts from several vessels in a world wide distribution from March 1, 1996 to...

Temperature profile data from surface seawater intake, bucket, and XBT casts in a world wide distribution from 1996-08-11 to 1997-07-16 (NODC Accession 9700213)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using surface seawater intake, bucket, and XBT casts in a world wide distribution by several vessels from August 11, 1996 to...

Temperature profiles from MBT casts from a World-Wide distribution from the ALASKA and other platforms from 1943-02-02 to 1964-10-10 (NODC Accession 9200027)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected from MBT casts from a a World-Wide distribution. Data were collected from the ALASKA and other platforms from 02 February...

Depth, chlorophyll, and total pigment data were collected using bottle casts in a world-wide distribution from 16 March 1997 to 30 January 1998 (NODC Accession 0000292)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Depth, chlorophyll, and total pigment data were collected using bottle casts from TIOGA and other platforms in a world-wide distribution from March 16, 1997 to...

Distributing flight dynamics products via the World Wide Web

Science.gov (United States)

Woodard, Mark; Matusow, David

1996-01-01

The NASA Flight Dynamics Products Center (FDPC), which make available selected operations products via the World Wide Web, is reported on. The FDPC can be accessed from any host machine connected to the Internet. It is a multi-mission service which provides Internet users with unrestricted access to the following standard products: antenna contact predictions; ground tracks; orbit ephemerides; mean and osculating orbital elements; earth sensor sun and moon interference predictions; space flight tracking data network summaries; and Shuttle transport system predictions. Several scientific data bases are available through the service.

Proteomic analysis of tissue from α1,3-galactosyltransferase knockout mice reveals that a wide variety of proteins and protein fragments change expression level.

Directory of Open Access Journals (Sweden)

Louise Thorlacius-Ussing

Full Text Available A barrier in a pig-to-man xenotransplantation is that the Galα1-3Galβ1-4GlcNAc-R carbohydrate (α-Gal epitope expressed on pig endothelial cells reacts with naturally occurring antibodies in the recipient's blood leading to rejection. Deletion of the α1,3-galactosyltransferase gene prevents the synthesis of the α-Gal epitope. Therefore, knockout models of the α1,3-galactosyltransferase gene are widely used to study xenotransplantation. We have performed proteomic studies on liver and pancreas tissues from wild type and α1,3-galactosyltransferase gene knockout mice. The tissues were analyzed by two-dimensional polyacrylamide gel electrophoresis and liquid chromatography-tandem mass spectrometry. The analyses revealed that a wide variety of proteins and protein fragments are differentially expressed suggesting that knockout of the α1,3-galactosyltransferase gene affects the expression of several other genes.

Temperature profile data from MBT casts from NAUKA and other platforms in a World-wide distribution from 26 July 1966 to 09 September 1990 (NODC Accession 0000228)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using MBT casts in a World-wide distribution from the NAUKA, FIOLENT, LESNOYE, and other platforms from 26 July 1966 to 09...

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Directory of Open Access Journals (Sweden)

Riaño-Pachón Diego

2007-08-01

Full Text Available Abstract Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs, ABRE and CE3, in thale cress (Arabidopsis thaliana and rice (Oryza sativa. Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

Science.gov (United States)

Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

2007-08-01

In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be

Temperature profile data from MBT casts from NAUKA and other platforms in a World-wide distribution from 18 June 1970 to 05 May 1989 (NODC Accession 0000229)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using MBT casts in a World-wide distribution from the NAUKA, AELITA, LESNOYE, and other platforms from 18 June 1970 to 05 May...

Two Paralogous Families of a Two-Gene Subtilisin Operon Are Widely Distributed in Oral Treponemes

Science.gov (United States)

Correia, Frederick F.; Plummer, Alvin R.; Ellen, Richard P.; Wyss, Chris; Boches, Susan K.; Galvin, Jamie L.; Paster, Bruce J.; Dewhirst, Floyd E.

2003-01-01

Certain oral treponemes express a highly proteolytic phenotype and have been associated with periodontal diseases. The periodontal pathogen Treponema denticola produces dentilisin, a serine protease of the subtilisin family. The two-gene operon prcA-prtP is required for expression of active dentilisin (PrtP), a putative lipoprotein attached to the treponeme's outer membrane or sheath. The purpose of this study was to examine the diversity and structure of treponemal subtilisin-like proteases in order to better understand their distribution and function. The complete sequences of five prcA-prtP operons were determined for Treponema lecithinolyticum, “Treponema vincentii,” and two canine species. Partial operon sequences were obtained for T. socranskii subsp. 04 as well as 450- to 1,000-base fragments of prtP genes from four additional treponeme strains. Phylogenetic analysis demonstrated that the sequences fall into two paralogous families. The first family includes the sequence from T. denticola. Treponemes possessing this operon family express chymotrypsin-like protease activity and can cleave the substrate N-succinyl-alanyl-alanyl-prolyl-phenylalanine-p-nitroanilide (SAAPFNA). Treponemes possessing the second paralog family do not possess chymotrypsin-like activity or cleave SAAPFNA. Despite examination of a range of protein and peptide substrates, the specificity of the second protease family remains unknown. Each of the fully sequenced prcA and prtP genes contains a 5′ hydrophobic leader sequence with a treponeme lipobox. The two paralogous families of treponeme subtilisins represent a new subgroup within the subtilisin family of proteases and are the only subtilisin lipoprotein family. The present study demonstrated that the subtilisin paralogs comprising a two-gene operon are widely distributed among treponemes. PMID:14617650

Wide-Scale Adoption of Photovoltaic Energy

DEFF Research Database (Denmark)

Yang, Yongheng; Enjeti, Prasad; Blaabjerg, Frede

2015-01-01

Current grid standards largely require that low-power (e.g., several kilowatts) single-phase photovoltaic (PV) systems operate at unity power factor (PF) with maximum power point tracking (MPPT), and disconnect from the grid under grid faults by means of islanding detection. However, in the case...... of wide-scale penetration of single-phase PV systems in the distributed grid, disconnection under grid faults can contribute to 1) voltage flickers, 2) power outages, and 3) system instability. This article explores grid code modifications for a wide-scale adoption of PV systems in the distribution grid....... In addition, based on the fact that Italy and Japan have recently undertaken a major review of standards for PV power conversion systems connected to low-voltage networks, the importance of low voltage ride-through (LVRT) for single-phase PV power systems under grid faults is considered, along with three...

Crowdsourcing-based nationwide tick collection reveals the distribution of Ixodes ricinus and I. persulcatus and associated pathogens in Finland.

Science.gov (United States)

Laaksonen, Maija; Sajanti, Eeva; Sormunen, Jani J; Penttinen, Ritva; Hänninen, Jari; Ruohomäki, Kai; Sääksjärvi, Ilari; Vesterinen, Eero J; Vuorinen, Ilppo; Hytönen, Jukka; Klemola, Tero

2017-05-10

A national crowdsourcing-based tick collection campaign was organized in 2015 with the objective of producing novel data on tick distribution and tick-borne pathogens in Finland. Nearly 20 000 Ixodes ticks were collected. The collected material revealed the nationwide distribution of I. persulcatus for the first time and a shift northwards in the distribution of I. ricinus in Finland. A subset of 2038 tick samples containing both species was screened for Borrelia burgdorferi sensu lato (the prevalence was 14.2% for I. ricinus and 19.8% for I. persulcatus), B. miyamotoi (0.2% and 0.4%, respectively) and tick-borne encephalitis virus (TBEV; 0.2% and 3.0%, respectively). We also report new risk areas for TBEV in Finland and, for the first time, the presence of B. miyamotoi in ticks from mainland Finland. Most importantly, our study demonstrates the overwhelming power of citizen science in accomplishing a collection effort that would have been impossible with the scientific community alone.

Wind direction/velocity and current direction/velocity data from current meter casts in a world wide distribution from 1970-12-06 to 1991-10-01 (NODC Accession 9700218)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Wind direction/velocity and current direction/velocity data were collected using current meter casts in a world wide distribution from December 6, 1970 to October 1,...

Genome-wide distribution comparative and composition analysis of the SSRs in Poaceae.

Science.gov (United States)

Wang, Yi; Yang, Chao; Jin, Qiaojun; Zhou, Dongjie; Wang, Shuangshuang; Yu, Yuanjie; Yang, Long

2015-02-15

The Poaceae family is of great importance to human beings since it comprises the cereal grasses which are the main sources for human food and animal feed. With the rapid growth of genomic data from Poaceae members, comparative genomics becomes a convinent method to study genetics of diffierent species. The SSRs (Simple Sequence Repeats) are widely used markers in the studies of Poaceae for their high abundance and stability. In this study, using the genomic sequences of 9 Poaceae species, we detected 11,993,943 SSR loci and developed 6,799,910 SSR primer pairs. The results show that SSRs are distributed on all the genomic elements in grass. Hexamer is the most frequent motif and AT/TA is the most frequent motif in dimer. The abundance of the SSRs has a positive linear relationship with the recombination rate. SSR sequences in the coding regions involve a higher GC content in the Poaceae than that in the other species. SSRs of 70-80 bp in length showed the highest AT/GC base ratio among all of these loci. The result shows the highest polymorphism rate belongs to the SSRs ranged from 30 bp to 40 bp. Using all the SSR primers of Japonica, nineteen universal primers were selected and located on the genome of the grass family. The information of SSR loci, the SSR primers and the tools of mining and analyzing SSR are provided in the PSSRD (Poaceae SSR Database, http://biodb.sdau.edu.cn/pssrd/). Our study and the PSSRD database provide a foundation for the comparative study in the Poaceae and it will accelerate the study on markers application, gene mapping and molecular breeding.

Temperature profile and oxygen data collected from multiple ships using CTD casts in a world wide distribution from 04 September 1979 to 15 April 1998 (NODC Accession 0002716)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and oxygen data were collected using CTD casts in a world wide distribution from multiple platforms from 04 September 1979 to 15 April 1998. Data...

Details of 1π sr wide acceptance angle electrostatic lens for electron energy and two-dimensional angular distribution analysis combined with real space imaging

International Nuclear Information System (INIS)

Tóth, László; Matsuda, Hiroyuki; Matsui, Fumihiko; Goto, Kentaro; Daimon, Hiroshi

2012-01-01

We propose a new 1π sr Wide Acceptance Angle Electrostatic Lens (WAAEL), which works as a photoemission electron microscope (PEEM), a highly sensitive display-type electron energy and two-dimensional angular distribution analyzer. It can display two-dimensional angular distributions of charged particles within the acceptance angle of ±60° that is much larger than the largest acceptance angle range so far and comparable to the display-type spherical mirror analyzer developed by Daimon et al. . It has good focusing capabilities with 5-times magnification and 27(4) μm lateral-resolution. The relative energy resolution is typically from 2 to 5×10 -3 depending on the diameter of energy aperture and the emission area on the sample. Although, the lateral resolution of the presented lens is far from those are available nowadays, but this is the first working model that can form images using charged particles collected from 1π sr wide acceptance angle. The realization of such lens system is one of the first possible steps towards reaching the field of imaging type atomic resolution electron microscopy Feynman et al. Here some preliminary results are shown.

DIRS1-like retrotransposons are widely distributed among Decapoda and are particularly present in hydrothermal vent organisms

Directory of Open Access Journals (Sweden)

Bonnivard Eric

2009-04-01

allowed for revealing for the first time a widespread distribution of these elements among a large phylum, here the order Decapoda. They also suggest some peculiar features of these retrotransposons in hydrothermal organisms where a great diversity of elements is already observed. Finally, this paper constitutes the first essential step which allows for considering further studies based on the dynamics of the DIRS1-like retrotransposons among several genomes.

Air/delta/sea surface temperature, pressure, and other data from MISS GAIL in a world-wide distribution from 21 October 1957 to 18 April 1961 (NODC Accession 0000366)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Air/delta/sea surface temperature, pressure, and other data were collected from the MISS GAIL in a world-wide distribution from October 21, 1957 to April 18, 1961....

Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster.

Directory of Open Access Journals (Sweden)

Sibylle Chantal Vonesch

2016-01-01

Full Text Available Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. We performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequenced lines. We find that the top associated variants differ between traits and sexes; do not map to canonical growth pathway genes, but can be linked to these by epistasis analysis; and are enriched for genes and putative enhancers. Performing GWA on well-studied developmental traits under controlled conditions expands our understanding of developmental processes underlying phenotypic diversity.

Temperature profiles from XBT casts from a world-wide distribution from the EMERALD INDAH and other platforms from 28 November 2000 to 29 May 2001 (NODC Accession 0000465)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — XBT and other data were collected from a world-wide distribution from the EMERALD INDAH and other platforms from 28 November 2000 to 29 May 2001. Data were submitted...

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants.

Science.gov (United States)

Rawal, H C; Singh, N K; Sharma, T R

2013-01-01

Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL) and peroxidase A (POX A) enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula), fruits (Vitis vinifera), cereals (Sorghum bicolor, Zea mays, and Oryza sativa), trees (Populus trichocarpa), and model dicot (Arabidopsis thaliana) and monocot (Brachypodium distachyon) species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Conservation, Divergence, and Genome-Wide Distribution of PAL and POX A Gene Families in Plants

Directory of Open Access Journals (Sweden)

H. C. Rawal

2013-01-01

Full Text Available Genome-wide identification and phylogenetic and syntenic comparison were performed for the genes responsible for phenylalanine ammonia lyase (PAL and peroxidase A (POX A enzymes in nine plant species representing very diverse groups like legumes (Glycine max and Medicago truncatula, fruits (Vitis vinifera, cereals (Sorghum bicolor, Zea mays, and Oryza sativa, trees (Populus trichocarpa, and model dicot (Arabidopsis thaliana and monocot (Brachypodium distachyon species. A total of 87 and 1045 genes in PAL and POX A gene families, respectively, have been identified in these species. The phylogenetic and syntenic comparison along with motif distributions shows a high degree of conservation of PAL genes, suggesting that these genes may predate monocot/eudicot divergence. The POX A family genes, present in clusters at the subtelomeric regions of chromosomes, might be evolving and expanding with higher rate than the PAL gene family. Our analysis showed that during the expansion of POX A gene family, many groups and subgroups have evolved, resulting in a high level of functional divergence among monocots and dicots. These results will act as a first step toward the understanding of monocot/eudicot evolution and functional characterization of these gene families in the future.

Multi-source analysis reveals latitudinal and altitudinal shifts in range of Ixodes ricinus at its northern distribution limit

Directory of Open Access Journals (Sweden)

Kristoffersen Anja B

2011-05-01

Full Text Available Abstract Background There is increasing evidence for a latitudinal and altitudinal shift in the distribution range of Ixodes ricinus. The reported incidence of tick-borne disease in humans is on the rise in many European countries and has raised political concern and attracted media attention. It is disputed which factors are responsible for these trends, though many ascribe shifts in distribution range to climate changes. Any possible climate effect would be most easily noticeable close to the tick's geographical distribution limits. In Norway- being the northern limit of this species in Europe- no documentation of changes in range has been published. The objectives of this study were to describe the distribution of I. ricinus in Norway and to evaluate if any range shifts have occurred relative to historical descriptions. Methods Multiple data sources - such as tick-sighting reports from veterinarians, hunters, and the general public - and surveillance of human and animal tick-borne diseases were compared to describe the present distribution of I. ricinus in Norway. Correlation between data sources and visual comparison of maps revealed spatial consistency. In order to identify the main spatial pattern of tick abundance, a principal component analysis (PCA was used to obtain a weighted mean of four data sources. The weighted mean explained 67% of the variation of the data sources covering Norway's 430 municipalities and was used to depict the present distribution of I. ricinus. To evaluate if any geographical range shift has occurred in recent decades, the present distribution was compared to historical data from 1943 and 1983. Results Tick-borne disease and/or observations of I. ricinus was reported in municipalities up to an altitude of 583 metres above sea level (MASL and is now present in coastal municipalities north to approximately 69°N. Conclusion I. ricinus is currently found further north and at higher altitudes than described in

System-wide power management control via clock distribution network

Science.gov (United States)

Coteus, Paul W.; Gara, Alan; Gooding, Thomas M.; Haring, Rudolf A.; Kopcsay, Gerard V.; Liebsch, Thomas A.; Reed, Don D.

2015-05-19

An apparatus, method and computer program product for automatically controlling power dissipation of a parallel computing system that includes a plurality of processors. A computing device issues a command to the parallel computing system. A clock pulse-width modulator encodes the command in a system clock signal to be distributed to the plurality of processors. The plurality of processors in the parallel computing system receive the system clock signal including the encoded command, and adjusts power dissipation according to the encoded command.

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study.

Science.gov (United States)

Wang, Quanxiu; Xie, Weibo; Xing, Hongkun; Yan, Ju; Meng, Xiangzhou; Li, Xinglei; Fu, Xiangkui; Xu, Jiuyue; Lian, Xingming; Yu, Sibin; Xing, Yongzhong; Wang, Gongwei

2015-06-01

Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

Science.gov (United States)

Alsop, Eric B; Boyd, Eric S; Raymond, Jason

2014-05-28

The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes

An Ultra-High Fluorescence Enhancement and High Throughput Assay for Revealing Expression and Internalization of Chemokine Receptor CXCR4.

Science.gov (United States)

He, Hua; Wang, Xiaojuan; Cheng, Tiantian; Xia, Yongqing; Lao, Jun; Ge, Baosheng; Ren, Hao; Khan, Naseer Ullah; Huang, Fang

2016-04-18

Revealing chemokine receptor CXCR4 expression, distribution, and internalization levels in different cancers helps to evaluate cancer progression or prognosis and to set personalized treatment strategy. We here describe a sensitive and high-throughput immunoassay for determining CXCR4 expression and distribution in cancer cells. The assay is accessible to a wide range of users in an ordinary lab only by dip-coating poly(styrene-co-N-isopropylacrylamide) spheres on the glass substrate. The self- assembled spheres form three-dimensional photonic colloidal crystals which enhance the fluorescence of CF647 and Alexa Fluor 647 by a factor of up to 1000. CXCR4 in cells is detected by using the sandwich immunoassay, where the primary antibody recognizes CXCR4 and the secondary antibody is labeled with CF647. With the newly established assay, we quantified the total expression of CXCR4, its distribution on the cell membrane and cytoplasm, and revealed their internalization level upon SDF-1α activation in various cancer cells, even for those with extremely low expression level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome-Wide Association Analysis Reveals Genetic Heterogeneity of Sjögren's Syndrome According to Ancestry.

Science.gov (United States)

Taylor, Kimberly E; Wong, Quenna; Levine, David M; McHugh, Caitlin; Laurie, Cathy; Doheny, Kimberly; Lam, Mi Y; Baer, Alan N; Challacombe, Stephen; Lanfranchi, Hector; Schiødt, Morten; Srinivasan, M; Umehara, Hisanori; Vivino, Frederick B; Zhao, Yan; Shiboski, Stephen C; Daniels, Troy E; Greenspan, John S; Shiboski, Caroline H; Criswell, Lindsey A

2017-06-01

The Sjögren's International Collaborative Clinical Alliance (SICCA) is an international data registry and biorepository derived from a multisite observational study of participants in whom genotyping was performed on the Omni2.5M platform and who had undergone deep phenotyping using common protocol-directed methods. The aim of this study was to examine the genetic etiology of Sjögren's syndrome (SS) across ancestry and disease subsets. We performed genome-wide association study analyses using SICCA subjects and external controls obtained from dbGaP data sets, one using all participants (1,405 cases, 1,622 SICCA controls, and 3,125 external controls), one using European participants (585, 966, and 580, respectively), and one using Asian participants (460, 224, and 901, respectively) with ancestry adjustments via principal components analyses. We also investigated whether subphenotype distributions differ by ethnicity, and whether this contributes to the heterogeneity of genetic associations. We observed significant associations in established regions of the major histocompatibility complex (MHC), IRF5, and STAT4 (P = 3 × 10 -42 , P = 3 × 10 -14 , and P = 9 × 10 -10 , respectively), and several novel suggestive regions (those with 2 or more associations at P ancestry (P = 4 × 10 -15 and P = 4 × 10 -5 , respectively), but that subphenotype differences did not explain most of the ancestry differences in genetic associations. Genetic associations with SS differ markedly according to ancestry; however, this is not explained by differences in subphenotypes. © 2017, The Authors. Arthritis & Rheumatology published by Wiley Periodicals, Inc. on behalf of American College of Rheumatology.

Accessing NASA Technology with the World Wide Web

Science.gov (United States)

Nelson, Michael L.; Bianco, David J.

1995-01-01

NASA Langley Research Center (LaRC) began using the World Wide Web (WWW) in the summer of 1993, becoming the first NASA installation to provide a Center-wide home page. This coincided with a reorganization of LaRC to provide a more concentrated focus on technology transfer to both aerospace and non-aerospace industry. Use of WWW and NCSA Mosaic not only provides automated information dissemination, but also allows for the implementation, evolution and integration of many technology transfer and technology awareness applications. This paper describes several of these innovative applications, including the on-line presentation of the entire Technology OPportunities Showcase (TOPS), an industrial partnering showcase that exists on the Web long after the actual 3-day event ended. The NASA Technical Report Server (NTRS) provides uniform access to many logically similar, yet physically distributed NASA report servers. WWW is also the foundation of the Langley Software Server (LSS), an experimental software distribution system which will distribute LaRC-developed software. In addition to the more formal technology distribution projects, WWW has been successful in connecting people with technologies and people with other people.

Continental-wide distribution of crayfish species in Europe: update and maps

Directory of Open Access Journals (Sweden)

Kouba A.

2014-01-01

Full Text Available Recently published astacological studies substantially improved available data on distribution of crayfish in various European regions. At the same time, spread of invasive species has been recorded, additional non-indigenous species became established in various countries, and losses of populations of native species due to crayfish plague and other negative factors were observed. We overview recent advances in this knowledge, and provide updated colour maps of the distribution of all crayfish species present in Europe. These maps are originally based on the data from the Atlas of Crayfish in Europe published in 2006 as a result of the CRAYNET project, and were further updated from more recently published reports, grey literature, and especially thanks to contributions and feedback of over 70 specialists from 32 countries. Separate maps are available for all indigenous crayfish species in Europe as well as for three most widespread non-indigenous crayfish species. Additionally, two maps give locations of known findings of crayfish species introduced to Europe after 1980. These newly established alien species have so far restricted distributions; however, the frequency of recent reports suggests that findings of such species resulting from releases of aquarium pets will further increase.

Geolocation Reveals Year-Round at-Sea Distribution and Activity of a Superabundant Tropical Seabird, the Sooty Tern Onychoprion fuscatus

Directory of Open Access Journals (Sweden)

Audrey Jaeger

2017-12-01

Full Text Available Migration is a fundamental aspect of the ecology and evolutionary history of many animals, driven by seasonal changes in resource availability and habitat structure. Seabird migration has been investigated extensively in highly seasonal temperate and polar environments. By contrast, the relationships between migration and seasonal environmental changes have rarely been studied in tropical marine habitats. The sooty tern Onychoprion fuscatus is the most abundant tropical seabirds, and has been ranked as the most important tropical species in terms of its annual estimated consumption of marine resources. We used global location sensing (GLS loggers to describe for the first time the year-round at-sea distribution and activity patterns of sooty terns from a large breeding colony in the western Indian Ocean (Bird Island, Seychelles. While breeding, they foraged within 1,074 ± 274 km of the colony. After breeding, birds undertook an extensive post-breeding migration throughout the Indian Ocean; average distances traveled exceeded 50,000 km per individual. Sooty terns used mainly four distinct core oceanic areas during the non-breeding period; in the Bay of Bengal (A, northeast to an area straddling the Chagos-Laccadive plateau (B, southeast to an area on each side of the 90 East Ridge (C and southwest to an area around Comoros (D. Individuals exhibited a high degree of fidelity to these core areas in successive years. We also established that they performed an unusual behavior for a non-Procellariiformes seabird; most individuals undertook a 1-month pre-laying exodus, during which they foraged in a specific area c. 2,000 km to the south-east of the colony. Year-round at-sea activity of sooty terns revealed that they spent only 3.72% of their time in contact with seawater, so indicating that they must sleep in flight. Activity parameters exhibited seasonal (breeding vs. non-breeding periods and daily variations; they notably never land on the water

A Proteome-wide, Quantitative Survey of In Vivo Ubiquitylation Sites Reveals Widespread Regulatory Roles

DEFF Research Database (Denmark)

Wagner, Sebastian Alexander; Beli, Petra; Weinert, Brian Tate

2011-01-01

Post-translational modification of proteins by ubiquitin is a fundamentally important regulatory mechanism. However, proteome-wide analysis of endogenous ubiquitylation remains a challenging task, and almost always has relied on cells expressing affinity tagged ubiquitin. Here we combine single...

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

Directory of Open Access Journals (Sweden)

De Marzo Angelo M

2011-06-01

Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

Temperature profile and water depth data collected from SAXON STAR and other platforms in a World wide distribution from 09 March 1983 to 12 November 1986 (NODC Accession 8700035)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and water depth data were collected using BT and XBT from the SAXON STAR and other platforms in a World wide distribution. Data were collected...

Environmental distribution and abundance of the facultative methanotroph Methylocella.

Science.gov (United States)

Rahman, Md Tanvir; Crombie, Andrew; Chen, Yin; Stralis-Pavese, Nancy; Bodrossy, Levente; Meir, Patrick; McNamara, Niall P; Murrell, J Colin

2011-06-01

Methylocella spp. are facultative methanotrophs, which are able to grow not only on methane but also on multicarbon substrates such as acetate, pyruvate or malate. Methylocella spp. were previously thought to be restricted to acidic soils such as peatlands, in which they may have a key role in methane oxidation. There is little information on the abundance and distribution of Methylocella spp. in the environment. New primers were designed, and a real-time quantitative PCR method was developed and validated targeting Methylocella mmoX (encoding the α-subunit of the soluble methane monooxygenase) that allowed the quantification of Methylocella spp. in environmental samples. We also developed and validated specific PCR assays, which target 16S rRNA genes of known Methylocella spp. These were used to investigate the distribution of Methylocella spp. in a variety of environmental samples. It was revealed that Methylocella species are widely distributed in nature and not restricted to acidic environments.

Temperature profile data from XBT casts in a World-wide distribution from NOAA Ship RESEARCHER and other platforms from 1982-05-24 to 1996-03-21 (NODC Accession 9600116)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT casts in a World-wide distribution from NOAA Ship RESEARCHER and other platforms from 24 May 1982 to 21 March 1996....

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa.

Science.gov (United States)

Duncan, Laramie; Yilmaz, Zeynep; Gaspar, Helena; Walters, Raymond; Goldstein, Jackie; Anttila, Verneri; Bulik-Sullivan, Brendan; Ripke, Stephan; Thornton, Laura; Hinney, Anke; Daly, Mark; Sullivan, Patrick F; Zeggini, Eleftheria; Breen, Gerome; Bulik, Cynthia M

2017-09-01

The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3) in 12 case-control cohorts comprising 3,495 anorexia nervosa cases and 10,982 controls, the authors performed standard association analysis followed by a meta-analysis across cohorts. Linkage disequilibrium score regression was used to calculate genome-wide common variant heritability (single-nucleotide polymorphism [SNP]-based heritability [h 2 SNP ]), partitioned heritability, and genetic correlations (r g ) between anorexia nervosa and 159 other phenotypes. Results were obtained for 10,641,224 SNPs and insertion-deletion variants with minor allele frequencies >1% and imputation quality scores >0.6. The h 2 SNP of anorexia nervosa was 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability arises from common genetic variation. The authors identified one genome-wide significant locus on chromosome 12 (rs4622308) in a region harboring a previously reported type 1 diabetes and autoimmune disorder locus. Significant positive genetic correlations were observed between anorexia nervosa and schizophrenia, neuroticism, educational attainment, and high-density lipoprotein cholesterol, and significant negative genetic correlations were observed between anorexia nervosa and body mass index, insulin, glucose, and lipid phenotypes. Anorexia nervosa is a complex heritable phenotype for which this study has uncovered the first genome-wide significant locus. Anorexia nervosa also has large and significant genetic correlations with both psychiatric phenotypes and metabolic traits. The study results encourage a reconceptualization of this frequently lethal disorder as one with both psychiatric and metabolic etiology.

Clustering patterns of LOD scores for asthma-related phenotypes revealed by a genome-wide screen in 295 French EGEA families.

Science.gov (United States)

Bouzigon, Emmanuelle; Dizier, Marie-Hélène; Krähenbühl, Christine; Lemainque, Arnaud; Annesi-Maesano, Isabella; Betard, Christine; Bousquet, Jean; Charpin, Denis; Gormand, Frédéric; Guilloud-Bataille, Michel; Just, Jocelyne; Le Moual, Nicole; Maccario, Jean; Matran, Régis; Neukirch, Françoise; Oryszczyn, Marie-Pierre; Paty, Evelyne; Pin, Isabelle; Rosenberg-Bourgin, Myriam; Vervloet, Daniel; Kauffmann, Francine; Lathrop, Mark; Demenais, Florence

2004-12-15

A genome-wide scan for asthma phenotypes was conducted in the whole sample of 295 EGEA families selected through at least one asthmatic subject. In addition to asthma, seven phenotypes involved in the main asthma physiopathological pathways were considered: SPT (positive skin prick test response to at least one of 11 allergens), SPTQ score being the number of positive skin test responses to 11 allergens, Phadiatop (positive specific IgE response to a mixture of allergens), total IgE levels, eosinophils, bronchial responsiveness (BR) to methacholine challenge and %predicted FEV(1). Four regions showed evidence for linkage (Pwide LOD scores. This analysis revealed clustering of LODs for asthma, SPT and Phadiatop on one axis and clustering of LODs for %FEV(1), BR and SPTQ on the other, while LODs for IgE and eosinophils appeared to be independent from all other LODs. These results provide new insights into the potential sharing of genetic determinants by asthma-related phenotypes.

From Genome-Wide Association Study to Phenome-Wide Association Study: New Paradigms in Obesity Research.

Science.gov (United States)

Zhang, Y-P; Zhang, Y-Y; Duan, D D

2016-01-01

Obesity is a condition in which excess body fat has accumulated over an extent that increases the risk of many chronic diseases. The current clinical classification of obesity is based on measurement of body mass index (BMI), waist-hip ratio, and body fat percentage. However, these measurements do not account for the wide individual variations in fat distribution, degree of fatness or health risks, and genetic variants identified in the genome-wide association studies (GWAS). In this review, we will address this important issue with the introduction of phenome, phenomics, and phenome-wide association study (PheWAS). We will discuss the new paradigm shift from GWAS to PheWAS in obesity research. In the era of precision medicine, phenomics and PheWAS provide the required approaches to better definition and classification of obesity according to the association of obese phenome with their unique molecular makeup, lifestyle, and environmental impact. Copyright © 2016 Elsevier Inc. All rights reserved.

Spatial distribution of intra-molecular water and polymeric components in polyelectrolyte dendrimers revealed by small angle scattering investigations

Science.gov (United States)

Wu, Bin; Li, Xin; Do, Changwoo; Kim, Tae-Hwan; Shew, Chwen-Yang; Liu, Yun; Yang, Jun; Hong, Kunlun; Porcar, Lionel; Chen, Chun-Yu; Liu, Emily L.; Smith, Gregory S.; Herwig, Kenneth W.; Chen, Wei-Ren

2011-10-01

An experimental scheme using contrast variation small angle neutron scattering technique is developed to investigate the structural characteristics of amine-terminated poly(amidoamine) dendrimers solutions. Using this methodology, we present the dependence of both the intra-dendrimer water and the polymer distribution on molecular protonation, which can be precisely adjusted by tuning the pH of the solution. Assuming spherical symmetry of the spatial arrangement of the constituent components of dendrimer, and that the atomic ratio of hydrogen-to-deuterium for the solvent residing within the cavities of dendrimer is identical to that for the solvent outside the dendrimer, the intra-dendrimer water distribution along the radial direction is determined. Our result clearly reveals an outward relocation of the peripheral groups, as well as enhanced intra-dendrimer hydration, upon increasing the molecular protonation and, therefore, allows the determination of segmental backfolding in a quantitative manner. The connection between these charge-induced structural changes and our recently observed progressively active segmental dynamics is also discussed.

A novel stress distribution analytical model of O-ring seals under different properties of materials

International Nuclear Information System (INIS)

Wu, Di; Wang, Shao Ping; Wang, Xing Jian

2017-01-01

The elastomeric O-ring seals have been widely used as sealing elements in hydraulic systems. The sealing performance of O-ring seals is related to stress distribution. The stresses distribution depends on the squeeze rate and internal pressure, and would vary with properties of O-ring seals materials. Thus, in order to study the sealing performance of O-ring seals, it is necessary to describe the analytic relationship between stress distribution and properties of O-ring seals materials. For this purpose, a novel Stress distribution analytical model (SDAM) is proposed in this paper. The analytical model utilizes two stress complex functions to describe the stress distribution of O-ring seals. The proposed SDAM can express not only the analytical relationship between stress distribution and Young’s modulus, but also the one between stress distribution and Poisson’s ratio. Finally, compared results between finite element analysis and the SDAM validate that the proposed model can effectively reveal the stress distribution under different properties for O-ring materials

A novel stress distribution analytical model of O-ring seals under different properties of materials

Energy Technology Data Exchange (ETDEWEB)

Wu, Di; Wang, Shao Ping; Wang, Xing Jian [School of Automation Science and Electrical Engineering, Beihang University, Beijing (China)

2017-01-15

The elastomeric O-ring seals have been widely used as sealing elements in hydraulic systems. The sealing performance of O-ring seals is related to stress distribution. The stresses distribution depends on the squeeze rate and internal pressure, and would vary with properties of O-ring seals materials. Thus, in order to study the sealing performance of O-ring seals, it is necessary to describe the analytic relationship between stress distribution and properties of O-ring seals materials. For this purpose, a novel Stress distribution analytical model (SDAM) is proposed in this paper. The analytical model utilizes two stress complex functions to describe the stress distribution of O-ring seals. The proposed SDAM can express not only the analytical relationship between stress distribution and Young’s modulus, but also the one between stress distribution and Poisson’s ratio. Finally, compared results between finite element analysis and the SDAM validate that the proposed model can effectively reveal the stress distribution under different properties for O-ring materials.

A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation

NARCIS (Netherlands)

Paul, Petra; van den Hoorn, Tineke; Jongsma, Marlieke L. M.; Bakker, Mark J.; Hengeveld, Rutger; Janssen, Lennert; Cresswell, Peter; Egan, David A.; van Ham, Marieke; ten Brinke, Anja; Ovaa, Huib; Beijersbergen, Roderick L.; Kuijl, Coenraad; Neefjes, Jacques

2011-01-01

MHC class II molecules (MHC-II) present peptides to T helper cells to facilitate immune responses and are strongly linked to autoimmune diseases. To unravel processes controlling MHC-II antigen presentation, we performed a genome-wide flow cytometry-based RNAi screen detecting MHC-II expression and

A genome-wide association study reveals variants in ARL15 that influence adiponectin levels

NARCIS (Netherlands)

J.B. Richards (Brent); D. Waterworth (Dawn); S. O'Rahilly (Stephen); M.-F. Hivert (Marie-France); R.J.F. Loos (Ruth); J.R.B. Perry (John); T. Tanaka (Toshiko); N.J. Timpson (Nicholas); R.K. Semple (Robert); N. Soranzo (Nicole); K. Song (Kijoung); N. Rocha (Nuno); E. Grundberg (Elin); J. Dupuis (Josée); J.C. Florez (Jose); C. Langenberg (Claudia); I. Prokopenko (Inga); R. Saxena (Richa); R. Sladek (Rob); Y.S. Aulchenko (Yurii); D.M. Evans (David); G. Waeber (Gérard); M.S. Burnett; N. Sattar (Naveed); J. Devaney (Joseph); C. Willenborg (Christina); A. Hingorani (Aroon); J.C.M. Witteman (Jacqueline); P. Vollenweider (Peter); B. Glaser (Beate); C. Hengstenberg (Christian); L. Ferrucci (Luigi); D. Melzer (David); K. Stark (Klaus); J. Deanfield (John); J. Winogradow (Janina); M. Grassl (Martina); A.S. Hall (Alistair); J.M. Egan (Josephine); J.R. Thompson (John); S.L. Ricketts (Sally); I.R. König (Inke); W. Reinhard (Wibke); S.M. Grundy (Scott); H.E. Wichmann (Heinz Erich); P. Barter (Phil); R. Mahley (Robert); Y.A. Kesaniemi (Antero); D.J. Rader (Daniel); M.P. Reilly (Muredach); S.E. Epstein (Stephen); A.F.R. Stewart (Alexandre); P. Tikka-Kleemola (Päivi); H. Schunkert (Heribert); K.A. Burling (Keith); J. Erdmann (Jeanette); P. Deloukas (Panagiotis); T. Pastinen (Tomi); N.J. Samani (Nilesh); R. McPherson (Ruth); G.D. Smith; T.M. Frayling (Timothy); N.J. Wareham (Nick); J.B. Meigs (James); V. Mooser (Vincent); T.D. Spector (Timothy)

2009-01-01

textabstractThe adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D) and coronary heart disease (CHD). We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531) and sought validation of

So Wide a Web, So Little Time.

Science.gov (United States)

McConville, David; And Others

1996-01-01

Discusses new trends in the World Wide Web. Highlights include multimedia; digitized audio-visual files; compression technology; telephony; virtual reality modeling language (VRML); open architecture; and advantages of Java, an object-oriented programming language, including platform independence, distributed development, and pay-per-use software.…

Extreme value distributions

CERN Document Server

Ahsanullah, Mohammad

2016-01-01

The aim of the book is to give a through account of the basic theory of extreme value distributions. The book cover a wide range of materials available to date. The central ideas and results of extreme value distributions are presented. The book rwill be useful o applied statisticians as well statisticians interrested to work in the area of extreme value distributions.vmonograph presents the central ideas and results of extreme value distributions.The monograph gives self-contained of theory and applications of extreme value distributions.

Architecture and Fault Identification of Wide-area Protection System

Directory of Open Access Journals (Sweden)

Yuxue Wang

2012-09-01

Full Text Available Wide-area protection system (WAPS is widely studied for the purpose of improvng the performance of conventional backup protection. In this paper, the system architecture of WAPS is proposed and its key technologies are discussed in view of engineering projects. So a mixed structurecentralized-distributed structure which is more suitable for WAPS in limited power grid region, is obtained based on the advantages of the centralized structure and distributed structure. Furthermore, regional distance protection algorithm was taken as an example to illustrate the functions of the constituent units. Faulted components can be detected based on multi-source imformation fuse in the algorithm. And the algorithm cannot only improve the selectivity, the rapidity, and the reliability of relaying protection but also has high fault tolerant capability. A simulation of 220 kV grid systems in Easter Hubei province shows the effectiveness of the wide-area protection system presented by this paper.

Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.

Directory of Open Access Journals (Sweden)

Sarit Edelheit

2013-06-01

Full Text Available The presence of 5-methylcytidine (m(5C in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago. However, detection of this modification was limited to specific, abundant, RNA species, due to the usage of low-throughput methods. To obtain a high resolution, systematic, and comprehensive transcriptome-wide overview of m(5C across the three domains of life, we used bisulfite treatment on total RNA from both gram positive (B. subtilis and gram negative (E. coli bacteria, an archaeon (S. solfataricus and a eukaryote (S. cerevisiae, followed by massively parallel sequencing. We were able to recover most previously documented m(5C sites on rRNA in the four organisms, and identified several novel sites in yeast and archaeal rRNAs. Our analyses also allowed quantification of methylated m(5C positions in 64 tRNAs in yeast and archaea, revealing stoichiometric differences between the methylation patterns of these organisms. Molecules of tRNAs in which m(5C was absent were also discovered. Intriguingly, we detected m(5C sites within archaeal mRNAs, and identified a consensus motif of AUCGANGU that directs methylation in S. solfataricus. Our results, which were validated using m(5C-specific RNA immunoprecipitation, provide the first evidence for mRNA modifications in archaea, suggesting that this mode of post-transcriptional regulation extends beyond the eukaryotic domain.

Temperature profile data from XBT casts from a world-wide distribution from the SEA-LAND NAVIGATOR and other platforms from 21 September 2000 to 18 March 2002 (NODC Accession 0000696)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profiles were collected by deploying XBT casts from the SEA-LAND NAVIGATOR and other platforms over a world-wide distribution from 21 September 2000 to...

Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells

Directory of Open Access Journals (Sweden)

Chad M. Toledo

2015-12-01

Full Text Available To identify therapeutic targets for glioblastoma (GBM, we performed genome-wide CRISPR-Cas9 knockout (KO screens in patient-derived GBM stem-like cells (GSCs and human neural stem/progenitors (NSCs, non-neoplastic stem cell controls, for genes required for their in vitro growth. Surprisingly, the vast majority GSC-lethal hits were found outside of molecular networks commonly altered in GBM and GSCs (e.g., oncogenic drivers. In vitro and in vivo validation of GSC-specific targets revealed several strong hits, including the wee1-like kinase, PKMYT1/Myt1. Mechanistic studies demonstrated that PKMYT1 acts redundantly with WEE1 to inhibit cyclin B-CDK1 activity via CDK1-Y15 phosphorylation and to promote timely completion of mitosis in NSCs. However, in GSCs, this redundancy is lost, most likely as a result of oncogenic signaling, causing GBM-specific lethality.

The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation.

Science.gov (United States)

Eckhart, V M; Geber, M A; Morris, W F; Fabio, E S; Tiffin, P; Moeller, D A

2011-10-01

Potential causes of species' geographic distribution limits fall into two broad classes: (1) limited adaptation across spatially variable environments and (2) limited opportunities to colonize unoccupied areas. Combining demographic studies, analyses of demographic responses to environmental variation, and species distribution models, we investigated the causes of range limits in a model system, the eastern border of the California annual plant Clarkia xantiana ssp. xantiana. Vital rates of 20 populations varied with growing season temperature and precipitation: fruit number and overwinter survival of 1-year-old seeds declined steeply, while current-year seed germination increased modestly along west-to-east gradients in decreasing temperature, decreasing mean precipitation, and increasing variation in precipitation. Long-term stochastic finite rate of increase, λ(s), exhibited a fourfold range and varied among geologic surface materials as well as with temperature and precipitation. Growth rate declined significantly toward the eastern border, falling below 1 in three of the five easternmost populations. Distribution models employing demographically important environmental variables predicted low habitat favorability beyond the eastern border. Models that filtered or weighted population presences by λ(s) predicted steeper eastward declines in favorability and assigned greater roles in setting the distribution to among-year variation in precipitation and to geologic surface material. These analyses reveal a species border likely set by limited adaptation to declining environmental quality.

A Metabolome-Wide Study of Dry Eye Disease Reveals Serum Androgens as Biomarkers.

Science.gov (United States)

Vehof, Jelle; Hysi, Pirro G; Hammond, Christopher J

2017-04-01

To test the association between serum metabolites and dry eye disease (DED) using a hypothesis-free metabolomics approach. Cross-sectional association study. A total of 2819 subjects from the population-representative TwinsUK cohort in the United Kingdom, with a mean age of 57 years (range, 17-82 years). We tested associations between 222 known serum metabolites and DED. All subjects underwent nontargeted metabolomic analysis of plasma samples using gas and liquid chromatography in combination with mass spectrometry (Metabolon Inc., Durham, NC). Dry eye disease was defined from the validated Short Questionnaire for Dry Eye Syndrome (SQDES) as a previous diagnosis of DED by a clinician or "often" or "constant" symptoms of dryness and irritation. Analyses were performed with linear mixed effect models that included age, BMI, and sex as covariates, corrected for multiple testing. Primary outcome was DED as defined by the SQDES, and secondary outcomes were symptom score of DED and a clinical diagnosis of DED. Prevalence of DED as defined by the SQDES was 15.5% (n = 436). A strong and metabolome-wide significant association with DED was found with decreased levels of the metabolites androsterone sulfate (P = 0.00030) and epiandrosterone sulfate (P = 0.00036). Three other metabolites involved in androgen metabolism, 4-androsten-3beta,17beta-diol disulfate 1 and 2, and dehydroepiandrosterone sulfate, were the next most strongly associated of the 222 metabolites, but did not reach metabolome-wide significance. Dryness and irritation symptoms, as opposed to a clinical diagnosis, were particularly strongly associated with decreased androgen steroid metabolites, with all reaching metabolome-wide significance (androsterone sulfate, P = 0.000000029; epiandrosterone sulfate, P = 0.0000040; 4-androsten-3beta,17beta-diol disulfate 1, P = 0.000016; 4-androsten-3beta,17beta-diol disulfate 2, P = 0.000064; and dehydroepiandrosterone sulfate, P = 0.00011). Of these 5

Temperature and nutrients data collected using bottle casts from the SKIF and other platforms in a World-wide distribution from 06 July 1962 to 08 January 1990 (NODC Accession 0000856)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and nutrients data were collected using bottle casts in a World-wide distribution from SKIF and other platforms. Data were collected from 06 July 1962 to...

Widely tunable Sampled Grating Distributed Bragg Reflector Quantum Cascade laser for gas spectroscopy applications

Science.gov (United States)

Diba, Abdou Salam

Since the advent of semiconductor lasers, the development of tunable laser sources has been subject of many efforts in industry and academia arenas. This interest towards broadly tunable lasers is mainly due to the great promise they have in many applications ranging from telecommunication, to environmental science and homeland security, just to name a few. After the first demonstration of quantum cascade laser (QCL) in the early nineties, QCL has experienced a rapid development, so much so that QCLs are now the most reliable and efficient laser source in the Mid-IR range covering between 3 microm to 30 microm region of the electromagnetic spectrum. QCLs have almost all the desirable characteristics of a laser for spectroscopy applications such as narrow spectral linewidth ideal for high selectivity measurement, high power enabling high sensitivity sensing and more importantly they emit in the finger-print region of most of the trace gases and large molecules. The need for widely tunable QCLs is now more pressing than ever before. A single mode quantum cascade laser (QCL) such as a distributed feedback (DFB) QCL, is an ideal light source for gas sensing in the MIR wavelength range. Despite their performance and reliability, DFB QCLs are limited by their relatively narrow wavelength tuning range determined by the thermal rollover of the laser. An external cavity (EC) QCL, on the other hand, is a widely tunable laser source, and so far is the choice mid-infrared single frequency light sources for detecting multiple species/large molecules. However, EC QCLs can be complex, bulky and expensive. In the quest for finding alternative broadly wavelength tunable sources in the mid-infrared, many monolithic tunable QCLs are recently proposed and fabricated, including SG-DBR, DFB-Arrays, Slot-hole etc. and they are all of potentially of interest as a candidate for multi-gas sensing and monitoring applications, due to their large tuning range (>50 cm-1), and potentially low

Sheep skeletal muscle transcriptome analysis reveals muscle growth regulatory lncRNAs.

Science.gov (United States)

Chao, Tianle; Ji, Zhibin; Hou, Lei; Wang, Jin; Zhang, Chunlan; Wang, Guizhi; Wang, Jianmin

2018-01-01

As widely distributed domestic animals, sheep are an important species and the source of mutton. In this study, we aimed to evaluate the regulatory lncRNAs associated with muscle growth and development between high production mutton sheep (Dorper sheep and Qianhua Mutton Merino sheep) and low production mutton sheep (Small-tailed Han sheep). In total, 39 lncRNAs were found to be differentially expressed. Using co-expression analysis and functional annotation, 1,206 co-expression interactions were found between 32 lncRNAs and 369 genes, and 29 of these lncRNAs were found to be associated with muscle development, metabolism, cell proliferation and apoptosis. lncRNA-mRNA interactions revealed 6 lncRNAs as hub lncRNAs. Moreover, three lncRNAs and their associated co-expressed genes were demonstrated by cis-regulatory gene analyses, and we also found a potential regulatory relationship between the pseudogene lncRNA LOC101121401 and its parent gene FTH1. This study provides a genome-wide resolution of lncRNA and mRNA regulation in muscles from mutton sheep.

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Science.gov (United States)

Berndt, Sonja I.; Gustafsson, Stefan; Mägi, Reedik; Ganna, Andrea; Wheeler, Eleanor; Feitosa, Mary F.; Justice, Anne E.; Monda, Keri L.; Croteau-Chonka, Damien C.; Day, Felix R.; Esko, Tõnu; Fall, Tove; Ferreira, Teresa; Gentilini, Davide; Jackson, Anne U.; Luan, Jian’an; Randall, Joshua C.; Vedantam, Sailaja; Willer, Cristen J.; Winkler, Thomas W.; Wood, Andrew R.; Workalemahu, Tsegaselassie; Hu, Yi-Juan; Lee, Sang Hong; Liang, Liming; Lin, Dan-Yu; Min, Josine L.; Neale, Benjamin M.; Thorleifsson, Gudmar; Yang, Jian; Albrecht, Eva; Amin, Najaf; Bragg-Gresham, Jennifer L.; Cadby, Gemma; den Heijer, Martin; Eklund, Niina; Fischer, Krista; Goel, Anuj; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jarick, Ivonne; Johansson, Åsa; Johnson, Toby; Kanoni, Stavroula; Kleber, Marcus E.; König, Inke R.; Kristiansson, Kati; Kutalik, Zoltán; Lamina, Claudia; Lecoeur, Cecile; Li, Guo; Mangino, Massimo; McArdle, Wendy L.; Medina-Gomez, Carolina; Müller-Nurasyid, Martina; Ngwa, Julius S.; Nolte, Ilja M.; Paternoster, Lavinia; Pechlivanis, Sonali; Perola, Markus; Peters, Marjolein J.; Preuss, Michael; Rose, Lynda M.; Shi, Jianxin; Shungin, Dmitry; Smith, Albert Vernon; Strawbridge, Rona J.; Surakka, Ida; Teumer, Alexander; Trip, Mieke D.; Tyrer, Jonathan; Van Vliet-Ostaptchouk, Jana V.; Vandenput, Liesbeth; Waite, Lindsay L.; Zhao, Jing Hua; Absher, Devin; Asselbergs, Folkert W.; Atalay, Mustafa; Attwood, Antony P.; Balmforth, Anthony J.; Basart, Hanneke; Beilby, John; Bonnycastle, Lori L.; Brambilla, Paolo; Bruinenberg, Marcel; Campbell, Harry; Chasman, Daniel I.; Chines, Peter S.; Collins, Francis S.; Connell, John M.; Cookson, William; de Faire, Ulf; de Vegt, Femmie; Dei, Mariano; Dimitriou, Maria; Edkins, Sarah; Estrada, Karol; Evans, David M.; Farrall, Martin; Ferrario, Marco M.; Ferrières, Jean; Franke, Lude; Frau, Francesca; Gejman, Pablo V.; Grallert, Harald; Grönberg, Henrik; Gudnason, Vilmundur; Hall, Alistair S.; Hall, Per; Hartikainen, Anna-Liisa; Hayward, Caroline; Heard-Costa, Nancy L.; Heath, Andrew C.; Hebebrand, Johannes; Homuth, Georg; Hu, Frank B.; Hunt, Sarah E.; Hyppönen, Elina; Iribarren, Carlos; Jacobs, Kevin B.; Jansson, John-Olov; Jula, Antti; Kähönen, Mika; Kathiresan, Sekar; Kee, Frank; Khaw, Kay-Tee; Kivimaki, Mika; Koenig, Wolfgang; Kraja, Aldi T.; Kumari, Meena; Kuulasmaa, Kari; Kuusisto, Johanna; Laitinen, Jaana H.; Lakka, Timo A.; Langenberg, Claudia; Launer, Lenore J.; Lind, Lars; Lindström, Jaana; Liu, Jianjun; Liuzzi, Antonio; Lokki, Marja-Liisa; Lorentzon, Mattias; Madden, Pamela A.; Magnusson, Patrik K.; Manunta, Paolo; Marek, Diana; März, Winfried; Mateo Leach, Irene; McKnight, Barbara; Medland, Sarah E.; Mihailov, Evelin; Milani, Lili; Montgomery, Grant W.; Mooser, Vincent; Mühleisen, Thomas W.; Munroe, Patricia B.; Musk, Arthur W.; Narisu, Narisu; Navis, Gerjan; Nicholson, George; Nohr, Ellen A.; Ong, Ken K.; Oostra, Ben A.; Palmer, Colin N.A.; Palotie, Aarno; Peden, John F.; Pedersen, Nancy; Peters, Annette; Polasek, Ozren; Pouta, Anneli; Pramstaller, Peter P.; Prokopenko, Inga; Pütter, Carolin; Radhakrishnan, Aparna; Raitakari, Olli; Rendon, Augusto; Rivadeneira, Fernando; Rudan, Igor; Saaristo, Timo E.; Sambrook, Jennifer G.; Sanders, Alan R.; Sanna, Serena; Saramies, Jouko; Schipf, Sabine; Schreiber, Stefan; Schunkert, Heribert; Shin, So-Youn; Signorini, Stefano; Sinisalo, Juha; Skrobek, Boris; Soranzo, Nicole; Stančáková, Alena; Stark, Klaus; Stephens, Jonathan C.; Stirrups, Kathleen; Stolk, Ronald P.; Stumvoll, Michael; Swift, Amy J.; Theodoraki, Eirini V.; Thorand, Barbara; Tregouet, David-Alexandre; Tremoli, Elena; Van der Klauw, Melanie M.; van Meurs, Joyce B.J.; Vermeulen, Sita H.; Viikari, Jorma; Virtamo, Jarmo; Vitart, Veronique; Waeber, Gérard; Wang, Zhaoming; Widén, Elisabeth; Wild, Sarah H.; Willemsen, Gonneke; Winkelmann, Bernhard R.; Witteman, Jacqueline C.M.; Wolffenbuttel, Bruce H.R.; Wong, Andrew; Wright, Alan F.; Zillikens, M. Carola; Amouyel, Philippe; Boehm, Bernhard O.; Boerwinkle, Eric; Boomsma, Dorret I.; Caulfield, Mark J.; Chanock, Stephen J.; Cupples, L. Adrienne; Cusi, Daniele; Dedoussis, George V.; Erdmann, Jeanette; Eriksson, Johan G.; Franks, Paul W.; Froguel, Philippe; Gieger, Christian; Gyllensten, Ulf; Hamsten, Anders; Harris, Tamara B.; Hengstenberg, Christian; Hicks, Andrew A.; Hingorani, Aroon; Hinney, Anke; Hofman, Albert; Hovingh, Kees G.; Hveem, Kristian; Illig, Thomas; Jarvelin, Marjo-Riitta; Jöckel, Karl-Heinz; Keinanen-Kiukaanniemi, Sirkka M.; Kiemeney, Lambertus A.; Kuh, Diana; Laakso, Markku; Lehtimäki, Terho; Levinson, Douglas F.; Martin, Nicholas G.; Metspalu, Andres; Morris, Andrew D.; Nieminen, Markku S.; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Ouwehand, Willem H.; Palmer, Lyle J.; Penninx, Brenda; Power, Chris; Province, Michael A.; Psaty, Bruce M.; Qi, Lu; Rauramaa, Rainer; Ridker, Paul M.; Ripatti, Samuli; Salomaa, Veikko; Samani, Nilesh J.; Snieder, Harold; Sørensen, Thorkild I.A.; Spector, Timothy D.; Stefansson, Kari; Tönjes, Anke; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; van der Harst, Pim; Vollenweider, Peter; Wallaschofski, Henri; Wareham, Nicholas J.; Watkins, Hugh; Wichmann, H.-Erich; Wilson, James F.; Abecasis, Goncalo R.; Assimes, Themistocles L.; Barroso, Inês; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; Fox, Caroline S.; Frayling, Timothy; Groop, Leif C.; Haritunian, Talin; Heid, Iris M.; Hunter, David; Kaplan, Robert C.; Karpe, Fredrik; Moffatt, Miriam; Mohlke, Karen L.; O’Connell, Jeffrey R.; Pawitan, Yudi; Schadt, Eric E.; Schlessinger, David; Steinthorsdottir, Valgerdur; Strachan, David P.; Thorsteinsdottir, Unnur; van Duijn, Cornelia M.; Visscher, Peter M.; Di Blasio, Anna Maria; Hirschhorn, Joel N.; Lindgren, Cecilia M.; Morris, Andrew P.; Meyre, David; Scherag, André; McCarthy, Mark I.; Speliotes, Elizabeth K.; North, Kari E.; Loos, Ruth J.F.; Ingelsson, Erik

2014-01-01

Approaches exploiting extremes of the trait distribution may reveal novel loci for common traits, but it is unknown whether such loci are generalizable to the general population. In a genome-wide search for loci associated with upper vs. lower 5th percentiles of body mass index, height and waist-hip ratio, as well as clinical classes of obesity including up to 263,407 European individuals, we identified four new loci (IGFBP4, H6PD, RSRC1, PPP2R2A) influencing height detected in the tails and seven new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3, ZZZ3) for clinical classes of obesity. Further, we show that there is large overlap in terms of genetic structure and distribution of variants between traits based on extremes and the general population and little etiologic heterogeneity between obesity subgroups. PMID:23563607

Governance and assessment in a widely distributed medical education program in Australia.

Science.gov (United States)

Solarsh, Geoff; Lindley, Jennifer; Whyte, Gordon; Fahey, Michael; Walker, Amanda

2012-06-01

The learning objectives, curriculum content, and assessment standards for distributed medical education programs must be aligned across the health care systems and community contexts in which their students train. In this article, the authors describe their experiences at Monash University implementing a distributed medical education program at metropolitan, regional, and rural Australian sites and an offshore Malaysian site, using four different implementation models. Standardizing learning objectives, curriculum content, and assessment standards across all sites while allowing for site-specific implementation models created challenges for educational alignment. At the same time, this diversity created opportunities to customize the curriculum to fit a variety of settings and for innovations that have enriched the educational system as a whole.Developing these distributed medical education programs required a detailed review of Monash's learning objectives and curriculum content and their relevance to the four different sites. It also required a review of assessment methods to ensure an identical and equitable system of assessment for students at all sites. It additionally demanded changes to the systems of governance and the management of the educational program away from a centrally constructed and mandated curriculum to more collaborative approaches to curriculum design and implementation involving discipline leaders at multiple sites.Distributed medical education programs, like that at Monash, in which cohorts of students undertake the same curriculum in different contexts, provide potentially powerful research platforms to compare different pedagogical approaches to medical education and the impact of context on learning outcomes.

Fractal nature of hydrocarbon deposits. 2. Spatial distribution

International Nuclear Information System (INIS)

Barton, C.C.; Schutter, T.A; Herring, P.R.; Thomas, W.J.; Scholz, C.H.

1991-01-01

Hydrocarbons are unevenly distributed within reservoirs and are found in patches whose size distribution is a fractal over a wide range of scales. The spatial distribution of the patches is also fractal and this can be used to constrain the design of drilling strategies also defined by a fractal dimension. Fractal distributions are scale independent and are characterized by a power-law scaling exponent termed the fractal dimension. The authors have performed fractal analyses on the spatial distribution of producing and showing wells combined and of dry wells in 1,600-mi 2 portions of the Denver and Powder River basins that were nearly completely drilled on quarter-mile square-grid spacings. They have limited their analyses to wells drilled to single stratigraphic intervals so that the map pattern revealed by drilling is representative of the spatial patchiness of hydrocarbons at depth. The fractal dimensions for the spatial patchiness of hydrocarbons in the two basins are 1.5 and 1.4, respectively. The fractal dimension for the pattern of all wells drilled is 1.8 for both basins, which suggests a drilling strategy with a fractal dimension significantly higher than the dimensions 1.5 and 1.4 sufficient to efficiently and economically explore these reservoirs. In fact, the fractal analysis reveals that the drilling strategy used in these basins approaches a fractal dimension of 2.0, which is equivalent to random drilling with no geologic input. Knowledge of the fractal dimension of a reservoir prior to drilling would provide a basis for selecting and a criterion for halting a drilling strategy for exploration whose fractal dimension closely matches that of the spatial fractal dimension of the reservoir, such a strategy should prove more efficient and economical than current practice

Binary star statistics: the mass ratio distribution for very wide systems

International Nuclear Information System (INIS)

Trimble, V.

1987-01-01

The distribution of mass ratios for a sample of common proper motion (CPM) binaries is determined and compared with that of 798 visual binaries (VB's) studied earlier, in hopes of answering the question: Can the member stars of these systems have been drawn at random from the normal initial mass function for single stars? The observed distributions peak strongly toward q = 1.0 for both kinds of systems, but less strongly for the CPM's than for the VB's. Due allowance having been made for assorted observational selection effects, it seems quite probable that the CPM's represent the observed part of a population drawn at random from the normal IMF, while the VB's are much more difficult to interpret that way and could, perhaps, result from a formation mechanism that somewhat favors sytems with roughly equal components. (author)

Wide-band low-noise distributed front-end for multi-gigabit CPFSK receivers

DEFF Research Database (Denmark)

Petersen, Anders Kongstad; Ebskamp, F; Pedersen, Rune Johan Skullerud

1994-01-01

In this paper a distributed optical front-end amplifier for a coherent optical CPFSK receiver is presented. The measured average input noise current density is 20 pA/√(Hz) in a 3-13 GHz bandwidth. This is the lowest value reported for a distributed optical front-end in this frequency range....... The front-end is tested in a system set-up at a bit rate of 2.5 Gbit/s and a receiver sensitivity of -41.5 dBm is achieved at a 10-9 bit error rate...

Physical, chemical, meteorological, and nutrients data from bottle casts from a world-wide distribution from the YERMAK and other platforms from 15 January 1873 to 15 June 1967 (NODC Accession 0000505)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical, meteorological, and nutrients data were collected from bottle casts from the YERMAK and other platforms from a world-wide distribution from 15 January 1873...

Pathway-based analysis of genome-wide siRNA screens reveals the regulatory landscape of APP processing.

Directory of Open Access Journals (Sweden)

Luiz Miguel Camargo

Full Text Available The progressive aggregation of Amyloid-β (Aβ in the brain is a major trait of Alzheimer's Disease (AD. Aβ is produced as a result of proteolytic processing of the β-amyloid precursor protein (APP. Processing of APP is mediated by multiple enzymes, resulting in the production of distinct peptide products: the non-amyloidogenic peptide sAPPα and the amyloidogenic peptides sAPPβ, Aβ40, and Aβ42. Using a pathway-based approach, we analyzed a large-scale siRNA screen that measured the production of different APP proteolytic products. Our analysis identified many of the biological processes/pathways that are known to regulate APP processing and have been implicated in AD pathogenesis, as well as revealing novel regulatory mechanisms. Furthermore, we also demonstrate that some of these processes differentially regulate APP processing, with some mechanisms favouring production of certain peptide species over others. For example, synaptic transmission having a bias towards regulating Aβ40 production over Aβ42 as well as processes involved in insulin and pancreatic biology having a bias for sAPPβ production over sAPPα. In addition, some of the pathways identified as regulators of APP processing contain genes (CLU, BIN1, CR1, PICALM, TREM2, SORL1, MEF2C, DSG2, EPH1A recently implicated with AD through genome wide association studies (GWAS and associated meta-analysis. In addition, we provide supporting evidence and a deeper mechanistic understanding of the role of diabetes in AD. The identification of these processes/pathways, their differential impact on APP processing, and their relationships to each other, provide a comprehensive systems biology view of the "regulatory landscape" of APP.

Evolutionary genomics revealed interkingdom distribution of Tcn1-like chromodomain-containing Gypsy LTR retrotransposons among fungi and plants

Directory of Open Access Journals (Sweden)

Blinov Alexander

2010-04-01

Full Text Available Abstract Background Chromodomain-containing Gypsy LTR retrotransposons or chromoviruses are widely distributed among eukaryotes and have been found in plants, fungi and vertebrates. The previous comprehensive survey of chromoviruses from mosses (Bryophyta suggested that genomes of non-seed plants contain the clade which is closely related to the retrotransposons from fungi. The origin, distribution and evolutionary history of this clade remained unclear mainly due to the absence of information concerning the diversity and distribution of LTR retrotransposons in other groups of non-seed plants as well as in fungal genomes. Results In present study we preformed in silico analysis of chromodomain-containing LTR retrotransposons in 25 diverse fungi and a number of plant species including spikemoss Selaginella moellendorffii (Lycopodiophyta coupled with an experimental survey of chromodomain-containing Gypsy LTR retrotransposons from diverse non-seed vascular plants (lycophytes, ferns, and horsetails. Our mining of Gypsy LTR retrotransposons in genomic sequences allowed identification of numerous families which have not been described previously in fungi. Two new well-supported clades, Galahad and Mordred, as well as several other previously unknown lineages of chromodomain-containing Gypsy LTR retrotransposons were described based on the results of PCR-mediated survey of LTR retrotransposon fragments from ferns, horsetails and lycophytes. It appeared that one of the clades, namely Tcn1 clade, was present in basidiomycetes and non-seed plants including mosses (Bryophyta and lycophytes (genus Selaginella. Conclusions The interkingdom distribution is not typical for chromodomain-containing LTR retrotransposons clades which are usually very specific for a particular taxonomic group. Tcn1-like LTR retrotransposons from fungi and non-seed plants demonstrated high similarity to each other which can be explained by strong selective constraints and the

Lake-wide distribution of Dreissena in Lake Michigan, 1999

Science.gov (United States)

Fleischer, Guy W.; DeSorcie, Timothy J.; Holuszko, Jeffrey D.

2001-01-01

The Great Lakes Science Center has conducted lake-wide bottom trawl surveys of the fish community in Lake Michigan each fall since 1973. These systematic surveys are performed at depths of 9 to 110 m at each of seven index sites around Lake Michigan. Zebra mussel (Dreissena polymorpha) populations have expanded to all survey locations and at a level to sufficiently contribute to the bottom trawl catches. The quagga (Dreissena bugensis), recently reported in Lake Michigan, was likely in the catches though not recognized. Dreissena spp. biomass ranged from about 0.6 to 15 kg/ha at the various sites in 1999. Dreissenid mussels were found at depths of 9 to 82 m, with their peak biomass at 27 to 46 m. The colonization of these exotic mussels has ecological implications as well as potential ramifications on the ability to sample fish consistently and effectively with bottom trawls in Lake Michigan.

Charged-particle multiplicity distributions over a wide pseudorapidity range in proton-proton collisions at √(s) = 0.9, 7, and 8 TeV

Energy Technology Data Exchange (ETDEWEB)

Acharya, S. [Variable Energy Cyclotron Centre, Kolkata (India); Adamova, D. [Academy of Sciences of the Czech Republic, Rez u Prahy (Czech Republic). Nuclear Physics Inst.; Adolfsson, J. [Lund Univ. (Sweden). Div. of Experimental High Energy Physics; Collaboration: ALICE Collaboration; and others

2017-12-15

We present the charged-particle multiplicity distributions over a wide pseudorapidity range (-3.4<η<5.0) for pp collisions at √(s) = 0.9, 7, and 8 TeV at the LHC. Results are based on information from the Silicon Pixel Detector and the Forward Multiplicity Detector of ALICE, extending the pseudorapidity coverage of the earlier publications and the high-multiplicity reach. The measurements are compared to results from the CMS experiment and to PYTHIA, PHOJET and EPOS LHC event generators, as well as IP-Glasma calculations. (orig.)

Genome-wide identification and analysis of the chicken basic helix-loop-helix factors.

Science.gov (United States)

Liu, Wu-Yi; Zhao, Chun-Jiang

2010-01-01

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ''orphans". A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase.

Science.gov (United States)

Ahmed, Wareed; Sala, Claudia; Hegde, Shubhada R; Jha, Rajiv Kumar; Cole, Stewart T; Nagaraja, Valakunja

2017-05-01

Movement of the transcription machinery along a template alters DNA topology resulting in the accumulation of supercoils in DNA. The positive supercoils generated ahead of transcribing RNA polymerase (RNAP) and the negative supercoils accumulating behind impose severe topological constraints impeding transcription process. Previous studies have implied the role of topoisomerases in the removal of torsional stress and the maintenance of template topology but the in vivo interaction of functionally distinct topoisomerases with heterogeneous chromosomal territories is not deciphered. Moreover, how the transcription-induced supercoils influence the genome-wide recruitment of DNA topoisomerases remains to be explored in bacteria. Using ChIP-Seq, we show the genome-wide occupancy profile of both topoisomerase I and DNA gyrase in conjunction with RNAP in Mycobacterium tuberculosis taking advantage of minimal topoisomerase representation in the organism. The study unveils the first in vivo genome-wide interaction of both the topoisomerases with the genomic regions and establishes that transcription-induced supercoils govern their recruitment at genomic sites. Distribution profiles revealed co-localization of RNAP and the two topoisomerases on the active transcriptional units (TUs). At a given locus, topoisomerase I and DNA gyrase were localized behind and ahead of RNAP, respectively, correlating with the twin-supercoiled domains generated. The recruitment of topoisomerases was higher at the genomic loci with higher transcriptional activity and/or at regions under high torsional stress compared to silent genomic loci. Importantly, the occupancy of DNA gyrase, sole type II topoisomerase in Mtb, near the Ter domain of the Mtb chromosome validates its function as a decatenase.

Physical and chemical data collected using bottle casts in a World-wide distribution from NOAA Ship RESEARCHER and other platforms from 1911-11-11 to 1990-03-18 (NODC Accession 9600072)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical and chemical data were collected using bottle casts in a World-wide distribution from NOAA Ship RESEARCHER and other platforms from 11 November 1911 to 18...

Genetic analyses place most Spanish isolates of Beauveria bassiana in a molecular group with word-wide distribution

Science.gov (United States)

2011-01-01

Background The entomopathogenic anamorphic fungus Beauveria bassiana is currently used as a biocontrol agent (BCA) of insects. Fifty-seven Beauveria bassiana isolates -53 from Spain- were characterized, integrating group I intron insertion patterns at the 3'-end of the nuclear large subunit ribosomal gene (LSU rDNA) and elongation factor 1-alpha (EF1-α) phylogenetic information, in order to assess the genetic structure and diversity of this Spanish collection of B. bassiana. Results Group I intron genotype analysis was based on the four highly conserved insertion sites of the LSU (Ec2653, Ec2449, Ec2066, Ec1921). Of the 16 possible combinations/genotypes, only four were detected, two of which were predominant, containing 44 and 9 members out of 57 isolates, respectively. Interestingly, the members of the latter two genotypes showed unique differences in their growth temperatures. In follow, EF1-α phylogeny served to classify most of the strains in the B. bassiana s.s. (sensu stricto) group and separate them into 5 molecular subgroups, all of which contained a group I intron belonging to the IC1 subtype at the Ec1921 position. A number of parameters such as thermal growth or origin (host, geographic location and climatic conditions) were also examined but in general no association could be found. Conclusion Most Spanish B. bassiana isolates (77.2%) are grouped into a major phylogenetic subgroup with word-wide distribution. However, high phylogenetic diversity was also detected among Spanish isolates from close geographic zones with low climatic variation. In general, no correlation was observed between the molecular distribution and geographic origin or climatic characteristics where the Spanish B. bassiana isolates were sampled. PMID:21521527

Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model

Science.gov (United States)

Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan O.; Hasan, Tayyaba

2010-09-01

Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with increasing mean size. At day 10, cultures are treated with either carboplatin or photodynamic therapy (PDT). We quantify size-dependent cytotoxic response for each treatment on a nodule by nodule basis using automated segmentation combined with ratiometric batch-processing of calcein and ethidium bromide fluorescence intensity data (indicating live and dead cells, respectively). Both treatments reduce viability, though carboplatin leaves micronodules largely structurally intact with a size distribution similar to untreated cultures. In contrast, PDT treatment disrupts micronodular structure, causing punctate regions of toxicity, shifting the distribution toward smaller sizes, and potentially increasing vulnerability to subsequent chemotherapeutic treatment.

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa

NARCIS (Netherlands)

Duncan, Laramie; Yilmaz, Zeynep; Gaspar, Helena; Walters, Raymond K.; Goldstein, Jackie; Anttila, Verneri; Bulik-Sullivan, Brendan; Ripke, Stephan; Thornton, Laura M.; Hinney, Anke; Daly, Mark J.; Sullivan, Patrick F; Zeggini, Eleftheria; Breen, Gerome; Bulik, Cynthia M.; Adan, RAH

2017-01-01

Objective: The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. Method: Following uniformquality control and imputation procedures using the 1000 Genomes Project (phase 3) in

Significant locus and metabolic genetic correlations revealed in genome-wide association study of anorexia nervosa

NARCIS (Netherlands)

Duncan, Laramie; Yilmaz, Zeynep; Gaspar, Helena; Walters, Raymond; Goldstein, Jackie; Anttila, Verneri; Bulik-Sullivan, Brendan; Ripke, Stephan; Thornton, Laura; Hinney, Anke; Daly, Mark; Sullivan, Patrick F; Zeggini, Eleftheria; Breen, Gerome; Bulik, Cynthia M; Kas, Martinus J.H.

2017-01-01

OBJECTIVE: The authors conducted a genome-wide association study of anorexia nervosa and calculated genetic correlations with a series of psychiatric, educational, and metabolic phenotypes. METHOD: Following uniform quality control and imputation procedures using the 1000 Genomes Project (phase 3)

Wide Area Network Access to CMS Data Using the Lustre Filesystem

CERN Document Server

Rodríguez, J L; Prescott, C; Wu, Y; Kim, B; Fu, Y; Bourilkov, D; Avery, P

2009-01-01

In this paper, we explore the use of the Lustre cluster filesystem over the wide area network to access Compact Muon Solenoid (CMS) data stored on physical devices located hundreds of kilometres away. We describe the experimental testbed and report on the I/O performance of applications writing and reading data on the distributed Lustre filesystem established across the WAN. We compare the I/O performance of a CMS application to the performance obtained with IOzone, a standard benchmark tool. We then examine the I/O performance of the CMS application running multiple processes on a single server. And compare the Lustre results to results obtained on data stored on local filesystems. Our measurements reveal that the IOzone benchmark tool, accessing data sequentially, can saturate the Gbps network link that connects our Lustre client in Miami Florida to the Lustre storage located in Gainesville, Florida. We also find that the I/O rates of the CMS application is significantly less than what can be obtained with ...

A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol.

Directory of Open Access Journals (Sweden)

Ida Surakka

2011-10-01

Full Text Available Recent genome-wide association (GWA studies described 95 loci controlling serum lipid levels. These common variants explain ∼25% of the heritability of the phenotypes. To date, no unbiased screen for gene-environment interactions for circulating lipids has been reported. We screened for variants that modify the relationship between known epidemiological risk factors and circulating lipid levels in a meta-analysis of genome-wide association (GWA data from 18 population-based cohorts with European ancestry (maximum N = 32,225. We collected 8 further cohorts (N = 17,102 for replication, and rs6448771 on 4p15 demonstrated genome-wide significant interaction with waist-to-hip-ratio (WHR on total cholesterol (TC with a combined P-value of 4.79×10(-9. There were two potential candidate genes in the region, PCDH7 and CCKAR, with differential expression levels for rs6448771 genotypes in adipose tissue. The effect of WHR on TC was strongest for individuals carrying two copies of G allele, for whom a one standard deviation (sd difference in WHR corresponds to 0.19 sd difference in TC concentration, while for A allele homozygous the difference was 0.12 sd. Our findings may open up possibilities for targeted intervention strategies for people characterized by specific genomic profiles. However, more refined measures of both body-fat distribution and metabolic measures are needed to understand how their joint dynamics are modified by the newly found locus.

Distributed Generation (DG) practices in the US

Energy Technology Data Exchange (ETDEWEB)

NONE

2002-05-20

This document forms an annex to a report, 'Technical solutions to enable embedded generation growth', which is one of a series of studies commissioned by the UK Department of Trade and Industry into various aspects of embedded generation with the aim of supporting the development and deployment of electrical sources (particularly their ease of connection to the network) in the UK. The annex describes current practice with distributed generation in the USA. The wide range of practices relating to distributed generation and the lack of a specific government policy to encourage distributed generation are noted. The USA has a wide range of utility practices and a wide range of distributed generation practices are being attempted. The present approach, which is set against the beginnings of deregulation in the USA relies on market forces with a few subsidies.

Weighted Lomax distribution.

Science.gov (United States)

Kilany, N M

2016-01-01

The Lomax distribution (Pareto Type-II) is widely applicable in reliability and life testing problems in engineering as well as in survival analysis as an alternative distribution. In this paper, Weighted Lomax distribution is proposed and studied. The density function and its behavior, moments, hazard and survival functions, mean residual life and reversed failure rate, extreme values distributions and order statistics are derived and studied. The parameters of this distribution are estimated by the method of moments and the maximum likelihood estimation method and the observed information matrix is derived. Moreover, simulation schemes are derived. Finally, an application of the model to a real data set is presented and compared with some other well-known distributions.

A genome wide survey of SNP variation reveals the genetic structure of sheep breeds.

Directory of Open Access Journals (Sweden)

James W Kijas

Full Text Available The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

Genetic evidence for a high diversity and wide distribution of endemic strains of the pathogenic chytrid fungus Batrachochytrium dendrobatidis in wild Asian amphibians.

Science.gov (United States)

Bataille, Arnaud; Fong, Jonathan J; Cha, Moonsuk; Wogan, Guinevere O U; Baek, Hae Jun; Lee, Hang; Min, Mi-Sook; Waldman, Bruce

2013-08-01

Population declines and extinctions of amphibians have been attributed to the chytrid fungus Batrachochytrium dendrobatidis (Bd), especially one globally emerging recombinant lineage ('Bd-GPL'). We used PCR assays that target the ribosomal internal transcribed spacer region (ITS) of Bd to determine the prevalence and genetic diversity of Bd in South Korea, where Bd is widely distributed but is not known to cause morbidity or mortality in wild populations. We isolated Korean Bd strains from native amphibians with low infection loads and compared them to known worldwide Bd strains using 19 polymorphic SNP and microsatellite loci. Bd prevalence ranged between 12.5 and 48.0%, in 11 of 17 native Korean species, and 24.7% in the introduced bullfrog Lithobates catesbeianus. Based on ITS sequence variation, 47 of the 50 identified Korean haplotypes formed a group closely associated with a native Brazilian Bd lineage, separated from the Bd-GPL lineage. However, multilocus genotyping of three Korean Bd isolates revealed strong divergence from both Bd-GPL and the native Brazilian Bd lineages. Thus, the ITS region resolves genotypes that diverge from Bd-GPL but otherwise generates ambiguous phylogenies. Our results point to the presence of highly diversified endemic strains of Bd across Asian amphibian species. The rarity of Bd-GPL-associated haplotypes suggests that either this lineage was introduced into Korea only recently or Bd-GPL has been outcompeted by native Bd strains. Our results highlight the need to consider possible complex interactions among native Bd lineages, Bd-GPL and their associated amphibian hosts when assessing the spread and impact of Bd-GPL on worldwide amphibian populations. © 2013 John Wiley & Sons Ltd.

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

Directory of Open Access Journals (Sweden)

Kevin C. Deitz

2016-09-01

Full Text Available Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

State Electricity Regulatory Policy and Distributed Resources: Accommodating Distributed Resources in Wholesale Markets

Energy Technology Data Exchange (ETDEWEB)

Weston, F.; Harrington, C.; Moskovitz, D.; Shirley, W.; Cowart, R.; Sedano, R.

2002-10-01

Distributed resources can provide cost-effective reliability and energy services - in many cases, obviating the need for more expensive investments in wires and central station electricity generating facilities. Given the unique features of distributed resources, the challenge facing policymakers today is how to restructure wholesale markets for electricity and related services so as to reveal the full value that distributed resources can provide to the electric power system (utility grid). This report looks at the functions that distributed resources can perform and examines the barriers to them. It then identifies a series of policy and operational approaches to promoting DR in wholesale markets. This report is one in the State Electricity Regulatory Policy and Distributed Resources series developed under contract to NREL (see Annual Technical Status Report of the Regulatory Assistance Project: September 2000-September 2001, NREL/SR-560-32733). Other titles in this series are: (1) Distributed Resource Distribution Credit Pilot Programs - Revealing the Value to Consumers and Vendors, NREL/SR-560-32499; (2) Distributed Resources and Electric System Reliability, NREL/SR-560-32498; (3) Distribution System Cost Methodologies for Distributed Generation, NREL/SR-560-32500; (4) Distribution System Cost Methodologies for Distributed Generation Appendices, NREL/SR-560-32501

Temperature, salinity, and nutrients data from CTD and bottle casts from a world-wide distribution from the ANDROMEDA and other platforms from 01 January 1923 to 31 December 1999 (NODC Accession 0000208)

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National Oceanic and Atmospheric Administration, Department of Commerce — CTD and bottle data were collected from the ANDROMEDA and other platforms from a world-wide distribution from 01 January 1923 to 31 December 1999. Data were...

Temperature profile data collected using XBT and BT casts in a World-wide distribution from NOAA Ship RESEARCHER and other platforms from 1970-09-30 to 1979-08-05 (NODC Accession 8300089)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT and BT casts from NOAA Ship RESEARCHER and other platforms in a World-wide distribution from 30 September 1970 to...

The Relationship Between Implementation of School-Wide Positive Behavior Intervention and Supports and Performance on State Accountability Measures

Directory of Open Access Journals (Sweden)

Adriana M. Marin

2013-10-01

Full Text Available This study examined data from 96 schools in a Southeastern U.S. state participating in training and/or coaching on School-Wide Positive Behavioral Interventions and Supports (SWPBIS provided by the State Personnel Development Grant (SPDG in their state. Schools studied either received training only (“non-intensive” sites or training and on-site coaching (“intensive” sites. Fidelity of implementation was self-evaluated by both types of schools using the Benchmarks of Quality (BOQ. Some schools were also externally evaluated using the School-Wide Evaluation Tool (SET, with those scoring 80% or higher determined “model sites.” Using an independent sample t-test, analyses revealed statistically significant differences between intensive and nonintensive schools’ Quality of Distribution Index (QDI scores and between model sites and nonmodel sites on QDI scores. Correlations were performed to determine whether the fidelity of implementation of SWPBIS as measured by the BOQ was related to any of the state’s accountability measures: performance classification, QDI, or growth.

A genome-wide association study reveals a novel candidate gene for sperm motility in pigs

NARCIS (Netherlands)

Diniz, D.B.; Lopes, M.S.; Broekhuijse, M.L.W.J.; Lopes, P.S.; Harlizius, B.; Guimaraes, S.E.F.; Duijvesteijn, N.; Knol, E.F.; Silva, F.F.

2014-01-01

Sperm motility is one of the most widely used parameters in order to evaluate boar semen quality. However, this trait can only be measured after puberty. Thus, the use of genomic information appears as an appealing alternative to evaluate and improve selection for boar fertility traits earlier in

Wide-field lifetime-based FRET imaging for the assessment of early functional distribution of transferrin-based delivery in breast tumor-bearing small animals

Science.gov (United States)

Sinsuebphon, Nattawut; Rudkouskaya, Alena; Barroso, Margarida; Intes, Xavier

2016-02-01

Targeted drug delivery is a critical aspect of successful cancer therapy. Assessment of dynamic distribution of the drug provides relative concentration and bioavailability at the target tissue. The most common approach of the assessment is intensity-based imaging, which only provides information about anatomical distribution. Observation of biomolecular interactions can be performed using Förster resonance energy transfer (FRET). Thus, FRET-based imaging can assess functional distribution and provide potential therapeutic outcomes. In this study, we used wide-field lifetime-based FRET imaging for the study of early functional distribution of transferrin delivery in breast cancer tumor models in small animals. Transferrin is a carrier for cancer drug delivery. Its interaction with its receptor is within a few nanometers, which is suitable for FRET. Alexa Fluor® 700 and Alexa Fluor® 750 were conjugated to holo-transferrin which were then administered via tail vein injection to the mice implanted with T47D breast cancer xenografts. Images were continuously acquired for 60 minutes post-injection. The results showed that transferrin was primarily distributed to the liver, the urinary bladder, and the tumor. The cellular uptake of transferrin, which was indicated by the level of FRET, was high in the liver but very low in the urinary bladder. The results also suggested that the fluorescence intensity and FRET signals were independent. The liver showed increasing intensity and increasing FRET during the observation period, while the urinary bladder showed increasing intensity but minimal FRET. Tumors gave varied results corresponding to their FRET progression. These results were relevant to the biomolecular events that occurred in the animals.

Distribution of unresolvable anisotropic microstructures revealed in visibility-contrast images using x-ray Talbot interferometry

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.

Distributed temperature and distributed acoustic sensing for remote and harsh environments

Science.gov (United States)

Mondanos, Michael; Parker, Tom; Milne, Craig H.; Yeo, Jackson; Coleman, Thomas; Farhadiroushan, Mahmoud

2015-05-01

Advances in opto-electronics and associated signal processing have enabled the development of Distributed Acoustic and Temperature Sensors. Unlike systems relying on discrete optical sensors a distributed system does not rely upon manufactured sensors but utilises passive custom optical fibre cables resistant to harsh environments, including high temperature applications (600°C). The principle of distributed sensing is well known from the distributed temperature sensor (DTS) which uses the interaction of the source light with thermal vibrations (Raman scattering) to determine the temperature at all points along the fibre. Distributed Acoustic Sensing (DAS) uses a novel digital optical detection technique to precisely capture the true full acoustic field (amplitude, frequency and phase) over a wide dynamic range at every point simultaneously. A number of signal processing techniques have been developed to process a large array of acoustic signals to quantify the coherent temporal and spatial characteristics of the acoustic waves. Predominantly these systems have been developed for the oil and gas industry to assist reservoir engineers in optimising the well lifetime. Nowadays these systems find a wide variety of applications as integrity monitoring tools in process vessels, storage tanks and piping systems offering the operator tools to schedule maintenance programs and maximize service life.

Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.

Science.gov (United States)

Shen, Kai; Sayeed, Sameera; Antalis, Patricia; Gladitz, John; Ahmed, Azad; Dice, Bethany; Janto, Benjamin; Dopico, Richard; Keefe, Randy; Hayes, Jay; Johnson, Sandra; Yu, Sujun; Ehrlich, Nathan; Jocz, Jennifer; Kropp, Laura; Wong, Ray; Wadowsky, Robert M; Slifkin, Malcolm; Preston, Robert A; Erdos, Geza; Post, J Christopher; Ehrlich, Garth D; Hu, Fen Z

2006-09-01

The distributed genome hypothesis (DGH) states that each strain within a bacterial species receives a unique distribution of genes from a population-based supragenome that is many times larger than the genome of any given strain. The observations that natural infecting populations are often polyclonal and that most chronic bacterial pathogens have highly developed mechanisms for horizontal gene transfer suggested the DGH and provided the means and the mechanisms to explain how chronic infections persist in the face of a mammalian host's adaptive defense mechanisms. Having previously established the validity of the DGH for obligate pathogens, we wished to evaluate its applicability to an opportunistic bacterial pathogen. This was accomplished by construction and analysis of a highly redundant pooled genomic library containing approximately 216,000 functional clones that was constructed from 12 low-passage clinical isolates of Pseudomonas aeruginosa, 6 otorrheic isolates and 6 from other body sites. Sequence analysis of 3,214 randomly picked clones (mean insert size, approximately 1.4 kb) from this library demonstrated that 348 (10.8%) of the clones were unique with respect to all genomic sequences of the P. aeruginosa prototype strain, PAO1. Hypothetical translations of the open reading frames within these unique sequences demonstrated protein homologies to a number of bacterial virulence factors and other proteins not previously identified in P. aeruginosa. PCR and reverse transcription-PCR-based assays were performed to analyze the distribution and expression patterns of a 70-open reading frame subset of these sequences among 11 of the clinical strains. These sequences were unevenly distributed among the clinical isolates, with nearly half (34/70) of the novel sequences being present in only one or two of the individual strains. Expression profiling revealed that a vast majority of these sequences are expressed, strongly suggesting they encode functional proteins.

Temperature profile data collected using XBT and BT casts in a world-wide distribution from NOAA Ship RESEARCHER and other platforms from 1982-08-18 to 1982-12-21 (NODC Accession 8300007)

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National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT and BT casts from NOAA Ship RESEARCHER and other platforms in a world-wide distribution from 18 August 1982 to 21...

Distribution

Science.gov (United States)

John R. Jones

1985-01-01

Quaking aspen is the most widely distributed native North American tree species (Little 1971, Sargent 1890). It grows in a great diversity of regions, environments, and communities (Harshberger 1911). Only one deciduous tree species in the world, the closely related Eurasian aspen (Populus tremula), has a wider range (Weigle and Frothingham 1911)....

A new method, with application, for analysis of the impacts on flood risk of widely distributed enhanced hillslope storage

Directory of Open Access Journals (Sweden)

P. Metcalfe

2018-04-01

Full Text Available Enhanced hillslope storage is utilised in natural flood management in order to retain overland storm run-off and to reduce connectivity between fast surface flow pathways and the channel. Examples include excavated ponds, deepened or bunded accumulation areas, and gullies and ephemeral channels blocked with wooden barriers or debris dams. The performance of large, distributed networks of such measures is poorly understood. Extensive schemes can potentially retain large quantities of run-off, but there are indications that much of their effectiveness can be attributed to desynchronisation of sub-catchment flood waves. Inappropriately sited measures may therefore increase, rather than mitigate, flood risk. Fully distributed hydrodynamic models have been applied in limited studies but introduce significant computational complexity. The longer run times of such models also restrict their use for uncertainty estimation or evaluation of the many potential configurations and storm sequences that may influence the timings and magnitudes of flood waves.Here a simplified overland flow-routing module and semi-distributed representation of enhanced hillslope storage is developed. It is applied to the headwaters of a large rural catchment in Cumbria, UK, where the use of an extensive network of storage features is proposed as a flood mitigation strategy. The models were run within a Monte Carlo framework against data for a 2-month period of extreme flood events that caused significant damage in areas downstream. Acceptable realisations and likelihood weightings were identified using the GLUE uncertainty estimation framework. Behavioural realisations were rerun against the catchment model modified with the addition of the hillslope storage. Three different drainage rate parameters were applied across the network of hillslope storage. The study demonstrates that schemes comprising widely distributed hillslope storage can be modelled effectively within such a

A new method, with application, for analysis of the impacts on flood risk of widely distributed enhanced hillslope storage

Science.gov (United States)

Metcalfe, Peter; Beven, Keith; Hankin, Barry; Lamb, Rob

2018-04-01

Enhanced hillslope storage is utilised in natural flood management in order to retain overland storm run-off and to reduce connectivity between fast surface flow pathways and the channel. Examples include excavated ponds, deepened or bunded accumulation areas, and gullies and ephemeral channels blocked with wooden barriers or debris dams. The performance of large, distributed networks of such measures is poorly understood. Extensive schemes can potentially retain large quantities of run-off, but there are indications that much of their effectiveness can be attributed to desynchronisation of sub-catchment flood waves. Inappropriately sited measures may therefore increase, rather than mitigate, flood risk. Fully distributed hydrodynamic models have been applied in limited studies but introduce significant computational complexity. The longer run times of such models also restrict their use for uncertainty estimation or evaluation of the many potential configurations and storm sequences that may influence the timings and magnitudes of flood waves. Here a simplified overland flow-routing module and semi-distributed representation of enhanced hillslope storage is developed. It is applied to the headwaters of a large rural catchment in Cumbria, UK, where the use of an extensive network of storage features is proposed as a flood mitigation strategy. The models were run within a Monte Carlo framework against data for a 2-month period of extreme flood events that caused significant damage in areas downstream. Acceptable realisations and likelihood weightings were identified using the GLUE uncertainty estimation framework. Behavioural realisations were rerun against the catchment model modified with the addition of the hillslope storage. Three different drainage rate parameters were applied across the network of hillslope storage. The study demonstrates that schemes comprising widely distributed hillslope storage can be modelled effectively within such a reduced complexity

Collaborative 3D Target Tracking in Distributed Smart Camera Networks for Wide-Area Surveillance

Directory of Open Access Journals (Sweden)

Xenofon Koutsoukos

2013-05-01

Full Text Available With the evolution and fusion of wireless sensor network and embedded camera technologies, distributed smart camera networks have emerged as a new class of systems for wide-area surveillance applications. Wireless networks, however, introduce a number of constraints to the system that need to be considered, notably the communication bandwidth constraints. Existing approaches for target tracking using a camera network typically utilize target handover mechanisms between cameras, or combine results from 2D trackers in each camera into 3D target estimation. Such approaches suffer from scale selection, target rotation, and occlusion, drawbacks typically associated with 2D tracking. In this paper, we present an approach for tracking multiple targets directly in 3D space using a network of smart cameras. The approach employs multi-view histograms to characterize targets in 3D space using color and texture as the visual features. The visual features from each camera along with the target models are used in a probabilistic tracker to estimate the target state. We introduce four variations of our base tracker that incur different computational and communication costs on each node and result in different tracking accuracy. We demonstrate the effectiveness of our proposed trackers by comparing their performance to a 3D tracker that fuses the results of independent 2D trackers. We also present performance analysis of the base tracker along Quality-of-Service (QoS and Quality-of-Information (QoI metrics, and study QoS vs. QoI trade-offs between the proposed tracker variations. Finally, we demonstrate our tracker in a real-life scenario using a camera network deployed in a building.

Two distinct mtDNA lineages of the blue crab reveal large-scale population structure in its native Atlantic distribution

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Alaniz Rodrigues, Marcos; Dumont, Luiz Felipe Cestari; dos Santos, Cléverson Rannieri Meira; D'Incao, Fernando; Weiss, Steven; Froufe, Elsa

2017-10-01

For the first time, a molecular approach was used to evaluate the phylogenetic structure of the disjunct native American distribution of the blue crab Callinectes sapidus. Population structure was investigated by sequencing 648bp of the Cytochrome oxidase subunit 1 (COI), in a total of 138 sequences stemming from individual samples from both the northern and southern hemispheres of the Western Atlantic distribution of the species. A Bayesian approach was used to construct a phylogenetic tree for all samples, and a 95% confidence parsimony network was created to depict the relationship among haplotypes. Results revealed two highly distinct lineages, one containing all samples from the United States and some from Brazil (lineage 1) and the second restricted to Brazil (lineage 2). In addition, gene flow (at least for females) was detected among estuaries at local scales and there is evidence for shared haplotypes in the south. Furthermore, the findings of this investigation support the contemporary introduction of haplotypes that have apparently spread from the south to the north Atlantic.

Genome-wide analysis reveals a cell cycle-dependent mechanism controlling centromere propagation.

Science.gov (United States)

Erhardt, Sylvia; Mellone, Barbara G; Betts, Craig M; Zhang, Weiguo; Karpen, Gary H; Straight, Aaron F

2008-12-01

Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division.

Genome Wide Association Analysis Reveals New Production Trait Genes in a Male Duroc Population.

Directory of Open Access Journals (Sweden)

Kejun Wang

Full Text Available In this study, 796 male Duroc pigs were used to identify genomic regions controlling growth traits. Three production traits were studied: food conversion ratio, days to 100 KG, and average daily gain, using a panel of 39,436 single nucleotide polymorphisms. In total, we detected 11 genome-wide and 162 chromosome-wide single nucleotide polymorphism trait associations. The Gene ontology analysis identified 14 candidate genes close to significant single nucleotide polymorphisms, with growth-related functions: six for days to 100 KG (WT1, FBXO3, DOCK7, PPP3CA, AGPAT9, and NKX6-1, seven for food conversion ratio (MAP2, TBX15, IVL, ARL15, CPS1, VWC2L, and VAV3, and one for average daily gain (COL27A1. Gene ontology analysis indicated that most of the candidate genes are involved in muscle, fat, bone or nervous system development, nutrient absorption, and metabolism, which are all either directly or indirectly related to growth traits in pigs. Additionally, we found four haplotype blocks composed of suggestive single nucleotide polymorphisms located in the growth trait-related quantitative trait loci and further narrowed down the ranges, the largest of which decreased by ~60 Mb. Hence, our results could be used to improve pig production traits by increasing the frequency of favorable alleles via artificial selection.

Using the Pareto principle in genome-wide breeding value estimation.

Science.gov (United States)

Yu, Xijiang; Meuwissen, Theo H E

2011-11-01

Genome-wide breeding value (GWEBV) estimation methods can be classified based on the prior distribution assumptions of marker effects. Genome-wide BLUP methods assume a normal prior distribution for all markers with a constant variance, and are computationally fast. In Bayesian methods, more flexible prior distributions of SNP effects are applied that allow for very large SNP effects although most are small or even zero, but these prior distributions are often also computationally demanding as they rely on Monte Carlo Markov chain sampling. In this study, we adopted the Pareto principle to weight available marker loci, i.e., we consider that x% of the loci explain (100 - x)% of the total genetic variance. Assuming this principle, it is also possible to define the variances of the prior distribution of the 'big' and 'small' SNP. The relatively few large SNP explain a large proportion of the genetic variance and the majority of the SNP show small effects and explain a minor proportion of the genetic variance. We name this method MixP, where the prior distribution is a mixture of two normal distributions, i.e. one with a big variance and one with a small variance. Simulation results, using a real Norwegian Red cattle pedigree, show that MixP is at least as accurate as the other methods in all studied cases. This method also reduces the hyper-parameters of the prior distribution from 2 (proportion and variance of SNP with big effects) to 1 (proportion of SNP with big effects), assuming the overall genetic variance is known. The mixture of normal distribution prior made it possible to solve the equations iteratively, which greatly reduced computation loads by two orders of magnitude. In the era of marker density reaching million(s) and whole-genome sequence data, MixP provides a computationally feasible Bayesian method of analysis.

Screening in larval zebrafish reveals tissue-specific distribution of fifteen fluorescent compounds

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Yuxiao Yao

2017-09-01

Full Text Available The zebrafish is a prominent vertebrate model for low-cost in vivo whole organism screening. In our recent screening of the distribution patterns of fluorescent compounds in live zebrafish larvae, fifteen compounds with tissue-specific distributions were identified. Several compounds were observed to accumulate in tissues where they were reported to induce side-effects, and compounds with similar structures tended to be enriched in the same tissues, with minor differences. In particular, we found three novel red fluorescent bone-staining dyes: purpurin, lucidin and 3-hydroxy-morindone; purpurin can effectively label bones in both larval and adult zebrafish, as well as in postnatal mice, without significantly affecting bone mass and density. Moreover, two structurally similar chemotherapeutic compounds, doxorubicin and epirubicin, were observed to have distinct distribution preferences in zebrafish. Epirubicin maintained a relatively higher concentration in the liver, and performed better in inhibiting hepatic hyperplasia caused by the over-expression of krasG12V. In total, our study suggests that the transparent zebrafish larvae serve as valuable tools for identifying tissue-specific distributions of fluorescent compounds.

Carbon: The Ultimate Electrode Choice for Widely Distributed Polymer Solar Cells

DEFF Research Database (Denmark)

Benatto, Gisele Alves dos Reis; Roth, Bérenger; Madsen, Morten Vesterager

2014-01-01

-, indium tin oxide (ITO)-, and silver-free solar cells in a fully packaged form using only roll-to-roll processing is reported. Replacing silver with carbon as electrode material signifi cantly lowers the manufacturing cost and makes the organic photovoltaic (OPV) modules environmentally safe while...... retaining their fl exibility, active area effi ciency, and stability. The substitution of silver with carbon does not affect the roll-to-roll manufacturing of the modules and allows for the same fast printing and coating. The use of carbon as electrode material is one step closer to the wide release of low...

Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection.

Science.gov (United States)

Yang, Guanhua; Billings, Gabriel; Hubbard, Troy P; Park, Joseph S; Yin Leung, Ka; Liu, Qin; Davis, Brigid M; Zhang, Yuanxing; Wang, Qiyao; Waldor, Matthew K

2017-10-03

Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE). From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant's fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen) collected over a 2-week infection period from a natural host (the flatfish turbot). PACE uncovered more genes that affect E. piscicida 's fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses. IMPORTANCE Transposon insertion sequencing (TIS) enables genome-wide mapping of the genetic determinants of fitness, typically based on observations at a single sampling point. Here, we move beyond analysis of endpoint TIS data to create a framework for analysis of time series TIS data, termed pattern analysis of conditional essentiality (PACE). We applied PACE to identify genes that contribute to colonization of a natural host by the fish pathogen

Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

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Wu-yi Liu

2010-01-01

Full Text Available Members of the basic helix-loop-helix (bHLH family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

Temperature profile data collected using BT and XBT casts in a World-wide distribution from NOAA Ship MALCOLM BALDRIGE and other platforms from 1989-03-10 to 1990-08-01 (NODC Accession 9000239)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT and BT casts from NOAA Ship MALCOLM BALDRDIGE and other platforms in a World-wide distribution from 10 March 1989...

Unsaturated hydraulic properties of Sphagnum moss and peat reveal trimodal pore-size distributions

Science.gov (United States)

Weber, Tobias K. D.; Iden, Sascha C.; Durner, Wolfgang

2017-01-01

In ombrotrophic peatlands, the moisture content of the vadose zone (acrotelm) controls oxygen diffusion rates, redox state, and the turnover of organic matter. Whether peatlands act as sinks or sources of atmospheric carbon thus relies on variably saturated flow processes. The Richards equation is the standard model for water flow in soils, but it is not clear whether it can be applied to simulate water flow in live Sphagnum moss. Transient laboratory evaporation experiments were conducted to observe evaporative water fluxes in the acrotelm, containing living Sphagnum moss, and a deeper layer containing decomposed moss peat. The experimental data were evaluated by inverse modeling using the Richards equation as process model for variably-saturated flow. It was tested whether water fluxes and time series of measured pressure heads during evaporation could be simulated. The results showed that the measurements could be matched very well providing the hydraulic properties are represented by a suitable model. For this, a trimodal parametrization of the underlying pore-size distribution was necessary which reflects three distinct pore systems of the Sphagnum constituted by inter-, intra-, and inner-plant water. While the traditional van Genuchten-Mualem model led to great discrepancies, the physically more comprehensive Peters-Durner-Iden model which accounts for capillary and noncapillary flow, led to a more consistent description of the observations. We conclude that the Richards equation is a valid process description for variably saturated moisture fluxes over a wide pressure range in peatlands supporting the conceptualization of the live moss as part of the vadose zone.

A Comprehensive Survey of Pelagic Megafauna: Their Distribution, Densities, and Taxonomic Richness in the Tropical Southwest Indian Ocean

Directory of Open Access Journals (Sweden)

Sophie Laran

2017-05-01

Full Text Available The distribution and density of pelagic megafauna (marine mammals, seabirds, elasmobranches, and sea turtles are important indicators of marine biodiversity, reflecting the condition of the underlying ecosystems. A dedicated aerial survey was conducted in the tropical Southwest Indian Ocean to map their distribution, the taxonomic diversity, and to estimate their densities to serve as a baseline for the area. This large survey across three ecological sub-regions revealed contrasting spatial distributions: maps of taxonomic richness of marine mammals and seabirds revealed different “hotspots” in the area. Densities were estimated for eight cetacean taxa with small and large Delphininae, or small Globicephalinae dominating, and for seven seabird taxa, with terns and noddies dominating. At the community level, the Southwest Indian Ocean megafauna was structured by the marine environment with strong differences between the Mozambique Channel and the Mascarene Islands, or between shelf and slope/oceanic habitats. Our results illustrate how multi-taxa aerial surveys are relevant and cost-effective monitoring tools for marine megafauna, allowing a community-wide approach.

Temperature profile data collected using BT and XBT casts in a World-wide distribution from NOAA Ship MALCOLM BALDRIGE and other platforms from 1988-02-03 to 1990-03-31 (NODC Accession 9000094)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile data were collected using XBT and BT casts from NOAA Ship MALCOLM BALDRIGE in a World-wide distribution from 03 February 1988 to 31 March 1990....

Distributed Leadership: Friend or Foe?

Science.gov (United States)

Harris, Alma

2013-01-01

Distributed leadership is now widely known and variously enacted in schools and school systems. Distributed leadership implies a fundamental re-conceptualisation of leadership as practice and challenges conventional wisdom about the relationship between formal leadership and organisational performance. There has been much debate, speculation and…

Tourism distribution channels

OpenAIRE

Camilleri, Mark Anthony

2017-01-01

The distribution channels link the customers with the businesses. For many years, the tourism businesses may have distributed their products and services through intermediaries. However, the latest advances in technology have brought significant changes in this regard. More individuals and corporate customers are increasingly benefiting of ubiquitous technologies, including digital media. The development of mobile devices and their applications, are offering a wide range of possibilities to t...

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA

NARCIS (Netherlands)

Amaral, A.J.; Ferretti, L.; Megens, H.J.W.C.; Crooijmans, R.P.M.A.; Nie, H.; Ramos-Onsins, S.E.; Perez-Enciso, M.; Schook, L.B.; Groenen, M.A.M.

2011-01-01

Background Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. Methodology/Main Findings Genome wide footprints of pig domestication and

Distributed power-line outage detection based on wide area measurement system.

Science.gov (United States)

Zhao, Liang; Song, Wen-Zhan

2014-07-21

In modern power grids, the fast and reliable detection of power-line outages is an important functionality, which prevents cascading failures and facilitates an accurate state estimation to monitor the real-time conditions of the grids. However, most of the existing approaches for outage detection suffer from two drawbacks, namely: (i) high computational complexity; and (ii) relying on a centralized means of implementation. The high computational complexity limits the practical usage of outage detection only for the case of single-line or double-line outages. Meanwhile, the centralized means of implementation raises security and privacy issues. Considering these drawbacks, the present paper proposes a distributed framework, which carries out in-network information processing and only shares estimates on boundaries with the neighboring control areas. This novel framework relies on a convex-relaxed formulation of the line outage detection problem and leverages the alternating direction method of multipliers (ADMM) for its distributed solution. The proposed framework invokes a low computational complexity, requiring only linear and simple matrix-vector operations. We also extend this framework to incorporate the sparse property of the measurement matrix and employ the LSQRalgorithm to enable a warm start, which further accelerates the algorithm. Analysis and simulation tests validate the correctness and effectiveness of the proposed approaches.

Genome-wide analysis reveals a cell cycle–dependent mechanism controlling centromere propagation

Science.gov (United States)

Erhardt, Sylvia; Mellone, Barbara G.; Betts, Craig M.; Zhang, Weiguo; Karpen, Gary H.; Straight, Aaron F.

2008-01-01

Centromeres are the structural and functional foundation for kinetochore formation, spindle attachment, and chromosome segregation. In this study, we isolated factors required for centromere propagation using genome-wide RNA interference screening for defects in centromere protein A (CENP-A; centromere identifier [CID]) localization in Drosophila melanogaster. We identified the proteins CAL1 and CENP-C as essential factors for CID assembly at the centromere. CID, CAL1, and CENP-C coimmunoprecipitate and are mutually dependent for centromere localization and function. We also identified the mitotic cyclin A (CYCA) and the anaphase-promoting complex (APC) inhibitor RCA1/Emi1 as regulators of centromere propagation. We show that CYCA is centromere localized and that CYCA and RCA1/Emi1 couple centromere assembly to the cell cycle through regulation of the fizzy-related/CDH1 subunit of the APC. Our findings identify essential components of the epigenetic machinery that ensures proper specification and propagation of the centromere and suggest a mechanism for coordinating centromere inheritance with cell division. PMID:19047461

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

Directory of Open Access Journals (Sweden)

Yong Guo

Full Text Available The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max. In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Genome-wide analysis of SU(VAR)3-9 distribution in chromosomes of Drosophila melanogaster.

Science.gov (United States)

Maksimov, Daniil A; Laktionov, Petr P; Posukh, Olga V; Belyakin, Stepan N; Koryakov, Dmitry E

2018-03-01

Histone modifications represent one of the key factors contributing to proper genome regulation. One of histone modifications involved in gene silencing is methylation of H3K9 residue. Present in the chromosomes across different eukaryotes, this epigenetic mark is controlled by SU(VAR)3-9 and its orthologs. Despite SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic (salivary glands and brain ganglia) and two germline (ovarian nurse cells and testes) tissues of Drosophila melanogaster. Analysis of tissue and developmental expression of SU(VAR)3-9-bound genes indicates that in the somatic tissues tested, as well as in the ovarian nurse cells, SU(VAR)3-9 tends to associate with transcriptionally silent genes. In contrast, in the testes, SU(VAR)3-9 shows preferential association with testis-specific genes, and its binding appears dynamic during spermatogenesis. In somatic cells, the mere presence/absence of SU(VAR)3-9 binding correlates with lower/higher expression. No such correlation is found in the male germline. Interestingly, transcription units in piRNA clusters (particularly flanks thereof) are frequently targeted by SU(VAR)3-9, and Su(var)3-9 mutation affects the expression of select piRNA species. Our analyses suggest a context-dependent role of SU(VAR)3-9. In euchromatin, SU(VAR)3-9 may serve to fine-tune the expression of individual genes, whereas in heterochromatin, chromosome 4, and piRNA clusters, it may act more broadly over large chromatin domains.

New mtDNA data reveal a wide distribution of the Japanese ginbuna Carassius langsdorfii in Europe

Czech Academy of Sciences Publication Activity Database

Kalous, L.; Rylková, K.; Bohlen, Jörg; Šanda, R.; Petrtýl, M.

2013-01-01

Roč. 82, č. 2 (2013), s. 703-707 ISSN 0022-1112 R&D Projects: GA ČR GA206/09/1154 Institutional research plan: CEZ:AV0Z50450515 Keywords : alien species * introduction * molecular genetics Subject RIV: EG - Zoology Impact factor: 1.734, year: 2013

Screening for Total Carotenoids and β-Carotene in Some Widely ...

African Journals Online (AJOL)

machinery and protect them against photo-damage. (Alexander, 1999). Carotenoids are notable for their wide distribution, structural diversity, and of various ... Squash (Curcurbita moschata), Spinach (Amaranthus gangeticus), Tomatoe (Lycopersicon esculentum) and. Waterleaf (Talinum triangulare) were purchased from.

Sexually dimorphic distribution of Prokr2 neurons revealed by the Prokr2-Cre mouse model.

Science.gov (United States)

Mohsen, Zaid; Sim, Hosung; Garcia-Galiano, David; Han, Xingfa; Bellefontaine, Nicole; Saunders, Thomas L; Elias, Carol F

2017-12-01

Prokineticin receptor 2 (PROKR2) is predominantly expressed in the mammalian central nervous system. Loss-of-function mutations of PROKR2 in humans are associated with Kallmann syndrome due to the disruption of gonadotropin releasing hormone neuronal migration and deficient olfactory bulb morphogenesis. PROKR2 has been also implicated in the neuroendocrine control of GnRH neurons post-migration and other physiological systems. However, the brain circuitry and mechanisms associated with these actions have been difficult to investigate mainly due to the widespread distribution of Prokr2-expressing cells, and the lack of animal models and molecular tools. Here, we describe the generation, validation and characterization of a new mouse model that expresses Cre recombinase driven by the Prokr2 promoter, using CRISPR-Cas9 technology. Cre expression was visualized using reporter genes, tdTomato and GFP, in males and females. Expression of Cre-induced reporter genes was found in brain sites previously described to express Prokr2, e.g., the paraventricular and the suprachiasmatic nuclei, and the area postrema. The Prokr2-Cre mouse model was further validated by colocalization of Cre-induced GFP and Prokr2 mRNA. No disruption of Prokr2 expression, GnRH neuronal migration or fertility was observed. Comparative analysis of Prokr2-Cre expression in male and female brains revealed a sexually dimorphic distribution confirmed by in situ hybridization. In females, higher Cre activity was found in the medial preoptic area, ventromedial nucleus of the hypothalamus, arcuate nucleus, medial amygdala and lateral parabrachial nucleus. In males, Cre was higher in the amygdalo-hippocampal area. The sexually dimorphic pattern of Prokr2 expression indicates differential roles in reproductive function and, potentially, in other physiological systems.

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

NARCIS (Netherlands)

K. Estrada Gil (Karol); U. Styrkarsdottir (Unnur); E. Evangelou (Evangelos); Y.-H. Hsu (Yi-Hsiang); E.L. Duncan (Emma); E.E. Ntzani (Evangelia); L. Oei (Ling); O.M.E. Albagha (Omar M.); N. Amin (Najaf); J.P. Kemp (John); D.L. Koller (Daniel); G. Li (Guo); C.-T. Liu (Ching-Ti); R.L. Minster (Ryan); A. Moayyeri (Alireza); L. Vandenput (Liesbeth); D. Willner (Dana); S.-M. Xiao (Su-Mei); L.M. Yerges-Armstrong (Laura); H.-F. Zheng (Hou-Feng); N. Alonso (Nerea); J. Eriksson (Joel); C.M. Kammerer (Candace); S. Kaptoge (Stephen); P.J. Leo (Paul); G. Thorleifsson (Gudmar); S.G. Wilson (Scott); J.F. Wilson (James); V. Aalto (Ville); T.A. van Alen (Theo); A.K. Aragaki (Aaron); T. Aspelund (Thor); J.R. Center (Jacqueline); Z. Dailiana (Zoe); C. Duggan; M. Garcia (Melissa); N. Garcia-Giralt (Natàlia); S. Giroux (Sylvie); G. Hallmans (Göran); L.J. Hocking (Lynne); L.B. Husted (Lise Bjerre); K. Jameson (Karen); R. Khusainova (Rita); G.S. Kim (Ghi Su); C. Kooperberg (Charles); T. Koromila (Theodora); M. Kruk (Marcin); M. Laaksonen (Marika); A.Z. LaCroix (Andrea); S.U. Lee (Seung); P.C. Leung (Ping); J.R. Lewis (Joshua); L. Masi (Laura); S. Mencej-Bedrac (Simona); T.V. Nguyen (Tuan); X. Nogues (Xavier); M.S. Patel (Millan); J. Prezelj (Janez); L.M. Rose (Lynda); S. Scollen (Serena); K. Siggeirsdottir (Kristin); G.D. Smith; O. Svensson (Olle); S. Trompet (Stella); O. Trummer (Olivia); N.M. van Schoor (Natasja); M.M. Woo (Margaret M.); K. Zhu (Kun); S. Balcells (Susana); M.L. Brandi; B.M. Buckley (Brendan M.); S. Cheng (Sulin); C. Christiansen; C. Cooper (Charles); G.V. Dedoussis (George); I. Ford (Ian); M. Frost (Morten); D. Goltzman (David); J. González-Macías (Jesús); M. Kähönen (Mika); M. Karlsson (Magnus); E.K. Khusnutdinova (Elza); J.-M. Koh (Jung-Min); P. Kollia (Panagoula); B.L. Langdahl (Bente); W.D. Leslie (William); P. Lips (Paul); O. Ljunggren (Östen); R. Lorenc (Roman); J. Marc (Janja); D. Mellström (Dan); B. Obermayer-Pietsch (Barbara); D. Olmos (David); U. Pettersson-Kymmer (Ulrika); D.M. Reid (David); J.A. Riancho (José); P.M. Ridker (Paul); M.F. Rousseau (Francois); P.E.S. Lagboom (P Eline); N.L.S. Tang (Nelson L.); R. Urreizti (Roser); W. Van Hul (Wim); J. Viikari (Jorma); M.T. Zarrabeitia (María); Y.S. Aulchenko (Yurii); M.C. Castaño Betancourt (Martha); E. Grundberg (Elin); L. Herrera (Lizbeth); T. Ingvarsson (Torvaldur); H. Johannsdottir (Hrefna); T. Kwan (Tony); R. Li (Rui); R.N. Luben (Robert); M.C. Medina-Gomez (Carolina); S. Th Palsson (Stefan); S. Reppe (Sjur); J.I. Rotter (Jerome); G. Sigurdsson (Gunnar); J.B.J. van Meurs (Joyce); D.J. Verlaan (Dominique); F.M. Williams (Frances); A.R. Wood (Andrew); Y. Zhou (Yanhua); K.M. Gautvik (Kaare); T. Pastinen (Tomi); S. Raychaudhuri (Soumya); J.A. Cauley (Jane); D.I. Chasman (Daniel); G.R. Clark (Graeme); S. Cummings; P. Danoy (Patrick); E.M. Dennison (Elaine); R. Eastell (Richard); J.A. Eisman (John); V. Gudnason (Vilmundur); A. Hofman (Albert); R.D. Jackson (Rebecca); G. Jones (Graeme); J.W. Jukema (Jan Wouter); K-T. Khaw (Kay-Tee); T. Lehtimäki (Terho); Y. Liu (YongMei); M. Lorentzon (Mattias); E.V. McCloskey (Eugene); B.D. Mitchell (Braxton); K. Nandakumar (Kannabiran); G.C. Nicholson (Geoffrey); B.A. Oostra (Ben); M. Peacock (Munro); H.A.P. Pols (Huib); R.L. Prince (Richard); O. Raitakari (Olli); I.R. Reid (Ian); J. Robbins (John); P.N. Sambrook (Philip); P.C. Sham (Pak); A.R. Shuldiner (Alan); F.A. Tylavsky (Frances); C.M. van Duijn (Cornelia); N.J. Wareham (Nick); L.A. Cupples (Adrienne); M.J. Econs (Michael); D.M. Evans (David); T.B. Harris (Tamara); A.W.C. Kung (Annie); B.M. Psaty (Bruce); J. Reeve (Jonathan); T.D. Spector (Timothy); E.A. Streeten (Elizabeth); M.C. Zillikens (Carola); U. Thorsteinsdottir (Unnur); C. Ohlsson (Claes); D. Karasik (David); J.B. Richards (Brent); M.A. Brown (Matthew); J-A. Zwart (John-Anker); A.G. Uitterlinden (André); S.H. Ralston (Stuart); J.P.A. Ioannidis (John); D.P. Kiel (Douglas); F. Rivadeneira Ramirez (Fernando)

2012-01-01

textabstractBone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top

Mechanistic species distribution modeling reveals a niche shift during invasion.

Science.gov (United States)

Chapman, Daniel S; Scalone, Romain; Štefanić, Edita; Bullock, James M

2017-06-01

Niche shifts of nonnative plants can occur when they colonize novel climatic conditions. However, the mechanistic basis for niche shifts during invasion is poorly understood and has rarely been captured within species distribution models. We quantified the consequence of between-population variation in phenology for invasion of common ragweed (Ambrosia artemisiifolia L.) across Europe. Ragweed is of serious concern because of its harmful effects as a crop weed and because of its impact on public health as a major aeroallergen. We developed a forward mechanistic species distribution model based on responses of ragweed development rates to temperature and photoperiod. The model was parameterized and validated from the literature and by reanalyzing data from a reciprocal common garden experiment in which native and invasive populations were grown within and beyond the current invaded range. It could therefore accommodate between-population variation in the physiological requirements for flowering, and predict the potentially invaded ranges of individual populations. Northern-origin populations that were established outside the generally accepted climate envelope of the species had lower thermal requirements for bud development, suggesting local adaptation of phenology had occurred during the invasion. The model predicts that this will extend the potentially invaded range northward and increase the average suitability across Europe by 90% in the current climate and 20% in the future climate. Therefore, trait variation observed at the population scale can trigger a climatic niche shift at the biogeographic scale. For ragweed, earlier flowering phenology in established northern populations could allow the species to spread beyond its current invasive range, substantially increasing its risk to agriculture and public health. Mechanistic species distribution models offer the possibility to represent niche shifts by varying the traits and niche responses of individual

Genome-wide identification and characterization of WRKY gene family in peanut

Directory of Open Access Journals (Sweden)

Hui eSong

2016-04-01

Full Text Available WRKY, an important transcription factor family, is widely distributed in the plant kingdom. Many reports focused on analysis of phylogenetic relationship and biological function of WRKY protein at the whole genome level in different plant species. However, little is known about WRKY proteins in the genome of Arachis species and their response to salicylic acid (SA and jasmonic acid (JA treatment. In this study, we identified 77 and 75 WRKY proteins from the two wild ancestral diploid genomes of cultivated tetraploid peanut, Arachis duranensis and Arachis ipaënsis, using bioinformatics approaches. Most peanut WRKY coding genes were located on A. duranensis chromosome A6 and A. ipaënsis chromosome B3, while the least number of WRKY genes was found in chromosome 9. The WRKY orthologous gene pairs in A. duranensis and A. ipaënsis chromosomes were highly syntenic. Our analysis indicated that segmental duplication events played a major role in AdWRKY and AiWRKY genes, and strong purifying selection was observed in gene duplication pairs. Furthermore, we translate the knowledge gained from the genome-wide analysis result of wild ancestral peanut to cultivated peanut to reveal that gene activities of specific cultivated peanut WRKY gene were changed due to SA and JA treatment. Peanut WRKY7, 8 and 13 genes were down-regulated, whereas WRKY1 and 12 genes were up-regulated with SA and JA treatment. These results could provide valuable information for peanut improvement.

Genome-Wide Identification and Characterization of WRKY Gene Family in Peanut.

Science.gov (United States)

Song, Hui; Wang, Pengfei; Lin, Jer-Young; Zhao, Chuanzhi; Bi, Yuping; Wang, Xingjun

2016-01-01

WRKY, an important transcription factor family, is widely distributed in the plant kingdom. Many reports focused on analysis of phylogenetic relationship and biological function of WRKY protein at the whole genome level in different plant species. However, little is known about WRKY proteins in the genome of Arachis species and their response to salicylic acid (SA) and jasmonic acid (JA) treatment. In this study, we identified 77 and 75 WRKY proteins from the two wild ancestral diploid genomes of cultivated tetraploid peanut, Arachis duranensis and Arachis ipaënsis, using bioinformatics approaches. Most peanut WRKY coding genes were located on A. duranensis chromosome A6 and A. ipaënsis chromosome B3, while the least number of WRKY genes was found in chromosome 9. The WRKY orthologous gene pairs in A. duranensis and A. ipaënsis chromosomes were highly syntenic. Our analysis indicated that segmental duplication events played a major role in AdWRKY and AiWRKY genes, and strong purifying selection was observed in gene duplication pairs. Furthermore, we translate the knowledge gained from the genome-wide analysis result of wild ancestral peanut to cultivated peanut to reveal that gene activities of specific cultivated peanut WRKY gene were changed due to SA and JA treatment. Peanut WRKY7, 8 and 13 genes were down-regulated, whereas WRKY1 and 12 genes were up-regulated with SA and JA treatment. These results could provide valuable information for peanut improvement.

Global Distribution and Vertical Structure of Clouds Revealed by CALIPSO

Science.gov (United States)

Yi, Y.; Minnis, P.; Winker, D.; Huang, J.; Sun-Mack, S.; Ayers, K.

2007-12-01

Understanding the effects of clouds on Earth's radiation balance, especially on longwave fluxes within the atmosphere, depends on having accurate knowledge of cloud vertical location within the atmosphere. The Cloud- Aerosol Lidar and Infrared Pathfinder Satellite Observations (CALIPSO) satellite mission provides the opportunity to measure the vertical distribution of clouds at a greater detail than ever before possible. The CALIPSO cloud layer products from June 2006 to June 2007 are analyzed to determine the occurrence frequency and thickness of clouds as functions of time, latitude, and altitude. In particular, the latitude-longitude and vertical distributions of single- and multi-layer clouds and the latitudinal movement of cloud cover with the changing seasons are examined. The seasonal variablities of cloud frequency and geometric thickness are also analyzed and compared with similar quantities derived from the Aqua Moderate Resolution Imaging Spectroradiometer (MODIS) using the Clouds and the Earth's Radiant Energy System (CERES) cloud retrieval algorithms. The comparisons provide an estimate of the errors in cloud fraction, top height, and thickness incurred by passive algorithms.

Genome-wide allelotyping of a new in vitro model system reveals early events in breast cancer progression.

Science.gov (United States)

Li, Zheng; Meng, Zhen Hang; Sayeed, Aejaz; Shalaby, Refaat; Ljung, Britt-Marie; Dairkee, Shanaz H

2002-10-15

Toward the goal of identifying early genetic losses, which mediate the release of human breast epithelium from replicative suppression leading to cellular immortalization, we have used a newly developed in vitro model system. This system consists of epithelial cultures derived from noncancerous breast tissue, treated with the chemical carcinogen N-ethyl-N-nitrosourea, and continuously passaged to yield cell populations culminating in the immortal phenotype. Genome-wide allelotyping of early passage N-ethyl-N-nitrosourea-exposed cell populations revealed aberrations at >10% (18 of 169) loci examined. Allelic losses encompassing chromosomes 6q24-6q27, implicating immortalization-associated candidate genes, hZAC and SEN6, occurred in two independently derived cell lines before the Hayflick limit. Additional LOH sites were present in one cell line at 3p11-3p26, 11p15, and 20p12-13. Allelic losses reported in this cell line preceded detectable levels of telomerase activity and the occurrence of p53-related aberrations. Information gained from the search for early immortalization-associated genetic deletions in cultured cells was applied in a novel approach toward the analysis of morphologically normal terminal ductal lobular units microdissected from 20 cases of ductal carcinoma in situ. Notably, clonal allelic losses at chromosome 3p24 and 6q24 were an early occurrence in adjoining terminal ductal lobular units of a proportion of primary tumors, which displayed loss of heterozygosity (3 of 11 and 3 of 6, respectively). The biological insights provided by the new model system reported here strongly suggest that early allelic losses delineated in immortalized cultures and validated in vivo could serve as surrogate endpoints to assist in the identification and intervention of high-risk benign breast tissue, which sustains the potential for continuous proliferation.

SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis.

Science.gov (United States)

Kang, Xincong; Hu, Liqin; Shen, Pengyuan; Li, Rui; Liu, Dongbo

2017-01-01

Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis , with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3 , 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis , and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO 2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture

DEFF Research Database (Denmark)

Estrada, Karol; Styrkarsdottir, Unnur; Evangelou, Evangelos

2012-01-01

Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associ...

Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer's disease.

Science.gov (United States)

Watson, Corey T; Roussos, Panos; Garg, Paras; Ho, Daniel J; Azam, Nidha; Katsel, Pavel L; Haroutunian, Vahram; Sharp, Andrew J

2016-01-19

Alzheimer's disease affects ~13% of people in the United States 65 years and older, making it the most common neurodegenerative disorder. Recent work has identified roles for environmental, genetic, and epigenetic factors in Alzheimer's disease risk. We performed a genome-wide screen of DNA methylation using the Illumina Infinium HumanMethylation450 platform on bulk tissue samples from the superior temporal gyrus of patients with Alzheimer's disease and non-demented controls. We paired a sliding window approach with multivariate linear regression to characterize Alzheimer's disease-associated differentially methylated regions (DMRs). We identified 479 DMRs exhibiting a strong bias for hypermethylated changes, a subset of which were independently associated with aging. DMR intervals overlapped 475 RefSeq genes enriched for gene ontology categories with relevant roles in neuron function and development, as well as cellular metabolism, and included genes reported in Alzheimer's disease genome-wide and epigenome-wide association studies. DMRs were enriched for brain-specific histone signatures and for binding motifs of transcription factors with roles in the brain and Alzheimer's disease pathology. Notably, hypermethylated DMRs preferentially overlapped poised promoter regions, marked by H3K27me3 and H3K4me3, previously shown to co-localize with aging-associated hypermethylation. Finally, the integration of DMR-associated single nucleotide polymorphisms with Alzheimer's disease genome-wide association study risk loci and brain expression quantitative trait loci highlights multiple potential DMRs of interest for further functional analysis. We have characterized changes in DNA methylation in the superior temporal gyrus of patients with Alzheimer's disease, highlighting novel loci that facilitate better characterization of pathways and mechanisms underlying Alzheimer's disease pathogenesis, and improve our understanding of epigenetic signatures that may contribute to the

A WIDE DISTRIBUTION OF A NEW VRN-B1c ALLELE OF WHEAT TRITICUM AESTIVUM L. IN RUSSIA, UKRAINE AND ADJACENT REGIONS: A LINK WITH THE HEADING TIME AND ADAPTIVE POTENTIAL

Directory of Open Access Journals (Sweden)

Shcherban A.

2012-08-01

Full Text Available The adaptation of common wheat (T. aestivum L. to diverse environmental conditions is greatly under the control of genes involved in determination of vernalization response (Vrn-1 genes. It was found that the variation in common wheat heading time is affected not only by combination of Vrn-1 homoeoalleles but also by multiple alleles at a separate Vrn-1 locus. Previously, we described the Vrn-B1c allele from T.aestivum cv. 'Saratovskaya 29' and found significant differences in the structure of the first (1st intron of this allele when compared to another highly abundant Vrn-B1a allele, specifically, the deletion of 0.8 kb coupled with the duplication of 0.4 kb. We suggested that the changes in the intron 1 of Vrn-B1c allele caused earlier ear emergence in the near-isogenic line and cultivars, carrying this allele. In this study we investigate the distribution of the Vrn-B1c allele in a wide set of spring wheat cultivars from Russia, Ukraine and adjacent regions. The analysis revealed that 40% of Russian and 53% of Ukranian spring wheat cultivars contain the Vrn-B1c allele. The high distribution of the Vrn-B1c allele can be explained by a frequent using of 'Saratovskaya 29' in the breeding process inside the studied area. From the other hand, the predominance of the Vrn-B1c allele among cultivars cultivated in West Siberia and Kazakhstan may be due to the selective advantage of this allele for the region where there is a high risk of early fall frosts.

Fitting statistical distributions the generalized lambda distribution and generalized bootstrap methods

CERN Document Server

Karian, Zaven A

2000-01-01

Throughout the physical and social sciences, researchers face the challenge of fitting statistical distributions to their data. Although the study of statistical modelling has made great strides in recent years, the number and variety of distributions to choose from-all with their own formulas, tables, diagrams, and general properties-continue to create problems. For a specific application, which of the dozens of distributions should one use? What if none of them fit well?Fitting Statistical Distributions helps answer those questions. Focusing on techniques used successfully across many fields, the authors present all of the relevant results related to the Generalized Lambda Distribution (GLD), the Generalized Bootstrap (GB), and Monte Carlo simulation (MC). They provide the tables, algorithms, and computer programs needed for fitting continuous probability distributions to data in a wide variety of circumstances-covering bivariate as well as univariate distributions, and including situations where moments do...

Transformation of an empirical distribution to normal distribution by the use of Johnson system of translation and symmetrical quantile method

OpenAIRE

Ludvík Friebel; Jana Friebelová

2006-01-01

This article deals with approximation of empirical distribution to standard normal distribution using Johnson transformation. This transformation enables us to approximate wide spectrum of continuous distributions with a normal distribution. The estimation of parameters of transformation formulas is based on percentiles of empirical distribution. There are derived theoretical probability distribution functions of random variable obtained on the base of backward transformation standard normal ...

Temperature, salinity, and nutrients data from CTD and bottle casts from a world-wide distribution from the CORNIDE DE SAAVEDRA and other platforms from 01 January 1914 to 12 December 1999 (NODC Accession 0000207)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — CTD, bottle, and other data were collected from the CORNIDE DE SAAVEDRA and other platforms from a world-wide distribution from 01 January 1914 to 31 December 1999....

Coal distribution, January--June 1990

Energy Technology Data Exchange (ETDEWEB)

1990-10-17

The Coal Distribution report provides information on coal production, distribution, and stocks in the United States to a wide audience including Congress, federal and state agencies, the coal industry, and the general public. This issue presents information for January through June 1990. Coal distribution data are shown (in tables 1--34) by coal-producing state of origin, consumer use, method of transportation, and state of destination. 6 figs., 34 tabs.

Distributed Energy Generation for Climate Resilience

Energy Technology Data Exchange (ETDEWEB)

Stout, Sherry; Hotchkiss, Eliza

2017-05-24

Distributed generation can play a critical role in supporting climate adaptation goals. This infographic style poster will showcase the role of distributed generation in achieving a wide range of technical and policy goals and social services associated with climate adaptation.

Nonmydriatic fluorescence-based quantitative imaging of human macular pigment distributions

Science.gov (United States)

Sharifzadeh, Mohsen; Bernstein, Paul S.; Gellermann, Werner

2006-10-01

We have developed a CCD-camera-based nonmydriatic instrument that detects fluorescence from retinal lipofuscin chromophores ("autofluorescence") as a means to indirectly quantify and spatially image the distribution of macular pigment (MP). The lipofuscin fluorescence intensity is reduced at all retinal locations containing MP, since MP has a competing absorption in the blue-green wavelength region. Projecting a large diameter, 488 nm excitation spot onto the retina, centered on the fovea, but extending into the macular periphery, and comparing lipofuscin fluorescence intensities outside and inside the foveal area, it is possible to spatially map out the distribution of MP. Spectrally selective detection of the lipofuscin fluorescence reveals an important wavelength dependence of the obtainable image contrast and deduced MP optical density levels, showing that it is important to block out interfering fluorescence contributions in the detection setup originating from ocular media such as the lens. Measuring 70 healthy human volunteer subjects with no ocular pathologies, we find widely varying spatial extent of MP, distinctly differing distribution patterns of MP, and strongly differing absolute MP levels among individuals. Our population study suggests that MP imaging based on lipofuscin fluorescence is useful as a relatively simple, objective, and quantitative noninvasive optical technique suitable to rapidly screen MP levels and distributions in healthy humans with undilated pupils.

The Geographic Distribution of Saccharomyces cerevisiae Isolates within three Italian Neighboring Winemaking Regions Reveals Strong Differences in Yeast Abundance, Genetic Diversity and Industrial Strain Dissemination

Directory of Open Access Journals (Sweden)

Alessia Viel

2017-08-01

Full Text Available In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota.

Genome-wide meta-analysis in alopecia areata resolves HLA associations and reveals two new susceptibility loci

NARCIS (Netherlands)

Betz, Regina C; Petukhova, Lynn; Ripke, Stephan; Huang, Hailiang; Menelaou, Androniki; Redler, Silke; Becker, Tim; Heilmann, Stefanie; Yamany, Tarek; Duvic, Madeliene; Hordinsky, Maria; Norris, David; Price, Vera H; Mackay-Wiggan, Julian; de Jong, Annemieke; DeStefano, Gina M; Moebus, Susanne; Böhm, Markus; Blume-Peytavi, Ulrike; Wolff, Hans; Lutz, Gerhard; Kruse, Roland; Bian, Li; Amos, Christopher I; Lee, Annette; Gregersen, Peter K; Blaumeiser, Bettina; Altshuler, David; Clynes, Raphael; de Bakker, Paul I W; Nöthen, Markus M; Daly, Mark J; Christiano, Angela M

2015-01-01

Alopecia areata (AA) is a prevalent autoimmune disease with 10 known susceptibility loci. Here we perform the first meta-analysis of research on AA by combining data from two genome-wide association studies (GWAS), and replication with supplemented ImmunoChip data for a total of 3,253 cases and

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution

DEFF Research Database (Denmark)

Heid, Iris M; Jackson, Anne U; Randall, Joshua C

2010-01-01

and CPEB4 (P = 1.9 × 10¿¿ to P = 1.8 × 10¿4°) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 × 10¿³ to P = 1.2 × 10¿¹³). These findings provide evidence for multiple loci that modulate...... body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions....

A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

Science.gov (United States)

Zila, Charles T.; Samayoa, L. Fernando; Santiago, Rogelio; Butrón, Ana; Holland, James B.

2013-01-01

Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 single-nucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0–100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools. PMID:24048647

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

Directory of Open Access Journals (Sweden)

Meghann K. Devlin-Durante

2017-11-01

Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

Science.gov (United States)

Devlin-Durante, Meghann K; Baums, Iliana B

2017-01-01

The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

A genome-wide association study reveals variants in ARL15 that influence adiponectin levels.

Directory of Open Access Journals (Sweden)

J Brent Richards

2009-12-01

Full Text Available The adipocyte-derived protein adiponectin is highly heritable and inversely associated with risk of type 2 diabetes mellitus (T2D and coronary heart disease (CHD. We meta-analyzed 3 genome-wide association studies for circulating adiponectin levels (n = 8,531 and sought validation of the lead single nucleotide polymorphisms (SNPs in 5 additional cohorts (n = 6,202. Five SNPs were genome-wide significant in their relationship with adiponectin (P< or =5x10(-8. We then tested whether these 5 SNPs were associated with risk of T2D and CHD using a Bonferroni-corrected threshold of P< or =0.011 to declare statistical significance for these disease associations. SNPs at the adiponectin-encoding ADIPOQ locus demonstrated the strongest associations with adiponectin levels (P-combined = 9.2x10(-19 for lead SNP, rs266717, n = 14,733. A novel variant in the ARL15 (ADP-ribosylation factor-like 15 gene was associated with lower circulating levels of adiponectin (rs4311394-G, P-combined = 2.9x10(-8, n = 14,733. This same risk allele at ARL15 was also associated with a higher risk of CHD (odds ratio [OR] = 1.12, P = 8.5x10(-6, n = 22,421 more nominally, an increased risk of T2D (OR = 1.11, P = 3.2x10(-3, n = 10,128, and several metabolic traits. Expression studies in humans indicated that ARL15 is well-expressed in skeletal muscle. These findings identify a novel protein, ARL15, which influences circulating adiponectin levels and may impact upon CHD risk.

Genome-wide association analysis reveals putative Alzheimer's disease susceptibility loci in addition to APOE.

Science.gov (United States)

Bertram, Lars; Lange, Christoph; Mullin, Kristina; Parkinson, Michele; Hsiao, Monica; Hogan, Meghan F; Schjeide, Brit M M; Hooli, Basavaraj; Divito, Jason; Ionita, Iuliana; Jiang, Hongyu; Laird, Nan; Moscarillo, Thomas; Ohlsen, Kari L; Elliott, Kathryn; Wang, Xin; Hu-Lince, Diane; Ryder, Marie; Murphy, Amy; Wagner, Steven L; Blacker, Deborah; Becker, K David; Tanzi, Rudolph E

2008-11-01

Alzheimer's disease (AD) is a genetically complex and heterogeneous disorder. To date four genes have been established to either cause early-onset autosomal-dominant AD (APP, PSEN1, and PSEN2(1-4)) or to increase susceptibility for late-onset AD (APOE5). However, the heritability of late-onset AD is as high as 80%, (6) and much of the phenotypic variance remains unexplained to date. We performed a genome-wide association (GWA) analysis using 484,522 single-nucleotide polymorphisms (SNPs) on a large (1,376 samples from 410 families) sample of AD families of self-reported European descent. We identified five SNPs showing either significant or marginally significant genome-wide association with a multivariate phenotype combining affection status and onset age. One of these signals (p = 5.7 x 10(-14)) was elicited by SNP rs4420638 and probably reflects APOE-epsilon4, which maps 11 kb proximal (r2 = 0.78). The other four signals were tested in three additional independent AD family samples composed of nearly 2700 individuals from almost 900 families. Two of these SNPs showed significant association in the replication samples (combined p values 0.007 and 0.00002). The SNP (rs11159647, on chromosome 14q31) with the strongest association signal also showed evidence of association with the same allele in GWA data generated in an independent sample of approximately 1,400 AD cases and controls (p = 0.04). Although the precise identity of the underlying locus(i) remains elusive, our study provides compelling evidence for the existence of at least one previously undescribed AD gene that, like APOE-epsilon4, primarily acts as a modifier of onset age.

Revealing hidden effect of earthworm on C distribution and enzyme activity

Science.gov (United States)

Razavi, Bahar S.; Hoang, Duyen; Kuzyakov, Yakov

2017-04-01

Despite its importance for terrestrial nutrient and carbon cycling, the spatial organization and localization of microbial activity in soil and in biopores is poorly understood. We hypothesized that biopores created by earthworm play a critical role in reducing the gap of SOM input and microbial activities between topsoil and subsoil. Accordingly, Carbon (C) allocation by earthworms was related to enzyme distribution along soil profile. For the first time we visualized spatial distribution of enzyme activities (β-glucosidase, chitinase and acid phosphatase) and C allocation (by 14C imaging) in earthworm biopores in topsoil and subsoil. Soil zymography (an in situ method for the analysis of the two-dimensional distribution of enzyme activity in soil) was accompanied with 14C imaging (a method that enables to trace distribution of litter and C in soil profile) to visualize change of enzyme activities along with SOM incorporation by earthworms from topsoil to subsoil. Experiment was set up acquiring rhizoboxes (9×1×50 cm) filled up with fresh soil and 3 earthworms (L. terrestris), which were then layered with 14C-labeled plant-litter of 0.3 MBq on the soil surface. 14C imaging and zymography have been carried out after one month. Activities of all enzymes regardless of their nutrient involvement (C, N, P) were higher in the biopores than in bulk soil, but the differences were larger in topsoil compared to subsoil. Among three enzymes, Phosphatase activity was 4-times higher in the biopore than in the bulk soil. Phosphatase activity was closely associated with edge of burrows and correlate positively with 14C activity. These results emphasized especial contribution of hotspheres such as biopores to C allocation in subsoil - which is limited in C input and nutrients - and in stimulation of microbial and enzymatic activity by input of organic residues, e.g. by earthworms. In conclusion, biopore increased enzymatic mobilization of nutrients (e.g. P) inducing allocation

GWAMA: software for genome-wide association meta-analysis

Directory of Open Access Journals (Sweden)

Mägi Reedik

2010-05-01

Full Text Available Abstract Background Despite the recent success of genome-wide association studies in identifying novel loci contributing effects to complex human traits, such as type 2 diabetes and obesity, much of the genetic component of variation in these phenotypes remains unexplained. One way to improving power to detect further novel loci is through meta-analysis of studies from the same population, increasing the sample size over any individual study. Although statistical software analysis packages incorporate routines for meta-analysis, they are ill equipped to meet the challenges of the scale and complexity of data generated in genome-wide association studies. Results We have developed flexible, open-source software for the meta-analysis of genome-wide association studies. The software incorporates a variety of error trapping facilities, and provides a range of meta-analysis summary statistics. The software is distributed with scripts that allow simple formatting of files containing the results of each association study and generate graphical summaries of genome-wide meta-analysis results. Conclusions The GWAMA (Genome-Wide Association Meta-Analysis software has been developed to perform meta-analysis of summary statistics generated from genome-wide association studies of dichotomous phenotypes or quantitative traits. Software with source files, documentation and example data files are freely available online at http://www.well.ox.ac.uk/GWAMA.

Escherichia coli type III secretion system 2 (ETT2) is widely distributed in avian pathogenic Escherichia coli isolates from Eastern China.

Science.gov (United States)

Wang, S; Liu, X; Xu, X; Zhao, Y; Yang, D; Han, X; Tian, M; Ding, C; Peng, D; Yu, S

2016-10-01

Pathogens utilize type III secretion systems to deliver effector proteins, which facilitate bacterial infections. The Escherichia coli type III secretion system 2 (ETT2) which plays a crucial role in bacterial virulence, is present in the majority of E. coli strains, although ETT2 has undergone widespread mutational attrition. We investigated the distribution and characteristics of ETT2 in avian pathogenic E. coli (APEC) isolates and identified five different ETT2 isoforms, including intact ETT2, in 57·6% (141/245) of the isolates. The ETT2 locus was present in the predominant APEC serotypes O78, O2 and O1. All of the ETT2 loci in the serotype O78 isolates were degenerate, whereas an intact ETT2 locus was mostly present in O1 and O2 serotype strains, which belong to phylogenetic groups B2 and D, respectively. Interestingly, a putative second type III secretion-associated locus (eip locus) was present only in the isolates with an intact ETT2. Moreover, ETT2 was more widely distributed in APEC isolates and exhibited more isoforms compared to ETT2 in human extraintestinal pathogenic E. coli, suggesting that APEC might be a potential risk to human health. However, there was no distinct correlation between ETT2 and other virulence factors in APEC.

Novel distributed strain sensing in polymeric materials

International Nuclear Information System (INIS)

Abot, Jandro L; Song, Yi; Medikonda, Sandeep; Rooy, Nathan; Schulz, Mark J

2010-01-01

Monitoring the state of strain throughout an entire structure is essential to determine its state of stress, detect potential residual stresses after fabrication, and also to help to establish its integrity. Several sensing technologies are presently available to determine the strain in the surface or inside a structure. Large sensor dimensions, complex signal conditioning equipment, and difficulty in achieving a widely distributed system have however hindered their development into robust structural health monitoring techniques. Recently, carbon nanotube forests were spun into a microscale thread that is electrically conductive, tough, and easily tailorable. The thread was integrated into polymeric materials and used for the first time as a piezoresistive sensor to monitor strain and also to detect damage in the material. It is revealed that the created self-sensing polymeric materials are sensitive to normal strains above 0.07% and that the sensor thread exhibits a perfectly linear delta resistance–strain response above 0.3%. The longitudinal gauge factors were determined to be in the 2–5 range. This low cost and simple built-in sensor thread may provide a new integrated and distributed sensor technology that enables robust real-time health monitoring of structures

Is the wide distribution of aspen a result of its stress tolerance?

Science.gov (United States)

V. J. Lieffers; S. M. Landhausser; E. H. Hogg

2001-01-01

Populus tremuloides is distributed from drought-prone fringes of the Great Plains to extremely cold sites at arctic treeline. To occupy these conditions aspen appears to be more tolerant of stress than the other North American species of the genus Populus. Cold winters, cold soil conditions during the growing season, periodic drought, insect defoliation, and...

Distributed Analysis in CMS

CERN Document Server

Fanfani, Alessandra; Sanches, Jose Afonso; Andreeva, Julia; Bagliesi, Giusepppe; Bauerdick, Lothar; Belforte, Stefano; Bittencourt Sampaio, Patricia; Bloom, Ken; Blumenfeld, Barry; Bonacorsi, Daniele; Brew, Chris; Calloni, Marco; Cesini, Daniele; Cinquilli, Mattia; Codispoti, Giuseppe; D'Hondt, Jorgen; Dong, Liang; Dongiovanni, Danilo; Donvito, Giacinto; Dykstra, David; Edelmann, Erik; Egeland, Ricky; Elmer, Peter; Eulisse, Giulio; Evans, Dave; Fanzago, Federica; Farina, Fabio; Feichtinger, Derek; Fisk, Ian; Flix, Josep; Grandi, Claudio; Guo, Yuyi; Happonen, Kalle; Hernandez, Jose M; Huang, Chih-Hao; Kang, Kejing; Karavakis, Edward; Kasemann, Matthias; Kavka, Carlos; Khan, Akram; Kim, Bockjoo; Klem, Jukka; Koivumaki, Jesper; Kress, Thomas; Kreuzer, Peter; Kurca, Tibor; Kuznetsov, Valentin; Lacaprara, Stefano; Lassila-Perini, Kati; Letts, James; Linden, Tomas; Lueking, Lee; Maes, Joris; Magini, Nicolo; Maier, Gerhild; McBride, Patricia; Metson, Simon; Miccio, Vincenzo; Padhi, Sanjay; Pi, Haifeng; Riahi, Hassen; Riley, Daniel; Rossman, Paul; Saiz, Pablo; Sartirana, Andrea; Sciaba, Andrea; Sekhri, Vijay; Spiga, Daniele; Tuura, Lassi; Vaandering, Eric; Vanelderen, Lukas; Van Mulders, Petra; Vedaee, Aresh; Villella, Ilaria; Wicklund, Eric; Wildish, Tony; Wissing, Christoph; Wurthwein, Frank

2009-01-01

The CMS experiment expects to manage several Pbytes of data each year during the LHC programme, distributing them over many computing sites around the world and enabling data access at those centers for analysis. CMS has identified the distributed sites as the primary location for physics analysis to support a wide community with thousands potential users. This represents an unprecedented experimental challenge in terms of the scale of distributed computing resources and number of user. An overview of the computing architecture, the software tools and the distributed infrastructure is reported. Summaries of the experience in establishing efficient and scalable operations to get prepared for CMS distributed analysis are presented, followed by the user experience in their current analysis activities.

DistAMo: A web-based tool to characterize DNA-motif distribution on bacterial chromosomes

Directory of Open Access Journals (Sweden)

Patrick eSobetzko

2016-03-01

Full Text Available Short DNA motifs are involved in a multitude of functions such as for example chromosome segregation, DNA replication or mismatch repair. Distribution of such motifs is often not random and the specific chromosomal pattern relates to the respective motif function. Computational approaches which quantitatively assess such chromosomal motif patterns are necessary. Here we present a new computer tool DistAMo (Distribution Analysis of DNA Motifs. The algorithm uses codon redundancy to calculate the relative abundance of short DNA motifs from single genes to entire chromosomes. Comparative genomics analyses of the GATC-motif distribution in γ-proteobacterial genomes using DistAMo revealed that (i genes beside the replication origin are enriched in GATCs, (ii genome-wide GATC distribution follows a distinct pattern and (iii genes involved in DNA replication and repair are enriched in GATCs. These features are specific for bacterial chromosomes encoding a Dam methyltransferase. The new software is available as a stand-alone or as an easy-to-use web-based server version at http://www.computational.bio.uni-giessen.de/distamo.

Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

Directory of Open Access Journals (Sweden)

Haft Daniel H

2011-01-01

Full Text Available Abstract Background Enzymes in the radical SAM (rSAM domain family serve in a wide variety of biological processes, including RNA modification, enzyme activation, bacteriocin core peptide maturation, and cofactor biosynthesis. Evolutionary pressures and relationships to other cellular constituents impose recognizable grammars on each class of rSAM-containing system, shaping patterns in results obtained through various comparative genomics analyses. Results An uncharacterized gene cluster found in many Actinobacteria and sporadically in Firmicutes, Chloroflexi, Deltaproteobacteria, and one Archaeal plasmid contains a PqqE-like rSAM protein family that includes Rv0693 from Mycobacterium tuberculosis. Members occur clustered with a strikingly well-conserved small polypeptide we designate "mycofactocin," similar in size to bacteriocins and PqqA, precursor of pyrroloquinoline quinone (PQQ. Partial Phylogenetic Profiling (PPP based on the distribution of these markers identifies the mycofactocin cluster, but also a second tier of high-scoring proteins. This tier, strikingly, is filled with up to thirty-one members per genome from three variant subfamilies that occur, one each, in three unrelated classes of nicotinoproteins. The pattern suggests these variant enzymes require not only NAD(P, but also the novel gene cluster. Further study was conducted using SIMBAL, a PPP-like tool, to search these nicotinoproteins for subsequences best correlated across multiple genomes to the presence of mycofactocin. For both the short chain dehydrogenase/reductase (SDR and iron-containing dehydrogenase families, aligning SIMBAL's top-scoring sequences to homologous solved crystal structures shows signals centered over NAD(P-binding sites rather than over substrate-binding or active site residues. Previous studies on some of these proteins have revealed a non-exchangeable NAD cofactor, such that enzymatic activity in vitro requires an artificial electron acceptor such

Multi Agent System Based Wide Area Protection against Cascading Events

DEFF Research Database (Denmark)

Liu, Zhou; Chen, Zhe; Liu, Leo

2012-01-01

In this paper, a multi-agent system based wide area protection scheme is proposed in order to prevent long term voltage instability induced cascading events. The distributed relays and controllers work as a device agent which not only executes the normal function automatically but also can...... the effectiveness of proposed protection strategy. The simulation results indicate that the proposed multi agent control system can effectively coordinate the distributed relays and controllers to prevent the long term voltage instability induced cascading events....

Genome Wide Expression Profiling of Cancer Cell Lines Cultured in Microgravity Reveals Significant Dysregulation of Cell Cycle and MicroRNA Gene Networks.

Directory of Open Access Journals (Sweden)

Prasanna Vidyasekar

Full Text Available Zero gravity causes several changes in metabolic and functional aspects of the human body and experiments in space flight have demonstrated alterations in cancer growth and progression. This study reports the genome wide expression profiling of a colorectal cancer cell line-DLD-1, and a lymphoblast leukemic cell line-MOLT-4, under simulated microgravity in an effort to understand central processes and cellular functions that are dysregulated among both cell lines. Altered cell morphology, reduced cell viability and an aberrant cell cycle profile in comparison to their static controls were observed in both cell lines under microgravity. The process of cell cycle in DLD-1 cells was markedly affected with reduced viability, reduced colony forming ability, an apoptotic population and dysregulation of cell cycle genes, oncogenes, and cancer progression and prognostic markers. DNA microarray analysis revealed 1801 (upregulated and 2542 (downregulated genes (>2 fold in DLD-1 cultures under microgravity while MOLT-4 cultures differentially expressed 349 (upregulated and 444 (downregulated genes (>2 fold under microgravity. The loss in cell proliferative capacity was corroborated with the downregulation of the cell cycle process as demonstrated by functional clustering of DNA microarray data using gene ontology terms. The genome wide expression profile also showed significant dysregulation of post transcriptional gene silencing machinery and multiple microRNA host genes that are potential tumor suppressors and proto-oncogenes including MIR22HG, MIR17HG and MIR21HG. The MIR22HG, a tumor-suppressor gene was one of the highest upregulated genes in the microarray data showing a 4.4 log fold upregulation under microgravity. Real time PCR validated the dysregulation in the host gene by demonstrating a 4.18 log fold upregulation of the miR-22 microRNA. Microarray data also showed dysregulation of direct targets of miR-22, SP1, CDK6 and CCNA2.

Temperature profile and chemical data collected using XBT and CTD casts from NOAA Ship MALCOLM BALDRIGE and other platforms in a World-wide distribution from 1991-09-17 to 1995-03-23 (NODC Accession 9500074)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profile and chemical data were collected using XBT and CTD casts in a World-wide distribution from NOAA Ship MALCOLM BALDRIGE and other platforms from 17...

Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis

Science.gov (United States)

Liu, Shuai; Zhou, Xiaosu; Hao, Lili; Piao, Xianyu; Hou, Nan; Chen, Qijun

2017-01-01

Alternative splicing (AS), as one of the most important topics in the post-genomic era, has been extensively studied in numerous organisms. However, little is known about the prevalence and characteristics of AS in Echinococcus species, which can cause significant health problems to humans and domestic animals. Based on high-throughput RNA-sequencing data, we performed a genome-wide survey of AS in two major pathogens of echinococcosis-Echinococcus granulosus and Echinococcus multilocularis. Our study revealed that the prevalence and characteristics of AS in protoscoleces of the two parasites were generally consistent with each other. A total of 6,826 AS events from 3,774 E. granulosus genes and 6,644 AS events from 3,611 E. multilocularis genes were identified in protoscolex transcriptomes, indicating that 33–36% of genes were subject to AS in the two parasites. Strikingly, intron retention instead of exon skipping was the predominant type of AS in Echinococcus species. Moreover, analysis of the Kyoto Encyclopedia of Genes and Genomes pathway indicated that genes that underwent AS events were significantly enriched in multiple pathways mainly related to metabolism (e.g., purine, fatty acid, galactose, and glycerolipid metabolism), signal transduction (e.g., Jak-STAT, VEGF, Notch, and GnRH signaling pathways), and genetic information processing (e.g., RNA transport and mRNA surveillance pathways). The landscape of AS obtained in this study will not only facilitate future investigations on transcriptome complexity and AS regulation during the life cycle of Echinococcus species, but also provide an invaluable resource for future functional and evolutionary studies of AS in platyhelminth parasites. PMID:28588571

Genome-wide identification of polycomb target genes reveals a functional association of Pho with Scm in Bombyx mori.

Science.gov (United States)

Li, Zhiqing; Cheng, Daojun; Mon, Hiroaki; Tatsuke, Tsuneyuki; Zhu, Li; Xu, Jian; Lee, Jae Man; Xia, Qingyou; Kusakabe, Takahiro

2012-01-01

Polycomb group (PcG) proteins are evolutionarily conserved chromatin modifiers and act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1), Polycomb repressive complex 2 (PRC2), and Pleiohomeotic repressive complex (PhoRC), to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori with holocentric centromere using genome-wide expression screening based on the knockdown of BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, the expressions of 29 genes were up-regulated after knocking down 4 PcG genes. Particularly, there is a significant overlap between targets of BmPho (331 out of 524) and BmScm (331 out of 532), and among these, 190 genes function as regulator factors playing important roles in development. We also found that BmPho, as well as BmScm, can interact with other Polycomb components examined in this study. Further detailed analysis revealed that the C-terminus of BmPho containing zinc finger domain is involved in the interaction between BmPho and BmScm. Moreover, the zinc finger domain in BmPho contributes to its inhibitory function and ectopic overexpression of BmScm is able to promote transcriptional repression by Gal4-Pho fusions including BmScm-interacting domain. Loss of BmPho expression causes relocalization of BmScm into the cytoplasm. Collectively, we provide evidence of a functional link between BmPho and BmScm, and propose two Polycomb-related repression mechanisms requiring only BmPho associated with BmScm or a whole set of PcG complexes.

Genome-Wide Association Mapping Reveals Multiple QTLs Governing Tolerance Response for Seedling Stage Chilling Stress in Indica Rice

Directory of Open Access Journals (Sweden)

Sharat K. Pradhan

2017-04-01

Full Text Available Rice crop is sensitive to cold stress at seedling stage. A panel of population representing 304 shortlisted germplasm lines was studied for seedling stage chilling tolerance in indica rice. Six phenotypic classes were exposed to six low temperature stress regimes under control phenotyping facility to investigate response pattern. A panel of 66 genotypes representing all phenotypic classes was used for ensuring genetic diversity, population structure and association mapping for the trait using 58 simple sequence repeat (SSR and 2 direct trait linked markers. A moderate level of genetic diversity was detected in the panel population for the trait. Deviation of Hardy-Weinberg's expectation was detected in the studied population using Wright's F statistic. The panel showed 30% variation among population and 70% among individuals. The entire population was categorized into three sub-populations through STRUCTURE analysis. This revealed tolerance for the trait had a common primary ancestor for each sub-population with few admix individuals. The panel population showed the presence of many QTLs for cold stress tolerance in the individuals representing like genome-wide expression of the trait. Nineteen SSR markers were significantly associated at chilling stress of 8°C to 4°C for 7–21 days duration. Thus, the primers linked to the seedling stage cold tolerance QTLs namely qCTS9, qCTS-2, qCTS6.1, qSCT2, qSCT11, qSCT1a, qCTS-3.1, qCTS11.1, qCTS12.1, qCTS-1b, and CTB2 need to be pyramided for development of strongly chilling tolerant variety.

Genome-wide identification of polycomb target genes reveals a functional association of Pho with Scm in Bombyx mori.

Directory of Open Access Journals (Sweden)

Zhiqing Li

Full Text Available Polycomb group (PcG proteins are evolutionarily conserved chromatin modifiers and act together in three multimeric complexes, Polycomb repressive complex 1 (PRC1, Polycomb repressive complex 2 (PRC2, and Pleiohomeotic repressive complex (PhoRC, to repress transcription of the target genes. Here, we identified Polycomb target genes in Bombyx mori with holocentric centromere using genome-wide expression screening based on the knockdown of BmSCE, BmESC, BmPHO, or BmSCM gene, which represent the distinct complexes. As a result, the expressions of 29 genes were up-regulated after knocking down 4 PcG genes. Particularly, there is a significant overlap between targets of BmPho (331 out of 524 and BmScm (331 out of 532, and among these, 190 genes function as regulator factors playing important roles in development. We also found that BmPho, as well as BmScm, can interact with other Polycomb components examined in this study. Further detailed analysis revealed that the C-terminus of BmPho containing zinc finger domain is involved in the interaction between BmPho and BmScm. Moreover, the zinc finger domain in BmPho contributes to its inhibitory function and ectopic overexpression of BmScm is able to promote transcriptional repression by Gal4-Pho fusions including BmScm-interacting domain. Loss of BmPho expression causes relocalization of BmScm into the cytoplasm. Collectively, we provide evidence of a functional link between BmPho and BmScm, and propose two Polycomb-related repression mechanisms requiring only BmPho associated with BmScm or a whole set of PcG complexes.

Lithuanian on-line periodicals on the World Wide Web

Directory of Open Access Journals (Sweden)

Lina Sarlauskiene

2001-01-01

Full Text Available Deals with Lithuanian full-text electronic periodicals distributed through the World Wide Web. An electronic periodical is usually defined as a regular publication on some particular topic distributed in digital form, chiefly through the Web, but also by electronic mail or digital disk. The author has surveyed 106 publications. Thirty-four are distributed only on the Web, and 72 have printed versions. The number of analysed publications is not very big, but four years of electronic publishing and the variety of periodicals enables us to establish the causes of this phenomenon, the main features of development, and some perspectives. Electronic periodicals were analysed according to their type, purpose, contents, publisher, regularity, language, starting date and place of publication, and other features.

Genome-Wide Spectra of Transcription Insertions and Deletions Reveal That Slippage Depends on RNA:DNA Hybrid Complementarity.

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Traverse, Charles C; Ochman, Howard

2017-08-29

Advances in sequencing technologies have enabled direct quantification of genome-wide errors that occur during RNA transcription. These errors occur at rates that are orders of magnitude higher than rates during DNA replication, but due to technical difficulties such measurements have been limited to single-base substitutions and have not yet quantified the scope of transcription insertions and deletions. Previous reporter gene assay findings suggested that transcription indels are produced exclusively by elongation complex slippage at homopolymeric runs, so we enumerated indels across the protein-coding transcriptomes of Escherichia coli and Buchnera aphidicola , which differ widely in their genomic base compositions and incidence of repeat regions. As anticipated from prior assays, transcription insertions prevailed in homopolymeric runs of A and T; however, transcription deletions arose in much more complex sequences and were rarely associated with homopolymeric runs. By reconstructing the relocated positions of the elongation complex as inferred from the sequences inserted or deleted during transcription, we show that continuation of transcription after slippage hinges on the degree of nucleotide complementarity within the RNA:DNA hybrid at the new DNA template location. IMPORTANCE The high level of mistakes generated during transcription can result in the accumulation of malfunctioning and misfolded proteins which can alter global gene regulation and in the expenditure of energy to degrade these nonfunctional proteins. The transcriptome-wide occurrence of base substitutions has been elucidated in bacteria, but information on transcription insertions and deletions-errors that potentially have more dire effects on protein function-is limited to reporter gene constructs. Here, we capture the transcriptome-wide spectrum of insertions and deletions in Escherichia coli and Buchnera aphidicola and show that they occur at rates approaching those of base substitutions

[Origination of Pareto distribution in complex dynamic systems].

Science.gov (United States)

Chernavskiĭ, D S; Nikitin, A P; Chernavskaia, O D

2008-01-01

The Pareto distribution, whose probability density function can be approximated at sufficiently great chi as rho(chi) - chi(-alpha), where alpha > or = 2, is of crucial importance from both the theoretical and practical point of view. The main reason is its qualitative distinction from the normal (Gaussian) distribution. Namely, the probability of high deviations appears to be significantly higher. The conception of the universal applicability of the Gauss law remains to be widely distributed despite the lack of objective confirmation of this notion in a variety of application areas. The origin of the Pareto distribution in dynamic systems located in the gaussian noise field is considered. A simple one-dimensional model is discussed where the system response in a rather wide interval of the variable can be quite precisely approximated by this distribution.

Distributed Storage Algorithm for Geospatial Image Data Based on Data Access Patterns.

Directory of Open Access Journals (Sweden)

Shaoming Pan

Full Text Available Declustering techniques are widely used in distributed environments to reduce query response time through parallel I/O by splitting large files into several small blocks and then distributing those blocks among multiple storage nodes. Unfortunately, however, many small geospatial image data files cannot be further split for distributed storage. In this paper, we propose a complete theoretical system for the distributed storage of small geospatial image data files based on mining the access patterns of geospatial image data using their historical access log information. First, an algorithm is developed to construct an access correlation matrix based on the analysis of the log information, which reveals the patterns of access to the geospatial image data. Then, a practical heuristic algorithm is developed to determine a reasonable solution based on the access correlation matrix. Finally, a number of comparative experiments are presented, demonstrating that our algorithm displays a higher total parallel access probability than those of other algorithms by approximately 10-15% and that the performance can be further improved by more than 20% by simultaneously applying a copy storage strategy. These experiments show that the algorithm can be applied in distributed environments to help realize parallel I/O and thereby improve system performance.

Distributed Storage Algorithm for Geospatial Image Data Based on Data Access Patterns.

Science.gov (United States)

Pan, Shaoming; Li, Yongkai; Xu, Zhengquan; Chong, Yanwen

2015-01-01

Declustering techniques are widely used in distributed environments to reduce query response time through parallel I/O by splitting large files into several small blocks and then distributing those blocks among multiple storage nodes. Unfortunately, however, many small geospatial image data files cannot be further split for distributed storage. In this paper, we propose a complete theoretical system for the distributed storage of small geospatial image data files based on mining the access patterns of geospatial image data using their historical access log information. First, an algorithm is developed to construct an access correlation matrix based on the analysis of the log information, which reveals the patterns of access to the geospatial image data. Then, a practical heuristic algorithm is developed to determine a reasonable solution based on the access correlation matrix. Finally, a number of comparative experiments are presented, demonstrating that our algorithm displays a higher total parallel access probability than those of other algorithms by approximately 10-15% and that the performance can be further improved by more than 20% by simultaneously applying a copy storage strategy. These experiments show that the algorithm can be applied in distributed environments to help realize parallel I/O and thereby improve system performance.

Characterization and detection of a widely distributed gene cluster that predicts anaerobic choline utilization by human gut bacteria.

Science.gov (United States)

Martínez-del Campo, Ana; Bodea, Smaranda; Hamer, Hilary A; Marks, Jonathan A; Haiser, Henry J; Turnbaugh, Peter J; Balskus, Emily P

2015-04-14

Elucidation of the molecular mechanisms underlying the human gut microbiota's effects on health and disease has been complicated by difficulties in linking metabolic functions associated with the gut community as a whole to individual microorganisms and activities. Anaerobic microbial choline metabolism, a disease-associated metabolic pathway, exemplifies this challenge, as the specific human gut microorganisms responsible for this transformation have not yet been clearly identified. In this study, we established the link between a bacterial gene cluster, the choline utilization (cut) cluster, and anaerobic choline metabolism in human gut isolates by combining transcriptional, biochemical, bioinformatic, and cultivation-based approaches. Quantitative reverse transcription-PCR analysis and in vitro biochemical characterization of two cut gene products linked the entire cluster to growth on choline and supported a model for this pathway. Analyses of sequenced bacterial genomes revealed that the cut cluster is present in many human gut bacteria, is predictive of choline utilization in sequenced isolates, and is widely but discontinuously distributed across multiple bacterial phyla. Given that bacterial phylogeny is a poor marker for choline utilization, we were prompted to develop a degenerate PCR-based method for detecting the key functional gene choline TMA-lyase (cutC) in genomic and metagenomic DNA. Using this tool, we found that new choline-metabolizing gut isolates universally possessed cutC. We also demonstrated that this gene is widespread in stool metagenomic data sets. Overall, this work represents a crucial step toward understanding anaerobic choline metabolism in the human gut microbiota and underscores the importance of examining this microbial community from a function-oriented perspective. Anaerobic choline utilization is a bacterial metabolic activity that occurs in the human gut and is linked to multiple diseases. While bacterial genes responsible for

The NILE system architecture: fault-tolerant, wide-area access to computing and data resources

International Nuclear Information System (INIS)

Ricciardi, Aleta; Ogg, Michael; Rothfus, Eric

1996-01-01

NILE is a multi-disciplinary project building a distributed computing environment for HEP. It provides wide-area, fault-tolerant, integrated access to processing and data resources for collaborators of the CLEO experiment, though the goals and principles are applicable to many domains. NILE has three main objectives: a realistic distributed system architecture design, the design of a robust data model, and a Fast-Track implementation providing a prototype design environment which will also be used by CLEO physicists. This paper focuses on the software and wide-area system architecture design and the computing issues involved in making NILE services highly-available. (author)

Gluon field distribution in baryons

International Nuclear Information System (INIS)

Bissey, F.; Cao, F-G.; Kitson, A.; Lasscock, B.G.; Leinweber, D.B.; Signal, A.I.; Williams, A.G.; Zanotti, J.M.

2005-01-01

Methods for revealing the distribution of gluon fields within the three-quark static-baryon potential are presented. In particular, we outline methods for studying the sensitivity of the source on the emerging vacuum response for the three-quark system. At the same time, we explore the possibility of revealing gluon-field distributions in three-quark systems in QCD without the use of gauge-dependent smoothing techniques. Renderings of flux tubes from a preliminary high-statistics study on a 12 3 x 24 lattice are presented

Wide area network access to CMS data using the LustreTM filesystem

Science.gov (United States)

Rodriguez, J. L.; Avery, P.; Brody, T.; Bourilkov, D.; Fu, Y.; Kim, B.; Prescott, C.; Wu, Y.

2010-04-01

In this paper, we explore the use of the LustreTM cluster filesystem over the wide area network to access Compact Muon Solenoid (CMS) data stored on physical devices located hundreds of kilometres away. We describe the experimental testbed and report on the I/O performance of applications writing and reading data on the distributed LustreTM filesystem established across the WAN. We compare the I/O performance of a CMS application to the performance obtained with IOzone, a standard benchmark tool. We then examine the I/O performance of the CMS application running multiple processes on a single server. And compare the Lustre results to results obtained on data stored on local filesystems. Our measurements reveal that the IOzone benchmark tool, accessing data sequentially, can saturate the Gbps network link that connects our Lustre client in Miami Florida to the Lustre storage located in Gainesville, Florida. We also find that the I/O rates of the CMS application is significantly less than what can be obtained with IOzone for sequential access to data.

Wide area network access to CMS data using the LustreTM filesystem

International Nuclear Information System (INIS)

Rodriguez, J L; Brody, T; Avery, P; Bourilkov, D; Fu, Y; Kim, B; Wu, Y; Prescott, C

2010-01-01

In this paper, we explore the use of the Lustre TM cluster filesystem over the wide area network to access Compact Muon Solenoid (CMS) data stored on physical devices located hundreds of kilometres away. We describe the experimental testbed and report on the I/O performance of applications writing and reading data on the distributed Lustre TM filesystem established across the WAN. We compare the I/O performance of a CMS application to the performance obtained with IOzone, a standard benchmark tool. We then examine the I/O performance of the CMS application running multiple processes on a single server. And compare the Lustre results to results obtained on data stored on local filesystems. Our measurements reveal that the IOzone benchmark tool, accessing data sequentially, can saturate the Gbps network link that connects our Lustre client in Miami Florida to the Lustre storage located in Gainesville, Florida. We also find that the I/O rates of the CMS application is significantly less than what can be obtained with IOzone for sequential access to data.

SQC: secure quality control for meta-analysis of genome-wide association studies.

Science.gov (United States)

Huang, Zhicong; Lin, Huang; Fellay, Jacques; Kutalik, Zoltán; Hubaux, Jean-Pierre

2017-08-01

Due to the limited power of small-scale genome-wide association studies (GWAS), researchers tend to collaborate and establish a larger consortium in order to perform large-scale GWAS. Genome-wide association meta-analysis (GWAMA) is a statistical tool that aims to synthesize results from multiple independent studies to increase the statistical power and reduce false-positive findings of GWAS. However, it has been demonstrated that the aggregate data of individual studies are subject to inference attacks, hence privacy concerns arise when researchers share study data in GWAMA. In this article, we propose a secure quality control (SQC) protocol, which enables checking the quality of data in a privacy-preserving way without revealing sensitive information to a potential adversary. SQC employs state-of-the-art cryptographic and statistical techniques for privacy protection. We implement the solution in a meta-analysis pipeline with real data to demonstrate the efficiency and scalability on commodity machines. The distributed execution of SQC on a cluster of 128 cores for one million genetic variants takes less than one hour, which is a modest cost considering the 10-month time span usually observed for the completion of the QC procedure that includes timing of logistics. SQC is implemented in Java and is publicly available at https://github.com/acs6610987/secureqc. jean-pierre.hubaux@epfl.ch. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A genome-wide map of hyper-edited RNA reveals numerous new sites

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Porath, Hagit T.; Carmi, Shai; Levanon, Erez Y.

2014-01-01

Adenosine-to-inosine editing is one of the most frequent post-transcriptional modifications, manifested as A-to-G mismatches when comparing RNA sequences with their source DNA. Recently, a number of RNA-seq data sets have been screened for the presence of A-to-G editing, and hundreds of thousands of editing sites identified. Here we show that existing screens missed the majority of sites by ignoring reads with excessive (‘hyper’) editing that do not easily align to the genome. We show that careful alignment and examination of the unmapped reads in RNA-seq studies reveal numerous new sites, usually many more than originally discovered, and in precisely those regions that are most heavily edited. Specifically, we discover 327,096 new editing sites in the heavily studied Illumina Human BodyMap data and more than double the number of detected sites in several published screens. We also identify thousands of new sites in mouse, rat, opossum and fly. Our results establish that hyper-editing events account for the majority of editing sites. PMID:25158696

An Analysis of Weakly Consistent Replication Systems in an Active Distributed Network

OpenAIRE

Amit Chougule; Pravin Ghewari

2011-01-01

With the sudden increase in heterogeneity and distribution of data in wide-area networks, more flexible, efficient and autonomous approaches for management and data distribution are needed. In recent years, the proliferation of inter-networks and distributed applications has increased the demand for geographically-distributed replicated databases. The architecture of Bayou provides features that address the needs of database storage of world-wide applications. Key is the use of weak consisten...

Body Size Distribution of the Dinosaurs

OpenAIRE

O?Gorman, Eoin J.; Hone, David W. E.

2012-01-01

The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutiona...

Distribution of crushing strength of tablets

DEFF Research Database (Denmark)

Sonnergaard, Jørn

2002-01-01

The distribution of a given set of data is important since most parametric statistical tests are based on the assumption that the studied data are normal distributed. In analysis of fracture mechanics the Weibull distribution is widely used and the derived Weibull modulus is interpreted as a mate...... data from nine model tablet formulations and four commercial tablets are shown to follow the normal distribution. The importance of proper cleaning of the crushing strength apparatus is demonstrated....

Distributions of Bacterial Generalists among the Guts of Birds ...

Science.gov (United States)

Complex distributions of bacterial taxa within diverse animal microbiomes have inspired ecological and biogeographical approaches to revealing the functions of taxa that may be most important for host health. Of particular interest are bacteria that find many diverse habitats suitable for growth and remain competitive amongst finely-tuned host specialists. While previous work has focused on identifying these specialists, here our aims were to 1) identify generalist taxa, 2) identify taxonomic clades with enriched generalist diversity, and 3) describe the distribution of the largest generalist groups among hosts. We analyzed existing bacterial rRNA tag-sequencing data (v6) available on VAMPs (vamps.mbl.edu) from the microbiomes of 12 host species (106 samples total) spanning birds, mammals, and fish for generalist taxa using the CLAM test. OTUs with approximately equal abundance and a minimum of 10 reads in two hosts were classified as generalists. Generalist OTUs (n=2,982) were found in all hosts tested. Bacterial families Alcaligenaceae and Burkholderiaceae were significantly enriched with generalists OTUs compared to other families. Bacterial families such as Bacteroidaceae and Lachnospiraceae significantly lacked generalists OTUs compared to other families. Enterobacteriaceae, Peptostreptococcaceae, and Erysipelotrichaceae more so than other bacterial families were widely distributed and abundant in birds, mammals, and fish suggesting that these taxa mainta

Are trait-scaling relationships invariant across contrasting elevations in the widely distributed treeline species Nothofagus pumilio?

Science.gov (United States)

Fajardo, Alex

2016-05-01

The study of scaling examines the relative dimensions of diverse organismal traits. Understanding whether global scaling patterns are paralleled within species is key to identify causal factors of universal scaling. I examined whether the foliage-stem (Corner's rules), the leaf size-number, and the leaf mass-leaf area scaling relationships remained invariant and isometric with elevation in a wide-distributed treeline species in the southern Chilean Andes. Mean leaf area, leaf mass, leafing intensity, and twig cross-sectional area were determined for 1-2 twigs of 8-15 Nothofagus pumilio individuals across four elevations (including treeline elevation) and four locations (from central Chile at 36°S to Tierra del Fuego at 54°S). Mixed effects models were fitted to test whether the interaction term between traits and elevation was nonsignificant (invariant). The leaf-twig cross-sectional area and the leaf mass-leaf area scaling relationships were isometric (slope = 1) and remained invariant with elevation, whereas the leaf size-number (i.e., leafing intensity) scaling was allometric (slope ≠ -1) and showed no variation with elevation. Leaf area and leaf number were consistently negatively correlated across elevation. The scaling relationships examined in the current study parallel those seen across species. It is plausible that the explanation of intraspecific scaling relationships, as trait combinations favored by natural selection, is the same as those invoked to explain across species patterns. Thus, it is very likely that the global interspecific Corner's rules and other leaf-leaf scaling relationships emerge as the aggregate of largely parallel intraspecific patterns. © 2016 Botanical Society of America.

Genome-wide linkage in a highly consanguineous pedigree reveals two novel loci on chromosome 7 for non-syndromic familial Premature Ovarian Failure.

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Sandrine Caburet

Full Text Available BACKGROUND: The human condition known as Premature Ovarian Failure (POF is characterized by loss of ovarian function before the age of 40. A majority of POF cases are sporadic, but 10-15% are familial, suggesting a genetic origin of the disease. Although several causal mutations have been identified, the etiology of POF is still unknown for about 90% of the patients. METHODOLOGY/PRINCIPAL FINDINGS: We report a genome-wide linkage and homozygosity analysis in one large consanguineous Middle-Eastern POF-affected family presenting an autosomal recessive pattern of inheritance. We identified two regions with a LOD(max of 3.26 on chromosome 7p21.1-15.3 and 7q21.3-22.2, which are supported as candidate regions by homozygosity mapping. Sequencing of the coding exons and known regulatory sequences of three candidate genes (DLX5, DLX6 and DSS1 included within the largest region did not reveal any causal mutations. CONCLUSIONS/SIGNIFICANCE: We detect two novel POF-associated loci on human chromosome 7, opening the way to the identification of new genes involved in the control of ovarian development and function.

A complex regulatory network coordinating cell cycles during C. elegans development is revealed by a genome-wide RNAi screen.

Science.gov (United States)

Roy, Sarah H; Tobin, David V; Memar, Nadin; Beltz, Eleanor; Holmen, Jenna; Clayton, Joseph E; Chiu, Daniel J; Young, Laura D; Green, Travis H; Lubin, Isabella; Liu, Yuying; Conradt, Barbara; Saito, R Mako

2014-02-28

The development and homeostasis of multicellular animals requires precise coordination of cell division and differentiation. We performed a genome-wide RNA interference screen in Caenorhabditis elegans to reveal the components of a regulatory network that promotes developmentally programmed cell-cycle quiescence. The 107 identified genes are predicted to constitute regulatory networks that are conserved among higher animals because almost half of the genes are represented by clear human orthologs. Using a series of mutant backgrounds to assess their genetic activities, the RNA interference clones displaying similar properties were clustered to establish potential regulatory relationships within the network. This approach uncovered four distinct genetic pathways controlling cell-cycle entry during intestinal organogenesis. The enhanced phenotypes observed for animals carrying compound mutations attest to the collaboration between distinct mechanisms to ensure strict developmental regulation of cell cycles. Moreover, we characterized ubc-25, a gene encoding an E2 ubiquitin-conjugating enzyme whose human ortholog, UBE2Q2, is deregulated in several cancers. Our genetic analyses suggested that ubc-25 acts in a linear pathway with cul-1/Cul1, in parallel to pathways employing cki-1/p27 and lin-35/pRb to promote cell-cycle quiescence. Further investigation of the potential regulatory mechanism demonstrated that ubc-25 activity negatively regulates CYE-1/cyclin E protein abundance in vivo. Together, our results show that the ubc-25-mediated pathway acts within a complex network that integrates the actions of multiple molecular mechanisms to control cell cycles during development. Copyright © 2014 Roy et al.

Autonomous operation of distributed storages in microgrids

DEFF Research Database (Denmark)

Loh, Poh Chiang; Chai, Yi Kai; Li, Ding

2014-01-01

Operation of distributed generators in microgrids has been widely discussed, but would not be fully autonomous if distributed energy storages are not considered. Storages are important since they provide energy buffering to load changes, energy levelling to source variations and ride-through enha......Operation of distributed generators in microgrids has been widely discussed, but would not be fully autonomous if distributed energy storages are not considered. Storages are important since they provide energy buffering to load changes, energy levelling to source variations and ride......-through enhancement to the microgrids. Recognising their importance, this study presents a scheme for sharing power among multiple distributed storages in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for local operating conditions, requesting for maximum...... to help with meeting the extra load demand. The described process takes place autonomously with energy eventually shared among the storages in proportion to their ratings. To test the concepts discussed, experiments have been performed with favourable results obtained for performance verification....

Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana

NARCIS (Netherlands)

Davila Olivas, Nelson H.; Kruijer, Willem; Gort, Gerrit; Wijnen, Cris L.; Loon, van Joop J.A.; Dicke, Marcel

2017-01-01

Plants are commonly exposed to abiotic and biotic stresses. We used 350 Arabidopsis thaliana accessions grown under controlled conditions. We employed genome-wide association analysis to investigate the genetic architecture and underlying loci involved in genetic variation in resistance to: two

Temperature profile data from XBT casts from a world-wide distribution from the SKOGAFOSS and other vessels as part of NOAA's Volunteer Observing Ships Program from 06 February 2002 to 10 April 2002 (NODC Accession 0000718)

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National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profiles were collected from XBT casts from the SKOGAFOSS and other platforms from a world-wide distribution from 06 February 2002 to 10 April 2002. Data...

Comparative Genomics Revealed Genetic Diversity and Species/Strain-Level Differences in Carbohydrate Metabolism of Three Probiotic Bifidobacterial Species

Directory of Open Access Journals (Sweden)

Toshitaka Odamaki

2015-01-01

Full Text Available Strains of Bifidobacterium longum, Bifidobacterium breve, and Bifidobacterium animalis are widely used as probiotics in the food industry. Although numerous studies have revealed the properties and functionality of these strains, it is uncertain whether these characteristics are species common or strain specific. To address this issue, we performed a comparative genomic analysis of 49 strains belonging to these three bifidobacterial species to describe their genetic diversity and to evaluate species-level differences. There were 166 common clusters between strains of B. breve and B. longum, whereas there were nine common clusters between strains of B. animalis and B. longum and four common clusters between strains of B. animalis and B. breve. Further analysis focused on carbohydrate metabolism revealed the existence of certain strain-dependent genes, such as those encoding enzymes for host glycan utilisation or certain membrane transporters, and many genes commonly distributed at the species level, as was previously reported in studies with limited strains. As B. longum and B. breve are human-residential bifidobacteria (HRB, whereas B. animalis is a non-HRB species, several of the differences in these species’ gene distributions might be the result of their adaptations to the nutrient environment. This information may aid both in selecting probiotic candidates and in understanding their potential function as probiotics.

Grid-optimized Web 3D applications on wide area network

Science.gov (United States)

Wang, Frank; Helian, Na; Meng, Lingkui; Wu, Sining; Zhang, Wen; Guo, Yike; Parker, Michael Andrew

2008-08-01

Geographical information system has come into the Web Service times now. In this paper, Web3D applications have been developed based on our developed Gridjet platform, which provides a more effective solution for massive 3D geo-dataset sharing in distributed environments. Web3D services enabling web users could access the services as 3D scenes, virtual geographical environment and so on. However, Web3D services should be shared by thousands of essential users that inherently distributed on different geography locations. Large 3D geo-datasets need to be transferred to distributed clients via conventional HTTP, NFS and FTP protocols, which often encounters long waits and frustration in distributed wide area network environments. GridJet was used as the underlying engine between the Web 3D application node and geo-data server that utilizes a wide range of technologies including the one of paralleling the remote file access, which is a WAN/Grid-optimized protocol and provides "local-like" accesses to remote 3D geo-datasets. No change in the way of using software is required since the multi-streamed GridJet protocol remains fully compatible with existing IP infrastructures. Our recent progress includes a real-world test that Web3D applications as Google Earth over the GridJet protocol beats those over the classic ones by a factor of 2-7 where the transfer distance is over 10,000 km.

Beyond-laboratory-scale prediction for channeling flows through subsurface rock fractures with heterogeneous aperture distributions revealed by laboratory evaluation

Science.gov (United States)

Ishibashi, Takuya; Watanabe, Noriaki; Hirano, Nobuo; Okamoto, Atsushi; Tsuchiya, Noriyoshi

2015-01-01

The present study evaluates aperture distributions and fluid flow characteristics for variously sized laboratory-scale granite fractures under confining stress. As a significant result of the laboratory investigation, the contact area in fracture plane was found to be virtually independent of scale. By combining this characteristic with the self-affine fractal nature of fracture surfaces, a novel method for predicting fracture aperture distributions beyond laboratory scale is developed. Validity of this method is revealed through reproduction of the results of laboratory investigation and the maximum aperture-fracture length relations, which are reported in the literature, for natural fractures. The present study finally predicts conceivable scale dependencies of fluid flows through joints (fractures without shear displacement) and faults (fractures with shear displacement). Both joint and fault aperture distributions are characterized by a scale-independent contact area, a scale-dependent geometric mean, and a scale-independent geometric standard deviation of aperture. The contact areas for joints and faults are approximately 60% and 40%. Changes in the geometric means of joint and fault apertures (µm), em, joint and em, fault, with fracture length (m), l, are approximated by em, joint = 1 × 102 l0.1 and em, fault = 1 × 103 l0.7, whereas the geometric standard deviations of both joint and fault apertures are approximately 3. Fluid flows through both joints and faults are characterized by formations of preferential flow paths (i.e., channeling flows) with scale-independent flow areas of approximately 10%, whereas the joint and fault permeabilities (m2), kjoint and kfault, are scale dependent and are approximated as kjoint = 1 × 10-12 l0.2 and kfault = 1 × 10-8 l1.1.

A kinome-wide RNAi screen in Drosophila Glia reveals that the RIO kinases mediate cell proliferation and survival through TORC2-Akt signaling in glioblastoma.

Directory of Open Access Journals (Sweden)

Renee D Read

Full Text Available Glioblastoma, the most common primary malignant brain tumor, is incurable with current therapies. Genetic and molecular analyses demonstrate that glioblastomas frequently display mutations that activate receptor tyrosine kinase (RTK and Pi-3 kinase (PI3K signaling pathways. In Drosophila melanogaster, activation of RTK and PI3K pathways in glial progenitor cells creates malignant neoplastic glial tumors that display many features of human glioblastoma. In both human and Drosophila, activation of the RTK and PI3K pathways stimulates Akt signaling along with other as-yet-unknown changes that drive oncogenesis. We used this Drosophila glioblastoma model to perform a kinome-wide genetic screen for new genes required for RTK- and PI3K-dependent neoplastic transformation. Human orthologs of novel kinases uncovered by these screens were functionally assessed in mammalian glioblastoma models and human tumors. Our results revealed that the atypical kinases RIOK1 and RIOK2 are overexpressed in glioblastoma cells in an Akt-dependent manner. Moreover, we found that overexpressed RIOK2 formed a complex with RIOK1, mTor, and mTor-complex-2 components, and that overexpressed RIOK2 upregulated Akt signaling and promoted tumorigenesis in murine astrocytes. Conversely, reduced expression of RIOK1 or RIOK2 disrupted Akt signaling and caused cell cycle exit, apoptosis, and chemosensitivity in glioblastoma cells by inducing p53 activity through the RpL11-dependent ribosomal stress checkpoint. These results imply that, in glioblastoma cells, constitutive Akt signaling drives RIO kinase overexpression, which creates a feedforward loop that promotes and maintains oncogenic Akt activity through stimulation of mTor signaling. Further study of the RIO kinases as well as other kinases identified in our Drosophila screen may reveal new insights into defects underlying glioblastoma and related cancers and may reveal new therapeutic opportunities for these cancers.

Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae.

Directory of Open Access Journals (Sweden)

Preeti Arya

Full Text Available Nucleotide binding site leucine-rich repeats (NBS-LRR disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR and coiled coil (CC (1 ∶ 1 was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.

Genome-wide identification and expression analysis of NBS-encoding genes in Malus x domestica and expansion of NBS genes family in Rosaceae.

Science.gov (United States)

Arya, Preeti; Kumar, Gulshan; Acharya, Vishal; Singh, Anil K

2014-01-01

Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1 ∶ 1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple.

REVEAL: Software Documentation and Platform Migration

Science.gov (United States)

Wilson, Michael A.; Veibell, Victoir T.; Freudinger, Lawrence C.

2008-01-01

The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA s Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This report specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as a final report for that internship. The topics discussed include: the documentation of REVEAL source code; the migration of REVEAL to other platforms; and an end-to-end field test that successfully validates the efforts.

Modeled distribution and abundance of a pelagic seabird reveal trends in relation to fisheries

Science.gov (United States)

Renner, Martin; Parrish, Julia K.; Piatt, John F.; Kuletz, Kathy J.; Edwards, Ann E.; Hunt, George L.

2013-01-01

The northern fulmar Fulmarus glacialis is one of the most visible and widespread seabirds in the eastern Bering Sea and Aleutian Islands. However, relatively little is known about its abundance, trends, or the factors that shape its distribution. We used a long-term pelagic dataset to model changes in fulmar at-sea distribution and abundance since the mid-1970s. We used an ensemble model, based on a weighted average of generalized additive model (GAM), multivariate adaptive regression splines (MARS), and random forest models to estimate the pelagic distribution and density of fulmars in the waters of the Aleutian Archipelago and Bering Sea. The most important predictor variables were colony effect, sea surface temperature, distribution of fisheries, location, and primary productivity. We calculated a time series from the ratio of observed to predicted values and found that fulmar at-sea abundance declined from the 1970s to the 2000s at a rate of 0.83% (± 0.39% SE) per annum. Interpolating fulmar densities on a spatial grid through time, we found that the center of fulmar distribution in the Bering Sea has shifted north, coinciding with a northward shift in fish catches and a warming ocean. Our study shows that fisheries are an important, but not the only factor, shaping fulmar distribution and abundance trends in the eastern Bering Sea and Aleutian Islands.

Hierarchical species distribution models

Science.gov (United States)

Hefley, Trevor J.; Hooten, Mevin B.

2016-01-01

Determining the distribution pattern of a species is important to increase scientific knowledge, inform management decisions, and conserve biodiversity. To infer spatial and temporal patterns, species distribution models have been developed for use with many sampling designs and types of data. Recently, it has been shown that count, presence-absence, and presence-only data can be conceptualized as arising from a point process distribution. Therefore, it is important to understand properties of the point process distribution. We examine how the hierarchical species distribution modeling framework has been used to incorporate a wide array of regression and theory-based components while accounting for the data collection process and making use of auxiliary information. The hierarchical modeling framework allows us to demonstrate how several commonly used species distribution models can be derived from the point process distribution, highlight areas of potential overlap between different models, and suggest areas where further research is needed.

Cross-cancer genome-wide analysis of lung, ovary, breast, prostate, and colorectal cancer reveals novel pleiotropic associations

NARCIS (Netherlands)

Fehringer, G. (Gordon); P. Kraft (Peter); P.D.P. Pharoah (Paul); R. Eeles (Rosalind); Chatterjee, N. (Nilanjan); F.R. Schumacher (Fredrick R); J.M. Schildkraut (Joellen); S. Lindstrom (Stephen); P. Brennan (Paul); H. Bickeböller (Heike); R. Houlston (Richard); M.T. Landi (Maria Teresa); N.E. Caporaso (Neil); Risch, A. (Angela); A.A. Al Olama (Ali Amin); S.I. Berndt (Sonja); Giovannucci, E.L. (Edward L.); H. Grönberg (Henrik); Z. Kote-Jarai; Ma, J. (Jing); K.R. Muir (K.); M.J. Stampfer (Meir J.); Stevens, V.L. (Victoria L.); F. Wiklund (Fredrik); W.C. Willett (Walter C.); E.L. Goode (Ellen); Permuth, J.B. (Jennifer B.); H. Risch (Harvey); Reid, B.M. (Brett M.); Bezieau, S. (Stephane); H. Brenner (Hermann); Chan, A.T. (Andrew T.); J. Chang-Claude (Jenny); T.J. Hudson (Thomas); Kocarnik, J.K. (Jonathan K.); P. Newcomb (Polly); Schoen, R.E. (Robert E.); Slattery, M.L. (Martha L.); White, E. (Emily); M.A. Adank (Muriel); H. Ahsan (Habibul); K. Aittomäki (Kristiina); Baglietto, L. (Laura); Blomquist, C. (Carl); F. Canzian (Federico); K. Czene (Kamila); I. dos Santos Silva (Isabel); Eliassen, A.H. (A. Heather); J.D. Figueroa (Jonine); D. Flesch-Janys (Dieter); O. Fletcher (Olivia); M. García-Closas (Montserrat); M.M. Gaudet (Mia); Johnson, N. (Nichola); P. Hall (Per); A. Hazra (Aditi); R. Hein (Rebecca); Hofman, A. (Albert); J.L. Hopper (John); A. Irwanto (Astrid); M. Johansson (Mattias); R. Kaaks (Rudolf); M.G. Kibriya (Muhammad); P. Lichtner (Peter); J. Liu (Jianjun); E. Lund (Eiliv); Makalic, E. (Enes); A. Meindl (Alfons); B. Müller-Myhsok (B.); Muranen, T.A. (Taru A.); H. Nevanlinna (Heli); P.H.M. Peeters; J. Peto (Julian); R. Prentice (Ross); N. Rahman (Nazneen); M.-J. Sanchez (Maria-Jose); D.F. Schmidt (Daniel); R.K. Schmutzler (Rita); M.C. Southey (Melissa); Tamimi, R. (Rulla); S.P.L. Travis (Simon); C. Turnbull (Clare); Uitterlinden, A.G. (Andre G.); Z. Wang (Zhaoming); A.S. Whittemore (Alice); X.R. Yang (Xiaohong); W. Zheng (Wei); D. Buchanan (Daniel); G. Casey (Graham); G. Conti (Giario); C.K. Edlund (Christopher); S. Gallinger (Steve); R. Haile (Robert); M. Jenkins (Mark); Marchand, L. (Loïcle); Li, L. (Li); N.M. Lindor (Noralane); Schmit, S.L. (Stephanie L.); S.N. Thibodeau (Stephen); M.O. Woods (Michael); T. Rafnar (Thorunn); J. Gudmundsson (Julius); S.N. Stacey (Simon); Stefansson, K. (Kari); P. Sulem (Patrick); Chen, Y.A. (Y. Ann); J.P. Tyrer (Jonathan); Christiani, D.C. (David C.); Wei, Y. (Yongyue); H. Shen (Hongbing); Z. Hu (Zhibin); X.-O. Shu (Xiao-Ou); Shiraishi, K. (Kouya); A. Takahashi (Atsushi); Y. Bossé (Yohan); M. Obeidat (Ma'en); D.C. Nickle (David); W. Timens (Wim); M. Freedman (Matthew); Li, Q. (Qiyuan); D. Seminara (Daniela); S.J. Chanock (Stephen); Gong, J. (Jian); U. Peters (Ulrike); S.B. Gruber (Stephen); Amos, C.I. (Christopher I.); T.A. Sellers (Thomas A.); D.F. Easton (Douglas F.); D. Hunter (David); C.A. Haiman (Christopher A.); B.E. Henderson (Brian); R.J. Hung (Rayjean)

2016-01-01

textabstractIdentifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Energy Technology Data Exchange (ETDEWEB)

Ma, Li Jun; van der Does, H. C.; Borkovich, Katherine A.; Coleman, Jeffrey J.; Daboussi, Marie-Jose; Di Pietro, Antonio; Dufresne, Marie; Freitag, Michael; Grabherr, Manfred; Henrissat, Bernard; Houterman, Petra M.; Kang, Seogchan; Shim, Won-Bo; Wolochuk, Charles; Xie, Xiaohui; Xu, Jin Rong; Antoniw, John; Baker, Scott E.; Bluhm, Burton H.; Breakspear, Andrew; Brown, Daren W.; Butchko, Robert A.; Chapman, Sinead; Coulson, Richard; Coutinho, Pedro M.; Danchin, Etienne G.; Diener, Andrew; Gale, Liane R.; Gardiner, Donald; Goff, Steven; Hammond-Kossack, Kim; Hilburn, Karen; Hua-Van, Aurelie; Jonkers, Wilfried; Kazan, Kemal; Kodira, Chinnappa D.; Koehrsen, Michael; Kumar, Lokesh; Lee, Yong Hwan; Li, Liande; Manners, John M.; Miranda-Saavedra, Diego; Mukherjee, Mala; Park, Gyungsoon; Park, Jongsun; Park, Sook Young; Proctor, Robert H.; Regev, Aviv; Ruiz-Roldan, M. C.; Sain, Divya; Sakthikumar, Sharadha; Sykes, Sean; Schwartz, David C.; Turgeon, Barbara G.; Wapinski, Ilan; Yoder, Olen; Young, Sarah; Zeng, Qiandong; Zhou, Shiguo; Galagan, James; Cuomo, Christina A.; Kistler, H. Corby; Rep, Martijn

2010-03-18

Fusarium species are among the most important phytopathogenic and toxigenic fungi, having significant impact on crop production and animal health. Distinctively, members of the F. oxysporum species complex exhibit wide host range but discontinuously distributed host specificity, reflecting remarkable genetic adaptability. To understand the molecular underpinnings of diverse phenotypic traits and their evolution in Fusarium, we compared the genomes of three economically important and phylogenetically related, yet phenotypically diverse plant-pathogenic species, F. graminearum, F. verticillioides and F. oxysporum f. sp. lycopersici. Our analysis revealed greatly expanded lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes, accounting for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity. Experimentally, we demonstrate for the first time the transfer of two LS chromosomes between strains of F. oxysporum, resulting in the conversion of a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in the F. oxysporum species complex, putting the evolution of fungal pathogenicity into a new perspective.

Brain-wide maps of Fos expression during fear learning and recall.

Science.gov (United States)

Cho, Jin-Hyung; Rendall, Sam D; Gray, Jesse M

2017-04-01

Fos induction during learning labels neuronal ensembles in the hippocampus that encode a specific physical environment, revealing a memory trace. In the cortex and other regions, the extent to which Fos induction during learning reveals specific sensory representations is unknown. Here we generate high-quality brain-wide maps of Fos mRNA expression during auditory fear conditioning and recall in the setting of the home cage. These maps reveal a brain-wide pattern of Fos induction that is remarkably similar among fear conditioning, shock-only, tone-only, and fear recall conditions, casting doubt on the idea that Fos reveals auditory-specific sensory representations. Indeed, novel auditory tones lead to as much gene induction in visual as in auditory cortex, while familiar (nonconditioned) tones do not appreciably induce Fos anywhere in the brain. Fos expression levels do not correlate with physical activity, suggesting that they are not determined by behavioral activity-driven alterations in sensory experience. In the thalamus, Fos is induced more prominently in limbic than in sensory relay nuclei, suggesting that Fos may be most sensitive to emotional state. Thus, our data suggest that Fos expression during simple associative learning labels ensembles activated generally by arousal rather than specifically by a particular sensory cue. © 2017 Cho et al.; Published by Cold Spring Harbor Laboratory Press.

Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.

OpenAIRE

Estrada, K.; Styrkarsdottir, U.; Evangelou, E.; Hsu, Y.H.; Duncan, E.L.; Ntzani, E.E.; Oei, L.; Albagha, O.M.; Amin, N.; Kemp, J.P.; Koller, D.L.; Li, G.; Liu, C.T.; Minster, R.L.; Moayyeri, A.

2012-01-01

Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We ident...

Wide distribution of autochthonous branched glycerol dialkyl glycerol tetraethers (bGDGTs in U.S. Great Basin hot springs

Directory of Open Access Journals (Sweden)

Brian P. Hedlund

2013-08-01

Full Text Available Branched glycerol dialkyl glycerol tetraethers (bGDGTs are membrane-spanning lipids that likely stabilize membranes of some bacteria. Although bGDGTs have been reported previously in certain geothermal environments, it has been suggested that they may derive from surrounding soils since bGDGTs are known to be produced by soil bacteria. To test the hypothesis that bGDGTs can be produced by thermophiles in geothermal environments, we examined the distribution and abundance of bGDGTs, along with extensive geochemical data, in 40 sediment and mat samples collected from geothermal systems in the U.S. Great Basin (temperature: 31-95°C; pH: 6.8-10.7. bGDGTs were found in 38 out of 40 samples at concentrations up to 824 ng/g sample dry mass and comprised up to 99.5% of total GDGTs (branched plus isoprenoidal. The wide distribution of bGDGTs in hot springs, strong correlation between core and polar lipid abundances, distinctness of bGDGT profiles compared to nearby soils, and higher concentration of bGDGTs in hot springs compared to nearby soils provided evidence of in situ production, particularly for the minimally methylated bGDGTs I, Ib, and Ic. Polar bGDGTs were found almost exclusively in samples ≤ 70°C and the absolute abundance of polar bGDGTs correlated negatively with properties of chemically reduced, high temperature spring sources (temperature, H2S/HS- and positively with properties of oxygenated, low temperature sites (O2, NO3-. Two-way cluster analysis and nonmetric multidimensional scaling based on relative abundance of polar bGDGTs supported these relationships and showed a negative relationship between the degree of methylation and temperature, suggesting a higher abundance for minimally methylated bGDGTs at high temperature. This study presents evidence of the widespread production of bGDGTs in mats and sediments of natural geothermal springs in the U.S. Great Basin, especially in oxygenated, low-temperature sites (≤ 70°C.

Wide distribution of autochthonous branched glycerol dialkyl glycerol tetraethers (bGDGTs) in U.S. Great Basin hot springs

Science.gov (United States)

Hedlund, Brian P.; Paraiso, Julienne J.; Williams, Amanda J.; Huang, Qiuyuan; Wei, Yuli; Dijkstra, Paul; Hungate, Bruce A.; Dong, Hailiang; Zhang, Chuanlun L.

2013-01-01

Branched glycerol dialkyl glycerol tetraethers (bGDGTs) are membrane-spanning lipids that likely stabilize membranes of some bacteria. Although bGDGTs have been reported previously in certain geothermal environments, it has been suggested that they may derive from surrounding soils since bGDGTs are known to be produced by soil bacteria. To test the hypothesis that bGDGTs can be produced by thermophiles in geothermal environments, we examined the distribution and abundance of bGDGTs, along with extensive geochemical data, in 40 sediment and mat samples collected from geothermal systems in the U.S. Great Basin (temperature: 31–95°C; pH: 6.8–10.7). bGDGTs were found in 38 out of 40 samples at concentrations up to 824 ng/g sample dry mass and comprised up to 99.5% of total GDGTs (branched plus isoprenoidal). The wide distribution of bGDGTs in hot springs, strong correlation between core and polar lipid abundances, distinctness of bGDGT profiles compared to nearby soils, and higher concentration of bGDGTs in hot springs compared to nearby soils provided evidence of in situ production, particularly for the minimally methylated bGDGTs I, Ib, and Ic. Polar bGDGTs were found almost exclusively in samples ≤70°C and the absolute abundance of polar bGDGTs correlated negatively with properties of chemically reduced, high temperature spring sources (temperature, H2S/HS−) and positively with properties of oxygenated, low temperature sites (O2, NO−3). Two-way cluster analysis and nonmetric multidimensional scaling based on relative abundance of polar bGDGTs supported these relationships and showed a negative relationship between the degree of methylation and temperature, suggesting a higher abundance for minimally methylated bGDGTs at high temperature. This study presents evidence of the widespread production of bGDGTs in mats and sediments of natural geothermal springs in the U.S. Great Basin, especially in oxygenated, low-temperature sites (≤70°C). PMID:23964271

Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations

NARCIS (Netherlands)

Fehringer, Gordon; Kraft, Peter; Pharoah, Paul D.; Eeles, Rosalind A.; Chatterjee, Nilanjan; Schumacher, Fredrick R.; Schildkraut, Joellen M.; Lindstrom, Sara; Brennan, Paul; Bickeboller, Heike; Houlston, Richard S.; Landi, Maria Teresa; Caporaso, Neil; Risch, Angela; Al Olama, Ali Amin; Berndt, Sonja I.; Giovannucci, Edward L.; Gronberg, Henrik; Kote-Jarai, Zsofia; Ma, Jing; Muir, Kenneth; Stampfer, Meir J.; Stevens, Victoria L.; Wiklund, Fredrik; Willett, Walter C.; Goode, Ellen L.; Permuth, Jennifer B.; Risch, Harvey A.; Reid, Brett M.; Bezieau, Stephane; Brenner, Hermann; Chan, Andrew T.; Chang-Claude, Jenny; Hudson, Thomas J.; Kocarnik, Jonathan K.; Newcomb, Polly A.; Schoen, Robert E.; Slattery, Martha L.; White, Emily; Adank, Muriel A.; Ahsan, Habibul; Aittomaki, Kristiina; Baglietto, Laura; Blomquist, Carl; Canzian, Federico; Czene, Kamila; dos-Santos-Silva, Isabel; Eliassen, A. Heather; Figueroa, Jonine D.; Timens, Wim

2016-01-01

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820

Cross-cancer genome-wide analysis of lung, ovary, breast, prostate, and colorectal cancer reveals novel pleiotropic associations

NARCIS (Netherlands)

Fehringer, Gordon; Kraft, Peter; Pharoah, Paul D.; Eeles, Rosalind A.; Chatterjee, Nilanjan; Schumacher, Fredrick R.; Schildkraut, Joellen M.; Lindström, Sara; Brennan, Paul; Bickeböller, Heike; Houlston, Richard S.; Landi, Maria Teresa; Caporaso, Neil; Risch, Angela; Al Olama, Ali Amin; Berndt, Sonja I.; Giovannucci, Edward L.; Grönberg, Henrik; Kote-Jarai, Zsofia; Ma, Jing; Muir, Kenneth; Stampfer, Meir J.; Stevens, Victoria L.; Wiklund, Fredrik; Willett, Walter C.; Goode, Ellen L.; Permuth, Jennifer B.; Risch, Harvey A.; Reid, Brett M.; Bezieau, Stephane; Brenner, Hermann; Chan, Andrew T.; Chang-Claude, Jenny; Hudson, Thomas J.; Kocarnik, Jonathan K.; Newcomb, Polly A.; Schoen, Robert E.; Slattery, Martha L.; White, Emily; Adank, Muriel A.; Ahsan, Habibul; Aittomäki, Kristiina; Baglietto, Laura; Blomquist, Carl; Canzian, Federico; Czene, Kamila; Dos-Santos-silva, Isabel; Eliassen, A. Heather; Figueroa, Jonine D.; Flesch-Janys, Dieter; Fletcher, Olivia; Garcia-Closas, Montserrat; Gaudet, Mia M.; Johnson, Nichola; Hall, Per; Hazra, Aditi; Hein, Rebecca; Hofman, Albert; Hopper, John L.; Irwanto, Astrid; Johansson, Mattias; Kaaks, Rudolf; Kibriya, Muhammad G.; Lichtner, Peter; Liu, Jianjun; Lund, Eiliv; Makalic, Enes; Meindl, Alfons; Müller-Myhsok, Bertram; Muranen, Taru A.; Nevanlinna, Heli; Peeters, Petra H.; Peto, Julian; Prentice, Ross L.; Rahman, Nazneen; Sanchez, Maria Jose; Schmidt, Daniel F.; Schmutzler, Rita K.; Southey, Melissa C.; Tamimi, Rulla; Travis, Ruth C.; Turnbull, Clare; Uitterlinden, Andre G.; Wang, Zhaoming; Whittemore, Alice S.; Yang, Xiaohong R.; Zheng, Wei; Buchanan, Daniel D.; Casey, Graham; Conti, David V.; Edlund, Christopher K.; Gallinger, Steven; Haile, Robert W.; Jenkins, Mark; Marchand, Loïcle; Li, Li; Lindor, Noralene M.; Schmit, Stephanie L.; Thibodeau, Stephen N.; Woods, Michael O.; Rafnar, Thorunn; Gudmundsson, Julius; Stacey, Simon N.; Stefansson, Kari; Sulem, Patrick; Chen, Y. Ann; Tyrer, Jonathan P.; Christiani, David C.; Wei, Yongyue; Shen, Hongbing; Hu, Zhibin; Shu, Xiao Ou; Shiraishi, Kouya; Takahashi, Atsushi; Bossé, Yohan; Obeidat, Ma'en; Nickle, David; Timens, Wim; Freedman, Matthew L.; Li, Qiyuan; Seminara, Daniela; Chanock, Stephen J.; Gong, Jian; Peters, Ulrike; Gruber, Stephen B.; Amos, Christopher I.; Sellers, Thomas A.; Easton, Douglas F.; Hunter, David J.; Haiman, Christopher A.; Henderson, Brian E.; Hung, Rayjean J.

2016-01-01

Identifying genetic variants with pleiotropic associations can uncover common pathways influencing multiple cancers. We took a two-stage approach to conduct genome-wide association studies for lung, ovary, breast, prostate, and colorectal cancer from the GAME-ON/GECCO Network (61,851 cases, 61,820

Development, Demonstration, and Field Testing of Enterprise-Wide Distributed Generation Energy Management System: Phase 1 Report

Energy Technology Data Exchange (ETDEWEB)

2003-04-01

This report describes RealEnergy's evolving distributed generation command and control system, called the"Distributed Energy Information System" (DEIS). This system uses algorithms to determine how to operate distributed generation systems efficiently and profitably. The report describes the system and RealEnergy's experiences in installing and applying the system to manage distributed generators for commercial building applications.The report is divided into six tasks. The first five describe the DEIS; the sixth describes RE's regulatory and contractual obligations: Task 1: Define Information and Communications Requirements; Task 2: Develop Command and Control Algorithms for Optimal Dispatch; Task 3: Develop Codes and Modules for Optimal Dispatch Algorithms; Task 4: Test Codes Using Simulated Data; Task 5: Install and Test Energy Management Software; Task 6: Contractual and Regulatory Issues.

A genome-wide association study by ImmunoChip reveals potential modifiers in myelodysplastic syndromes.

Science.gov (United States)

Danjou, Fabrice; Fozza, Claudio; Zoledziewska, Magdalena; Mulas, Antonella; Corda, Giovanna; Contini, Salvatore; Dore, Fausto; Galleu, Antonio; Di Tucci, Anna Angela; Caocci, Giovanni; Gaviano, Eleonora; Latte, Giancarlo; Gabbas, Attilio; Casula, Paolo; Delogu, Lucia Gemma; La Nasa, Giorgio; Angelucci, Emanuele; Cucca, Francesco; Longinotti, Maurizio

2016-11-01

Because different findings suggest that an immune dysregulation plays a role in the pathogenesis of myelodysplastic syndrome (MDS), we analyzed a large cohort of patients from a homogeneous Sardinian population using ImmunoChip, a genotyping array exploring 147,954 single-nucleotide polymorphisms (SNPs) localized in genomic regions displaying some degree of association with immune-mediated diseases or pathways. The population studied included 133 cases and 3,894 controls, and a total of 153,978 autosomal markers and 971 non-autosomal markers were genotyped. After association analysis, only one variant passed the genome-wide significance threshold: rs71325459 (p = 1.16 × 10 -12 ), which is situated on chromosome 20. The variant is in high linkage disequilibrium with rs35640778, an untested missense variant situated in the RTEL1 gene, an interesting candidate that encodes for an ATP-dependent DNA helicase implicated in telomere-length regulation, DNA repair, and maintenance of genomic stability. The second most associated signal is composed of five variants that fall slightly below the genome-wide significance threshold but point out another interesting gene candidate. These SNPs, with p values between 2.53 × 10 -6 and 3.34 × 10 -6 , are situated in the methylene tetrahydrofolate reductase (MTHFR) gene. The most associated of these variants, rs1537514, presents an increased frequency of the derived C allele in cases, with 11.4% versus 4.4% in controls. MTHFR is the rate-limiting enzyme in the methyl cycle and genetic variations in this gene have been strongly associated with the risk of neoplastic diseases. The current understanding of the MDS biology, which is based on the hypothesis of the sequential development of multiple subclonal molecular lesions, fits very well with the demonstration of a possible role for RTEL1 and MTHFR gene polymorphisms, both of which are related to a variable risk of genomic instability. Copyright © 2016 ISEH - International

Plesionika edwardsi (Brandt, 1851) is a marine species of wide ...

African Journals Online (AJOL)

spamer

Plesionika edwardsi (Brandt, 1851) is a marine species of wide distribution at low latitudes. It is known from the Western Pacific (Philippines,. Indonesia), the Western Atlantic (from South. Carolina and North Bahamas to the Gulf of Mexico), the Eastern Atlantic (from North-West Spain to. Sierra Leone, including the ...

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

Science.gov (United States)

Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

Science.gov (United States)

Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

2016-01-01

Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

Physical, biological, and chemical data from radiometer, profiling reflectance radiometer, and CTD casts in a world-wide distribution as part of the SeaWiFS/SIMBIOS project from 13 September 1981 to 16 December 1999 (NODC Accession 0000632)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Physical, biological, and chemical data were collected using radiometer, profiling reflectance radiometer, and CTD casts in a world-wide distribution from 13...

The absolute magnitude distribution of Kuiper Belt objects

International Nuclear Information System (INIS)

Fraser, Wesley C.; Brown, Michael E.; Morbidelli, Alessandro; Parker, Alex; Batygin, Konstantin

2014-01-01

Here we measure the absolute magnitude distributions (H-distribution) of the dynamically excited and quiescent (hot and cold) Kuiper Belt objects (KBOs), and test if they share the same H-distribution as the Jupiter Trojans. From a compilation of all useable ecliptic surveys, we find that the KBO H-distributions are well described by broken power laws. The cold population has a bright-end slope, α 1 =1.5 −0.2 +0.4 , and break magnitude, H B =6.9 −0.2 +0.1 (r'-band). The hot population has a shallower bright-end slope of, α 1 =0.87 −0.2 +0.07 , and break magnitude H B =7.7 −0.5 +1.0 . Both populations share similar faint-end slopes of α 2 ∼ 0.2. We estimate the masses of the hot and cold populations are ∼0.01 and ∼3 × 10 –4 M ⊕ . The broken power-law fit to the Trojan H-distribution has α 1 = 1.0 ± 0.2, α 2 = 0.36 ± 0.01, and H B = 8.3. The Kolmogorov-Smirnov test reveals that the probability that the Trojans and cold KBOs share the same parent H-distribution is less than 1 in 1000. When the bimodal albedo distribution of the hot objects is accounted for, there is no evidence that the H-distributions of the Trojans and hot KBOs differ. Our findings are in agreement with the predictions of the Nice model in terms of both mass and H-distribution of the hot and Trojan populations. Wide-field survey data suggest that the brightest few hot objects, with H r ′ ≲3, do not fall on the steep power-law slope of fainter hot objects. Under the standard hierarchical model of planetesimal formation, it is difficult to account for the similar break diameters of the hot and cold populations given the low mass of the cold belt.

Time-Resolved Transposon Insertion Sequencing Reveals Genome-Wide Fitness Dynamics during Infection

Directory of Open Access Journals (Sweden)

Guanhua Yang

2017-10-01

Full Text Available Transposon insertion sequencing (TIS is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection. Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE. From a temporal series of TIS data, PACE derives a quantitative assessment of each mutant’s fitness over the course of an experiment and identifies mutants with related fitness profiles. In so doing, PACE circumvents major limitations of existing methodologies, specifically the need for artificial effect size thresholds and enumeration of bacterial population expansion. We used PACE to analyze TIS samples of Edwardsiella piscicida (a fish pathogen collected over a 2-week infection period from a natural host (the flatfish turbot. PACE uncovered more genes that affect E. piscicida’s fitness in vivo than were detected using a cutoff at a terminal sampling point, and it identified subpopulations of mutants with distinct fitness profiles, one of which informed the design of new live vaccine candidates. Overall, PACE enables efficient mining of time series TIS data and enhances the power and sensitivity of TIS-based analyses.

Genome-wide analysis in Brazilian Xavante Indians reveals low degree of admixture.

Science.gov (United States)

Kuhn, Patricia C; Horimoto, Andréa R V Russo; Sanches, José Maurício; Vieira Filho, João Paulo B; Franco, Luciana; Fabbro, Amaury Dal; Franco, Laercio Joel; Pereira, Alexandre C; Moises, Regina S

2012-01-01

Characterization of population genetic variation and structure can be used as tools for research in human genetics and population isolates are of great interest. The aim of the present study was to characterize the genetic structure of Xavante Indians and compare it with other populations. The Xavante, an indigenous population living in Brazilian Central Plateau, is one of the largest native groups in Brazil. A subset of 53 unrelated subjects was selected from the initial sample of 300 Xavante Indians. Using 86,197 markers, Xavante were compared with all populations of HapMap Phase III and HGDP-CEPH projects and with a Southeast Brazilian population sample to establish its population structure. Principal Components Analysis showed that the Xavante Indians are concentrated in the Amerindian axis near other populations of known Amerindian ancestry such as Karitiana, Pima, Surui and Maya and a low degree of genetic admixture was observed. This is consistent with the historical records of bottlenecks experience and cultural isolation. By calculating pair-wise F(st) statistics we characterized the genetic differentiation between Xavante Indians and representative populations of the HapMap and from HGDP-CEPH project. We found that the genetic differentiation between Xavante Indians and populations of Ameridian, Asian, European, and African ancestry increased progressively. Our results indicate that the Xavante is a population that remained genetically isolated over the past decades and can offer advantages for genome-wide mapping studies of inherited disorders.

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

Science.gov (United States)

Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

2014-09-01

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Financing Distributed Generation

International Nuclear Information System (INIS)

Walker, A.

2001-01-01

This paper introduces the engineer who is undertaking distributed generation projects to a wide range of financing options. Distributed generation systems (such as internal combustion engines, small gas turbines, fuel cells and photovoltaics) all require an initial investment, which is recovered over time through revenues or savings. An understanding of the cost of capital and financing structures helps the engineer develop realistic expectations and not be offended by the common requirements of financing organizations. This paper discusses several mechanisms for financing distributed generation projects: appropriations; debt (commercial bank loan); mortgage; home equity loan; limited partnership; vendor financing; general obligation bond; revenue bond; lease; Energy Savings Performance Contract; utility programs; chauffage (end-use purchase); and grants. The paper also discusses financial strategies for businesses focusing on distributed generation: venture capital; informal investors (''business angels''); bank and debt financing; and the stock market

Markets for energy efficiency: Exploring the implications of an EU-wide 'Tradable White Certificate' scheme

International Nuclear Information System (INIS)

Mundaca, Luis

2008-01-01

Recent developments in European energy policy reveal an increasing interest in implementing the so-called 'Tradable White Certificate' (TWC) schemes to improve energy efficiency. Based on three evaluation criteria (cost-effectiveness, environmental effectiveness and distributional equity) this paper analyses the implications of implementing a European-wide TWC scheme targeting the household and commercial sectors. Using a bottom-up model, quantitative results show significant cost-effective potentials for improvements (ca. 1400 TWh in cumulative energy savings by 2020), with the household sector, gas and space heating representing most of the TWC supply in terms of eligible sector, fuel and energy service demand, respectively. If a single market price of negative externalities is considered, a societal cost-effective potential of energy savings above 30% (compared to the baseline) is observed. In environmental terms, the resulting greenhouse gas emission reductions are around 200 Mt CO 2-eq by 2010, representing nearly 60% of the EU-Kyoto-target. From the qualitative perspective, several embedded ancillary benefits are identified (e.g. employment generation, improved comfort level, reduced 'fuel poverty', security of energy supply). Whereas an EU-wide TWC increases liquidity and reduces the risks of market power, autarky compliance strategies may be expected in order to capture co-benefits nationally. Cross subsidies could occur due to investment recovery mechanisms and there is a risk that effects may be regressive for low-income households. Assumptions undertaken by the modelling approach strongly indicate that high effectiveness of other policy instruments is needed for an EU-wide TWC scheme to be cost-effective

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

NARCIS (Netherlands)

Mooijman, Dylan; Dey, Siddharth S; Boisset, Jean-Charles; Crosetto, Nicola; van Oudenaarden, Alexander

2016-01-01

The epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) has crucial roles in development and gene regulation. Quantifying the abundance of this epigenetic mark at the single-cell level could enable us to understand its roles. We present a single-cell, genome-wide and strand-specific 5hmC

World wide web implementation of the Langley technical report server

Science.gov (United States)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.

1994-01-01

On January 14, 1993, NASA Langley Research Center (LaRC) made approximately 130 formal, 'unclassified, unlimited' technical reports available via the anonymous FTP Langley Technical Report Server (LTRS). LaRC was the first organization to provide a significant number of aerospace technical reports for open electronic dissemination. LTRS has been successful in its first 18 months of operation, with over 11,000 reports distributed and has helped lay the foundation for electronic document distribution for NASA. The availability of World Wide Web (WWW) technology has revolutionized the Internet-based information community. This paper describes the transition of LTRS from a centralized FTP site to a distributed data model using the WWW, and suggests how the general model for LTRS can be applied to other similar systems.

Languages, compilers and run-time environments for distributed memory machines

CERN Document Server

Saltz, J

1992-01-01

Papers presented within this volume cover a wide range of topics related to programming distributed memory machines. Distributed memory architectures, although having the potential to supply the very high levels of performance required to support future computing needs, present awkward programming problems. The major issue is to design methods which enable compilers to generate efficient distributed memory programs from relatively machine independent program specifications. This book is the compilation of papers describing a wide range of research efforts aimed at easing the task of programmin

Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

Directory of Open Access Journals (Sweden)

Johannes Asplund-Samuelsson

Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

Collaborative Information Agents on the World Wide Web

Science.gov (United States)

Chen, James R.; Mathe, Nathalie; Wolfe, Shawn; Koga, Dennis J. (Technical Monitor)

1998-01-01

In this paper, we present DIAMS, a system of distributed, collaborative information agents which help users access, collect, organize, and exchange information on the World Wide Web. Personal agents provide their owners dynamic displays of well organized information collections, as well as friendly information management utilities. Personal agents exchange information with one another. They also work with other types of information agents such as matchmakers and knowledge experts to facilitate collaboration and communication.

Multilocus dataset reveals demographic histories of two peat mosses in Europe

Directory of Open Access Journals (Sweden)

Hock Zsófia

2007-08-01

Full Text Available Abstract Background Revealing the past and present demographic history of populations is of high importance to evaluate the conservation status of species. Demographic data can be obtained by direct monitoring or by analysing data of historical and recent collections. Although these methods provide the most detailed information they are very time consuming. Another alternative way is to make use of the information accumulated in the species' DNA over its history. Recent development of the coalescent theory makes it possible to reconstruct the demographic history of species using nucleotide polymorphism data. To separate the effect of natural selection and demography, multilocus analysis is needed because these two forces can produce similar patterns of polymorphisms. In this study we investigated the amount and pattern of sequence variability of a Europe wide sample set of two peat moss species (Sphagnum fimbriatum and S. squarrosum with similar distributions and mating systems but presumably contrasting historical demographies using 3 regions of the nuclear genome (appr. 3000 bps. We aimed to draw inferences concerning demographic, and phylogeographic histories of the species. Results All three nuclear regions supported the presence of an Atlantic and Non-Atlantic clade of S. fimbriatum suggesting glacial survival of the species along the Atlantic coast of Europe. Contrarily, S. squarrosum haplotypes showed three clades but no geographic structure at all. Maximum likelihood, mismatch and Bayesian analyses supported a severe historical bottleneck and a relatively recent demographic expansion of the Non-Atlantic clade of S. fimbriatum, whereas size of S. squarrosum populations has probably decreased in the past. Species wide molecular diversity of the two species was nearly the same with an excess of replacement mutations in S. fimbriatum. Similar levels of molecular diversity, contrasting phylogeographic patterns and excess of replacement

Transition from Exponential to Power Law Income Distributions in a Chaotic Market

Science.gov (United States)

Pellicer-Lostao, Carmen; Lopez-Ruiz, Ricardo

Economy is demanding new models, able to understand and predict the evolution of markets. To this respect, Econophysics offers models of markets as complex systems, that try to comprehend macro-, system-wide states of the economy from the interaction of many agents at micro-level. One of these models is the gas-like model for trading markets. This tries to predict money distributions in closed economies and quite simply, obtains the ones observed in real economies. However, it reveals technical hitches to explain the power law distribution, observed in individuals with high incomes. In this work, nonlinear dynamics is introduced in the gas-like model in an effort to overcomes these flaws. A particular chaotic dynamics is used to break the pairing symmetry of agents (i, j) ⇔ (j, i). The results demonstrate that a "chaotic gas-like model" can reproduce the Exponential and Power law distributions observed in real economies. Moreover, it controls the transition between them. This may give some insight of the micro-level causes that originate unfair distributions of money in a global society. Ultimately, the chaotic model makes obvious the inherent instability of asymmetric scenarios, where sinks of wealth appear and doom the market to extreme inequality.

Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure

NARCIS (Netherlands)

Visconti, A. (Alessia); D.L. Duffy (David); F. Liu (Fan); G. Zhu (Gu); Wu, W. (Wenting); C. Yan (Chen); P.G. Hysi (Pirro); C. Zeng (Changqing); Sanna, M. (Marianna); M.M. Iles (Mark M.); P.P. Kanetsky (Peter P.); F. Demenais (Florence); M.A. Hamer (Merel); A.G. Uitterlinden (André); M.A. Ikram (Arfan); T.E.C. Nijsten (Tamar); N.G. Martin (Nicholas); M.H. Kayser (Manfred); T.D. Spector (Timothy); J. Han (Jiali); V. Bataille (Veronique); M. Falchi (Mario)

2018-01-01

textabstractThe skin's tendency to sunburn rather than tan is a major risk factor for skin cancer. Here we report a large genome-wide association study of ease of skin tanning in 176,678 subjects of European ancestry. We identify significant association with tanning ability at 20 loci. We confirm

Synthesizing genome-wide association studies and expression microarray reveals novel genes that act in the human growth plate to modulate height.

Science.gov (United States)

Lui, Julian C; Nilsson, Ola; Chan, Yingleong; Palmer, Cameron D; Andrade, Anenisia C; Hirschhorn, Joel N; Baron, Jeffrey

2012-12-01

Previous meta-analysis of genome-wide association (GWA) studies has identified 180 loci that influence adult height. However, each GWA locus typically comprises a set of contiguous genes, only one of which presumably modulates height. We reasoned that many of the causative genes within these loci influence height because they are expressed in and function in the growth plate, a cartilaginous structure that causes bone elongation and thus determines stature. Therefore, we used expression microarray studies of mouse and rat growth plate, human disease databases and a mouse knockout phenotype database to identify genes within the GWAS loci that are likely required for normal growth plate function. Each of these approaches identified significantly more genes within the GWA height loci than at random genomic locations (P analysis strongly implicates 78 genes in growth plate function, including multiple genes that participate in PTHrP-IHH, BMP and CNP signaling, and many genes that have not previously been implicated in the growth plate. Thus, this analysis reveals a large number of novel genes that regulate human growth plate chondrogenesis and thereby contribute to the normal variations in human adult height. The analytic approach developed for this study may be applied to GWA studies for other common polygenic traits and diseases, thus providing a new general strategy to identify causative genes within GWA loci and to translate genetic associations into mechanistic biological insights.

MALDI-MS Imaging Analysis of Fungicide Residue Distributions on Wheat Leaf Surfaces.

Science.gov (United States)

Annangudi, Suresh P; Myung, Kyung; Avila Adame, Cruz; Gilbert, Jeffrey R

2015-05-05

Improved retention and distribution of agrochemicals on plant surfaces is an important attribute in the biological activity of pesticide. Although retention of agrochemicals on plants after spray application can be quantified using traditional analytical techniques including LC or GC, the spatial distribution of agrochemicals on the plants surfaces has received little attention. Matrix assisted laser desorption/ionization (MALDI) imaging technology has been widely used to determine the distribution of proteins, peptides and metabolites in different tissue sections, but its application to environmental research has been limited. Herein, we probed the potential utility of MALDI imaging in characterizing the distribution of three commercial fungicides on wheat leaf surfaces. Using this MALDI imaging method, we were able to detect 500 ng of epoxiconazole, azoxystrobin, and pyraclostrobin applied in 1 μL drop on the leaf surfaces using MALDI-MS. Subsequent dilutions of pyraclostrobin revealed that the compound can be chemically imaged on the leaf surfaces at levels as low as 60 ng of total applied in the area of 1 μL droplet. After application of epoxiconazole, azoxystrobin, and pyraclostrobin at a field rate of 100 gai/ha in 200 L water using a track sprayer system, residues of these fungicides on the leaf surfaces were sufficiently visualized. These results suggest that MALDI imaging can be used to monitor spatial distribution of agrochemicals on leaf samples after pesticide application.

Genome-wide identification and expression analysis of MAPK and MAPKK gene family in Malus domestica.

Science.gov (United States)

Zhang, Shizhong; Xu, Ruirui; Luo, Xiaocui; Jiang, Zesheng; Shu, Huairui

2013-12-01

MAPK signal transduction modules play crucial roles in regulating many biological processes in plants, which are composed of three classes of hierarchically organized protein kinases, namely MAPKKKs, MAPKKs, and MAPKs. Although genome-wide analysis of this family has been carried out in some species, little is known about MAPK and MAPKK genes in apple (Malus domestica). In this study, a total of 26 putative apple MAPK genes (MdMPKs) and 9 putative apple MAPKK genes (MdMKKs) have been identified and located within the apple genome. Phylogenetic analysis revealed that MdMAPKs and MdMAPKKs could be divided into 4 subfamilies (groups A, B, C and D), respectively. The predicted MdMAPKs and MdMAPKKs were distributed across 13 out of 17 chromosomes with different densities. In addition, analysis of exon-intron junctions and of intron phase inside the predicted coding region of each candidate gene has revealed high levels of conservation within and between phylogenetic groups. According to the microarray and expressed sequence tag (EST) analysis, the different expression patterns indicate that they may play different roles during fruit development and rootstock-scion interaction process. Moreover, MAPK and MAPKK genes were performed expression profile analyses in different tissues (root, stem, leaf, flower and fruit), and all of the selected genes were expressed in at least one of the tissues tested, indicating that the MAPKs and MAPKKs are involved in various aspects of physiological and developmental processes of apple. To our knowledge, this is the first report of a genome-wide analysis of the apple MAPK and MAPKK gene family. This study provides valuable information for understanding the classification and putative functions of the MAPK signal in apple. © 2013.

Pollen limitation and reduced reproductive success are associated with local genetic effects in Prunus virginiana, a widely distributed self-incompatible shrub.

Science.gov (United States)

Suarez-Gonzalez, Adriana; Good, Sara V

2014-03-01

A vast quantity of empirical evidence suggests that insufficient quantity or quality of pollen may lead to a reduction in fruit set, in particular for self-incompatible species. This study uses an integrative approach that combines field research with marker gene analysis to understand the factors affecting reproductive success in a widely distributed self-incompatible species, Prunus virginiana (Rosaceae). Twelve patches of P. virginiana distributed within three populations that differed in degree of disturbance were examined. Two of the sites were small (7-35 km(2)) remnants of forest in an intensively used agricultural landscape, while the third was continuous (350 km(2)) and less disturbed. Field studies (natural and hand cross-pollinations) were combined with marker gene analyses (microsatellites and S-locus) in order to explore potential factors affecting pollen delivery and consequently reproductive success at landscape (between populations) and fine scales (within populations). Reductions in reproductive output were found in the two fragments compared with the continuous population, and suggest that pollen is an important factor limiting fruit production. Genetic analyses carried out in one of the fragments and in the continuous site suggest that even though S-allele diversity is high in both populations, the fragment exhibits an increase in biparental inbreeding and correlated paternity. The increase in biparental inbreeding in the fragment is potentially attributable to variation in the density of individuals and/or the spatial distribution of genotypes among populations, both of which could alter mating dynamics. By using a novel integrative approach, this study shows that even though P. virginiana is a widespread species, fragmented populations can experience significant reductions in fruit set and pollen limitation in the field. Deatiled examination of one fragmented population suggests that these linitations may be explained by an increase in

LD Score regression distinguishes confounding from polygenicity in genome-wide association studies

DEFF Research Database (Denmark)

Bulik-Sullivan, Brendan K.; Loh, Po-Ru; Finucane, Hilary K.

2015-01-01

Both polygenicity (many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield an inflated distribution of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from...

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Science.gov (United States)

vonHoldt, Bridgett M.; Pollinger, John P.; Lohmueller, Kirk E.; Han, Eunjung; Parker, Heidi G.; Quignon, Pascale; Degenhardt, Jeremiah D.; Boyko, Adam R.; Earl, Dent A.; Auton, Adam; Reynolds, Andy; Bryc, Kasia; Brisbin, Abra; Knowles, James C.; Mosher, Dana S.; Spady, Tyrone C.; Elkahloun, Abdel; Geffen, Eli; Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Greco, Claudia; Randi, Ettore; Bannasch, Danika; Wilton, Alan; Shearman, Jeremy; Musiani, Marco; Cargill, Michelle; Jones, Paul G.; Qian, Zuwei; Huang, Wei; Ding, Zhao-Li; Zhang, Ya-ping; Bustamante, Carlos D.; Ostrander, Elaine A.; Novembre, John; Wayne, Robert K.

2010-01-01

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1,2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity. PMID:20237475

Stress distribution and topography of Tellus Regio, Venus

Science.gov (United States)

Williams, David R.; Greeley, Ronald

1989-01-01

The Tellus Regio area of Venus represents a subset of a narrow latitude band where Pioneer Venus Orbiter (PVO) altimetry data, line-of-sight (LOS) gravity data, and Venera 15/16 radar images have all been obtained with good resolution. Tellus Regio also has a wide variety of surface morphologic features, elevations ranging up to 2.5 km, and a relatively low LOS gravity anomaly. This area was therefore chosen in order to examine the theoretical stress distributions resulting from various models of compensation of the observed topography. These surface stress distributions are then compared with the surface morphology revealed in the Venera 15/16 radar images. Conclusions drawn from these comparisons will enable constraints to be put on various tectonic parameters relevant to Tellus Regio. The stress distribution is calculated as a function of the topography, the equipotential anomaly, and the assumed model parameters. The topography data is obtained from the PVO altimetry. The equipotential anomaly is estimated from the PVO LOS gravity data. The PVO LOS gravity represents the spacecraft accelerations due to mass anomalies within the planet. These accelerations are measured at various altitudes and angles to the local vertical and therefore do not lend themselves to a straightforward conversion. A minimum variance estimator of the LOS gravity data is calculated, taking into account the various spacecraft altitudes and LOS angles and using the measured PVO topography as an a priori constraint. This results in an estimated equivalent surface mass distribution, from which the equipotential anomaly is determined.

Stress distribution and topography of Tellus Regio, Venus

International Nuclear Information System (INIS)

Williams, D.R.; Greeley, R.

1989-01-01

The Tellus Regio area of Venus represents a subset of a narrow latitude band where Pioneer Venus Orbiter (PVO) altimetry data, line-of-sight (LOS) gravity data, and Venera 15/16 radar images have all been obtained with good resolution. Tellus Regio also has a wide variety of surface morphologic features, elevations ranging up to 2.5 km, and a relatively low LOS gravity anomaly. This area was therefore chosen in order to examine the theoretical stress distributions resulting from various models of compensation of the observed topography. These surface stress distributions are then compared with the surface morphology revealed in the Venera 15/16 radar images. Conclusions drawn from these comparisons will enable constraints to be put on various tectonic parameters relevant to Tellus Regio. The stress distribution is calculated as a function of the topography, the equipotential anomaly, and the assumed model parameters. The topography data is obtained from the PVO altimetry. The equipotential anomaly is estimated from the PVO LOS gravity data. The PVO LOS gravity represents the spacecraft accelerations due to mass anomalies within the planet. These accelerations are measured at various altitudes and angles to the local vertical and therefore do not lend themselves to a straightforward conversion. A minimum variance estimator of the LOS gravity data is calculated, taking into account the various spacecraft altitudes and LOS angles and using the measured PVO topography as an a priori constraint. This results in an estimated equivalent surface mass distribution, from which the equipotential anomaly is determined

Exome-wide association study reveals novel susceptibility genes to sporadic dilated cardiomyopathy.

Directory of Open Access Journals (Sweden)

Ulrike Esslinger

Full Text Available Dilated cardiomyopathy (DCM is an important cause of heart failure with a strong familial component. We performed an exome-wide array-based association study (EWAS to assess the contribution of missense variants to sporadic DCM.116,855 single nucleotide variants (SNVs were analyzed in 2796 DCM patients and 6877 control subjects from 6 populations of European ancestry. We confirmed two previously identified associations with SNVs in BAG3 and ZBTB17 and discovered six novel DCM-associated loci (Q-value<0.01. The lead-SNVs at novel loci are common and located in TTN, SLC39A8, MLIP, FLNC, ALPK3 and FHOD3. In silico fine mapping identified HSPB7 as the most likely candidate at the ZBTB17 locus. Rare variant analysis (MAF<0.01 demonstrated significant association for TTN variants only (P = 0.0085. All candidate genes but one (SLC39A8 exhibit preferential expression in striated muscle tissues and mutations in TTN, BAG3, FLNC and FHOD3 are known to cause familial cardiomyopathy. We also investigated a panel of 48 known cardiomyopathy genes. Collectively, rare (n = 228, P = 0.0033 or common (n = 36, P = 0.019 variants with elevated in silico severity scores were associated with DCM, indicating that the spectrum of genes contributing to sporadic DCM extends beyond those identified here.We identified eight loci independently associated with sporadic DCM. The functions of the best candidate genes at these loci suggest that proteostasis regulation might play a role in DCM pathophysiology.

Applied techniques for high bandwidth data transfers across wide area networks

International Nuclear Information System (INIS)

Lee, J.; Gunter, D.; Tierney, B.; Allcock, B.; Bester, J.; Bresnahan, J.; Tuecke, S.

2001-01-01

Large distributed systems such as Computational/Data Grids require large amounts of data to be co-located with the computing facilities for processing. From their work developing a scalable distributed network cache, the authors have gained experience with techniques necessary to achieve high data throughput over high bandwidth Wide Area Networks (WAN). The authors discuss several hardware and software design techniques, and then describe their application to an implementation of an enhanced FTP protocol called GridFTP. The authors describe results from the Supercomputing 2000 conference

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

OpenAIRE

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gen...

Quantification and genome-wide mapping of DNA double-strand breaks.

Science.gov (United States)

Grégoire, Marie-Chantal; Massonneau, Julien; Leduc, Frédéric; Arguin, Mélina; Brazeau, Marc-André; Boissonneault, Guylain

2016-12-01

DNA double-strand breaks (DSBs) represent a major threat to the genetic integrity of the cell. Knowing both their genome-wide distribution and number is important for a better assessment of genotoxicity at a molecular level. Available methods may have underestimated the extent of DSBs as they are based on markers specific to those undergoing active repair or may not be adapted for the large diversity of naturally occurring DNA ends. We have established conditions for an efficient first step of DNA nick and gap repair (NGR) allowing specific determination of DSBs by end labeling with terminal transferase. We used DNA extracted from HeLa cells harboring an I-SceI cassette to induce a targeted nick or DSB and demonstrated by immunocapture of 3'-OH that a prior step of NGR allows specific determination of loci-specific or genome wide DSBs. This method can be applied to the global determination of DSBs using radioactive end labeling and can find several applications aimed at understanding the distribution and kinetics of DSBs formation and repair. Copyright © 2016 Elsevier B.V. All rights reserved.

GeoCENS: a geospatial cyberinfrastructure for the world-wide sensor web.

Science.gov (United States)

Liang, Steve H L; Huang, Chih-Yuan

2013-10-02

The world-wide sensor web has become a very useful technique for monitoring the physical world at spatial and temporal scales that were previously impossible. Yet we believe that the full potential of sensor web has thus far not been revealed. In order to harvest the world-wide sensor web's full potential, a geospatial cyberinfrastructure is needed to store, process, and deliver large amount of sensor data collected worldwide. In this paper, we first define the issue of the sensor web long tail followed by our view of the world-wide sensor web architecture. Then, we introduce the Geospatial Cyberinfrastructure for Environmental Sensing (GeoCENS) architecture and explain each of its components. Finally, with demonstration of three real-world powered-by-GeoCENS sensor web applications, we believe that the GeoCENS architecture can successfully address the sensor web long tail issue and consequently realize the world-wide sensor web vision.

Genome-wide association study reveals greater polygenic loading for schizophrenia in cases with a family history of illness

DEFF Research Database (Denmark)

Bigdeli, Tim B.; Ripke, Stephan; Bacanu, Silviu-Alin

2016-01-01

Genome-wide association studies (GWAS) of schizophrenia have yielded more than 100 common susceptibility variants, and strongly support a substantial polygenic contribution of a large number of small allelic effects. It has been hypothesized that familial schizophrenia is largely a consequence...... of inherited rather than environmental factors. We investigated the extent to which familiality of schizophrenia is associated with enrichment for common risk variants detectable in a large GWAS. We analyzed single nucleotide polymorphism (SNP) data for cases reporting a family history of psychotic illness (N...... history subgroup. Comparison of genome-wide polygenic risk scores based on GWAS summary statistics indicated a significant enrichment for SNP effects among family history positive compared to family history negative cases (Nagelkerke's R2=0.0021; P=0.00331; P-value threshold

A multi-agent system for distribution grid congestion management with electric vehicles

DEFF Research Database (Denmark)

Hu, Junjie; Saleem, Arshad; You, Shi

2015-01-01

Electric vehicles (EVs) are widely regarded as valuable assets in the smart grid as distributed energy resources in addition to their primary transportation function. However, connecting EVs to the distribution network and recharging the EV batteries without any control may overload the transform......Electric vehicles (EVs) are widely regarded as valuable assets in the smart grid as distributed energy resources in addition to their primary transportation function. However, connecting EVs to the distribution network and recharging the EV batteries without any control may overload...

Predictive modelling of grain size distributions from marine electromagnetic profiling data using end-member analysis and a radial basis function network

Science.gov (United States)

Baasch, B.; M"uller, H.; von Dobeneck, T.

2018-04-01

In this work we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine learning techniques. Nonnegative matrix factorisation is used to determine grain-size end-members from sediment surface samples. Four end-members were found which well represent the variety of sediments in the study area. A radial-basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.

Single quantum dot tracking reveals the impact of nanoparticle surface on intracellular state.

Science.gov (United States)

Zahid, Mohammad U; Ma, Liang; Lim, Sung Jun; Smith, Andrew M

2018-05-08

Inefficient delivery of macromolecules and nanoparticles to intracellular targets is a major bottleneck in drug delivery, genetic engineering, and molecular imaging. Here we apply live-cell single-quantum-dot imaging and tracking to analyze and classify nanoparticle states after intracellular delivery. By merging trajectory diffusion parameters with brightness measurements, multidimensional analysis reveals distinct and heterogeneous populations that are indistinguishable using single parameters alone. We derive new quantitative metrics of particle loading, cluster distribution, and vesicular release in single cells, and evaluate intracellular nanoparticles with diverse surfaces following osmotic delivery. Surface properties have a major impact on cell uptake, but little impact on the absolute cytoplasmic numbers. A key outcome is that stable zwitterionic surfaces yield uniform cytosolic behavior, ideal for imaging agents. We anticipate that this combination of quantum dots and single-particle tracking can be widely applied to design and optimize next-generation imaging probes, nanoparticle therapeutics, and biologics.

Financing Distributed Generation

Energy Technology Data Exchange (ETDEWEB)

Walker, A.

2001-06-29

This paper introduces the engineer who is undertaking distributed generation projects to a wide range of financing options. Distributed generation systems (such as internal combustion engines, small gas turbines, fuel cells and photovoltaics) all require an initial investment, which is recovered over time through revenues or savings. An understanding of the cost of capital and financing structures helps the engineer develop realistic expectations and not be offended by the common requirements of financing organizations. This paper discusses several mechanisms for financing distributed generation projects: appropriations; debt (commercial bank loan); mortgage; home equity loan; limited partnership; vendor financing; general obligation bond; revenue bond; lease; Energy Savings Performance Contract; utility programs; chauffage (end-use purchase); and grants. The paper also discusses financial strategies for businesses focusing on distributed generation: venture capital; informal investors (''business angels''); bank and debt financing; and the stock market.

Vertical Distribution of Pasteuria penetrans Parasitizing Meloidogyne incognita on Pittosporum tobira in Florida.

Science.gov (United States)

Baidoo, Richard; Mengistu, Tesfamariam Mekete; Brito, Janete A; McSorley, Robert; Stamps, Robert H; Crow, William T

2017-09-01

Pasteuria penetrans is considered as the primary agent responsible for soil suppressiveness to root-knot nematodes widely distributed in many agricultural fields. A preliminary survey on a Pittosporum tobira field where the grower had experienced a continuous decline in productivity caused by Meloidogyne incognita showed that the nematode was infected with Pasteuria penetrans . For effective control of the nematode, the bacterium and the host must coexist in the same root zone. The vertical distribution of Pasteuria penetrans and its relationship with the nematode host in the soil was investigated to identify (i) the vertical distribution of P. penetrans endospores in an irrigated P. tobira field and (ii) the relationship among P. penetrans endospore density, M. incognita J2 population density, and host plant root distribution over time. Soil bioassays revealed that endospore density was greater in the upper 18 cm of the top soil compared with the underlying depths. A correlation analysis showed that the endospore density was positively related to the J2 population density and host plant root distribution. Thus, the vertical distribution of P. penetrans was largely dependent on its nematode host which in turn was determined by the distribution of the host plant roots. The Pasteuria was predominant mostly in the upper layers of the soil where their nematode host and the plant host roots are abundant, a factor which may be a critical consideration when using P. penetrans as a nematode biological control agent.

Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

Science.gov (United States)

Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

2016-06-01

Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

Use DNA to learn from the past: how modern and ancient DNA studies may help reveal the past and predict the future distribution of species

Science.gov (United States)

Edwards, M. E.; Alsos, I. G.; Sjögren, P.; Coissac, E.; Gielly, L.; Yoccoz, N.; Føreid, M. K.; Taberlet, P.

2015-12-01

Knowledge of how climate change affected species distribution in the past may help us predict the effect of ongoing environmental changes. We explore how the use of modern (AFLP fingerprinting techniques) and ancient DNA (metabarcoding P6 loop of chloroplast DNA) help to reveal past distribution of vascular plant species, dispersal processes, and effect of species traits. Based on studies of modern DNA combined with species distribution models, we show the dispersal routes and barriers to dispersal throughout the circumarctic/circumboreal region, likely dispersal vectors, the cost of dispersal in term of loss of genetic diversity, and how these relates to species traits, dispersal distance, and size of colonized region. We also estimate the expected future distribution and loss of genetic diversity and show how this relates to life form and adaptations to dispersal. To gain more knowledge on time lags in past range change events, we rely on palaeorecords. Current data on past distribution are limited by the taxonomic and time resolution of macrofossil and pollen records. We show how this may be improved by studying ancient DNA of lake sediments. DNA of lake sediments recorded about half of the flora surrounding the lake. Compared to macrofossil, the taxonomic resolution is similar but the detection rate is considerable improved. By taking into account main determinants of founder effect, dispersal vectors, and dispersal lags, we may improve our ability to forecast effects of climate change, whereas more studies on ancient DNA may provide us with knowledge on distribution time lags.

Temperature profile data from XBT casts from a world-wide distribution from the SEA-LAND HAWAII and other platforms as part of NOAA's Volunteer Observing Ships Program from 05 January 2000 to 26 February 2002 (NODC Accession 0000679)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature profiles were collected by using XBT casts from the SEA-LAND HAWAII and other platforms from a world-wide distribution from 05 January 2000 to 26...

Transformation of Bayesian posterior distribution into a basic analytical distribution

International Nuclear Information System (INIS)

Jordan Cizelj, R.; Vrbanic, I.

2002-01-01

Bayesian estimation is well-known approach that is widely used in Probabilistic Safety Analyses for the estimation of input model reliability parameters, such as component failure rates or probabilities of failure upon demand. In this approach, a prior distribution, which contains some generic knowledge about a parameter is combined with likelihood function, which contains plant-specific data about the parameter. Depending on the type of prior distribution, the resulting posterior distribution can be estimated numerically or analytically. In many instances only a numerical Bayesian integration can be performed. In such a case the posterior is provided in the form of tabular discrete distribution. On the other hand, it is much more convenient to have a parameter's uncertainty distribution that is to be input into a PSA model to be provided in the form of some basic analytical probability distribution, such as lognormal, gamma or beta distribution. One reason is that this enables much more convenient propagation of parameters' uncertainties through the model up to the so-called top events, such as plant system unavailability or core damage frequency. Additionally, software tools used to run PSA models often require that parameter's uncertainty distribution is defined in the form of one among the several allowed basic types of distributions. In such a case the posterior distribution that came as a product of Bayesian estimation needs to be transformed into an appropriate basic analytical form. In this paper, some approaches on transformation of posterior distribution to a basic probability distribution are proposed and discussed. They are illustrated by an example from NPP Krsko PSA model.(author)

The features of modelling semiconductor lasers with a wide contact

Directory of Open Access Journals (Sweden)

Rzhanov Alexey

2017-01-01

Full Text Available The aspects of calculating the dynamics and statics of powerful semiconductor laser diodes radiation are investigated. It takes into account the main physical mechanisms influencing power, spectral composition, far and near field of laser radiation. It outlines a dynamic distributed model of a semiconductor laser with a wide contact and possible algorithms for its implementation.

Genome-wide population structure and admixture analysis reveals weak differentiation among Ugandan goat breeds.

Science.gov (United States)

Onzima, R B; Upadhyay, M R; Mukiibi, R; Kanis, E; Groenen, M A M; Crooijmans, R P M A

2018-02-01

Uganda has a large population of goats, predominantly from indigenous breeds reared in diverse production systems, whose existence is threatened by crossbreeding with exotic Boer goats. Knowledge about the genetic characteristics and relationships among these Ugandan goat breeds and the potential admixture with Boer goats is still limited. Using a medium-density single nucleotide polymorphism (SNP) panel, we assessed the genetic diversity, population structure and admixture in six goat breeds in Uganda: Boer, Karamojong, Kigezi, Mubende, Small East African and Sebei. All the animals had genotypes for about 46 105 SNPs after quality control. We found high proportions of polymorphic SNPs ranging from 0.885 (Kigezi) to 0.928 (Sebei). The overall mean observed (H O ) and expected (H E ) heterozygosity across breeds was 0.355 ± 0.147 and 0.384 ± 0.143 respectively. Principal components, genetic distances and admixture analyses revealed weak population sub-structuring among the breeds. Principal components separated Kigezi and weakly Small East African from other indigenous goats. Sebei and Karamojong were tightly entangled together, whereas Mubende occupied a more central position with high admixture from all other local breeds. The Boer breed showed a unique cluster from the Ugandan indigenous goat breeds. The results reflect common ancestry but also some level of geographical differentiation. admixture and f 4 statistics revealed gene flow from Boer and varying levels of genetic admixture among the breeds. Generally, moderate to high levels of genetic variability were observed. Our findings provide useful insights into maintaining genetic diversity and designing appropriate breeding programs to exploit within-breed diversity and heterozygote advantage in crossbreeding schemes. © 2018 The Authors. Animal Genetics published by John Wiley & Sons Ltd on behalf of Stichting International Foundation for Animal Genetics.

Whole-genome characterization of Uruguayan strains of avian infectious bronchitis virus reveals extensive recombination between the two major South American lineages.

Science.gov (United States)

Marandino, Ana; Tomás, Gonzalo; Panzera, Yanina; Greif, Gonzalo; Parodi-Talice, Adriana; Hernández, Martín; Techera, Claudia; Hernández, Diego; Pérez, Ruben

2017-10-01

Infectious bronchitis virus (Gammacoronavirus, Coronaviridae) is a genetically variable RNA virus that causes one of the most persistent respiratory diseases in poultry. The virus is classified in genotypes and lineages with different epidemiological relevance. Two lineages of the GI genotype (11 and 16) have been widely circulating for decades in South America. GI-11 is an exclusive South American lineage while the GI-16 lineage is distributed in Asia, Europe and South America. Here, we obtained the whole genome of two Uruguayan strains of the GI-11 and GI-16 lineages using Illumina high-throughput sequencing. The strains here sequenced are the first obtained in South America for the infectious bronchitis virus and provide new insights into the origin, spreading and evolution of viral variants. The complete genome of the GI-11 and GI-16 strains have 27,621 and 27,638 nucleotides, respectively, and possess the same genomic organization. Phylogenetic incongruence analysis reveals that both strains have a mosaic genome that arose by recombination between Euro Asiatic strains of the GI-16 lineage and ancestral South American GI-11 viruses. The recombination occurred in South America and produced two viral variants that have retained the full-length S1 sequences of the parental lineages but are extremely similar in the rest of their genomes. These recombinant virus have been extraordinary successful, persisting in the continent for several years with a notorious wide geographic distribution. Our findings reveal a singular viral dynamics and emphasize the importance of complete genomic characterization to understand the emergence and evolutionary history of viral variants. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatially Explicit Modeling Reveals Cephalopod Distributions Match Contrasting Trophic Pathways in the Western Mediterranean Sea.

Directory of Open Access Journals (Sweden)

Patricia Puerta

Full Text Available Populations of the same species can experience different responses to the environment throughout their distributional range as a result of spatial and temporal heterogeneity in habitat conditions. This highlights the importance of understanding the processes governing species distribution at local scales. However, research on species distribution often averages environmental covariates across large geographic areas, missing variability in population-environment interactions within geographically distinct regions. We used spatially explicit models to identify interactions between species and environmental, including chlorophyll a (Chla and sea surface temperature (SST, and trophic (prey density conditions, along with processes governing the distribution of two cephalopods with contrasting life-histories (octopus and squid across the western Mediterranean Sea. This approach is relevant for cephalopods, since their population dynamics are especially sensitive to variations in habitat conditions and rarely stable in abundance and location. The regional distributions of the two cephalopod species matched two different trophic pathways present in the western Mediterranean Sea, associated with the Gulf of Lion upwelling and the Ebro river discharges respectively. The effects of the studied environmental and trophic conditions were spatially variant in both species, with usually stronger effects along their distributional boundaries. We identify areas where prey availability limited the abundance of cephalopod populations as well as contrasting effects of temperature in the warmest regions. Despite distributional patterns matching productive areas, a general negative effect of Chla on cephalopod densities suggests that competition pressure is common in the study area. Additionally, results highlight the importance of trophic interactions, beyond other common environmental factors, in shaping the distribution of cephalopod populations. Our study presents

Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

Directory of Open Access Journals (Sweden)

Karima Fadhlaoui-Zid

Full Text Available The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

Genome-wide and paternal diversity reveal a recent origin of human populations in North Africa.

Science.gov (United States)

Fadhlaoui-Zid, Karima; Haber, Marc; Martínez-Cruz, Begoña; Zalloua, Pierre; Benammar Elgaaied, Amel; Comas, David

2013-01-01

The geostrategic location of North Africa as a crossroad between three continents and as a stepping-stone outside Africa has evoked anthropological and genetic interest in this region. Numerous studies have described the genetic landscape of the human population in North Africa employing paternal, maternal, and biparental molecular markers. However, information from these markers which have different inheritance patterns has been mostly assessed independently, resulting in an incomplete description of the region. In this study, we analyze uniparental and genome-wide markers examining similarities or contrasts in the results and consequently provide a comprehensive description of the evolutionary history of North Africa populations. Our results show that both males and females in North Africa underwent a similar admixture history with slight differences in the proportions of admixture components. Consequently, genome-wide diversity show similar patterns with admixture tests suggesting North Africans are a mixture of ancestral populations related to current Africans and Eurasians with more affinity towards the out-of-Africa populations than to sub-Saharan Africans. We estimate from the paternal lineages that most North Africans emerged ∼15,000 years ago during the last glacial warming and that population splits started after the desiccation of the Sahara. Although most North Africans share a common admixture history, the Tunisian Berbers show long periods of genetic isolation and appear to have diverged from surrounding populations without subsequent mixture. On the other hand, continuous gene flow from the Middle East made Egyptians genetically closer to Eurasians than to other North Africans. We show that genetic diversity of today's North Africans mostly captures patterns from migrations post Last Glacial Maximum and therefore may be insufficient to inform on the initial population of the region during the Middle Paleolithic period.

Identification of Promising Mutants Associated with Egg Production Traits Revealed by Genome-Wide Association Study.

Directory of Open Access Journals (Sweden)

Jingwei Yuan

Full Text Available Egg number (EN, egg laying rate (LR and age at first egg (AFE are important production traits related to egg production in poultry industry. To better understand the knowledge of genetic architecture of dynamic EN during the whole laying cycle and provide the precise positions of associated variants for EN, LR and AFE, laying records from 21 to 72 weeks of age were collected individually for 1,534 F2 hens produced by reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken, and their genotypes were assayed by chicken 600 K Affymetrix high density genotyping arrays. Subsequently, pedigree and SNP-based genetic parameters were estimated and a genome-wide association study (GWAS was conducted on EN, LR and AFE. The heritability estimates were similar between pedigree and SNP-based estimates varying from 0.17 to 0.36. In the GWA analysis, we identified nine genome-wide significant loci associated with EN of the laying periods from 21 to 26 weeks, 27 to 36 weeks and 37 to 72 weeks. Analysis of GTF2A1 and CLSPN suggested that they influenced the function of ovary and uterus, and may be considered as relevant candidates. The identified SNP rs314448799 for accumulative EN from 21 to 40 weeks on chromosome 5 created phenotypic differences of 6.86 eggs between two homozygous genotypes, which could be potentially applied to the molecular breeding for EN selection. Moreover, our finding showed that LR was a moderate polygenic trait. The suggestive significant region on chromosome 16 for AFE suggested the relationship between sex maturity and immune in the current population. The present study comprehensively evaluates the role of genetic variants in the development of egg laying. The findings will be helpful to investigation of causative genes function and future marker-assisted selection and genomic selection in chickens.

Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication.

Science.gov (United States)

Xia, Xinyao; Luan, Lin Lin; Qin, Guanghua; Yu, Li Fang; Wang, Zhi Wei; Dong, Wan Chen; Song, Yumin; Qiao, Yuling; Zhang, Xian Sheng; Sang, Ya Lin; Yang, Long

2017-12-20

Molecular markers are efficient tools for breeding and genetic studies. However, despite their ecological and economic importance, their development and application have long been hampered. In this study, we identified 524,170 simple sequence repeat (SSR), 267,636 intron length polymorphism (ILP), and 11,872 potential intron polymorphism (PIP) markers from 16 tree species based on recently available genome sequences. Larger motifs, including hexamers and heptamers, accounted for most of the seven different types of SSR loci. Within these loci, A/T bases comprised a significantly larger proportion of sequence than G/C. SSR and ILP markers exhibited an alternative distribution pattern. Most SSRs were monomorphic markers, and the proportions of polymorphic markers were positively correlated with genome size. By verifying with all 16 tree species, 54 SSR, 418 ILP, and four PIP universal markers were obtained, and their efficiency was examined by PCR. A combination of five SSR and six ILP markers were used for the phylogenetic analysis of 30 willow samples, revealing a positive correlation between genetic diversity and geographic distance. We also found that SSRs can be used as tools for duplication analysis. Our findings provide important foundations for the development of breeding and genetic studies in tree species.

Compound-Specific Radiocarbon Dating Reveals the Age Distribution of Plant-Wax Biomarkers Exported to the Bengal Fan

Science.gov (United States)

Galy, V.; French, K. L.; Hein, C. J.; Haghipour, N.; Wacker, L.; Kudrass, H.; Eglinton, T. I.

2017-12-01

The stable isotope composition of leaf-wax compounds preserved in lacustrine and marine sediments has been widely used to reconstruct terrestrial paleo-environments. However, the timescales of plant-wax storage in continental reservoirs before riverine export are not well known, representing a key uncertainty in paleo-environment studies. We couple numerical models with bulk and leaf-wax fatty acid organic 13C and 14C signatures hosted in a high-deposition-rate sediment core from the Bengal shelf canyon in order to estimate storage timescales within the Ganges-Brahmaputra catchment area. The fatty acid 14C record reveals a muted nuclear weapons bomb spike, requiring that the Ganges-Brahmaputra river system exports a mixture of young and old (pre-aged) leaf-wax compounds. According to numerical simulations, 79-83% of the leaf-wax fatty acids in this core are sourced from continental reservoirs that store organic carbon on an average of 1000-1200 calendar years, while the remainder has an average age of 15 years. These results demonstrate that a majority of the leaf-wax compounds produced in the Ganges-Brahmaputra river basin was stored in soils, floodplains, and wetlands prior to its export to the Bengal Fan. We will discuss the implications of these findings for plant-wax based paleoenvironmental records.

Implementation of force distribution analysis for molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Seifert Christian

2011-04-01

Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

Applying machine learning to global surface ocean and seabed data to reveal the controls on the distribution of deep-sea sediments

Science.gov (United States)

Dutkiewicz, Adriana; Müller, Dietmar; O'Callaghan, Simon

2017-04-01

World's ocean basins contain a rich and nearly continuous record of environmental fluctuations preserved as different types of deep-sea sediments. The sediments represent the largest carbon sink on Earth and its largest geological deposit. Knowing the controls on the distribution of these sediments is essential for understanding the history of ocean-climate dynamics, including changes in sea-level and ocean circulation, as well as biological perturbations. Indeed, the bulk of deep-sea sediments comprises the remains of planktonic organisms that originate in the photic zone of the global ocean implying a strong connection between the seafloor and the sea surface. Machine-learning techniques are perfectly suited to unravelling these controls as they are able to handle large sets of spatial data and they often outperform traditional spatial analysis approaches. Using a support vector machine algorithm we recently created the first digital map of seafloor lithologies (Dutkiewicz et al., 2015) based on 14,400 surface samples. This map reveals significant deviations in distribution of deep-sea lithologies from hitherto hand-drawn maps based on far fewer data points. It also allows us to explore quantitatively, for the first time, the relationship between oceanographic parameters at the sea surface and lithologies on the seafloor. We subsequently coupled this global point sample dataset of 14,400 seafloor lithologies to bathymetry and oceanographic grids (sea-surface temperature, salinity, dissolved oxygen and dissolved inorganic nutrients) and applied a probabilistic Gaussian process classifier in an exhaustive combinatorial fashion (Dutkiewicz et al., 2016). We focused on five major lithologies (calcareous sediment, diatom ooze, radiolarian ooze, clay and lithogenous sediment) and used a computationally intensive five-fold cross-validation, withholding 20% of the data at each iteration, to assess the predictive performance of the machine learning method. We find that

Temperature profile data from STD/CTD casts from the KNORR from a world-wide distribution during the International Decade of Ocean Exploration / Geochemical Ocean Section Study (IDOE/GEOSECS) project, 24 July 1972 - 09 June 1974 (NODC Accession 8200010)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Temperature and salinity profile data were collected using STD/CTD casts from KNORR in a world-wide distribution from July 24, 1972 to June 9, 1974. Data were...

The role of environment and core-margin effects on range-wide phenotypic variation in a montane grasshopper.

Science.gov (United States)

Noguerales, V; García-Navas, V; Cordero, P J; Ortego, J

2016-11-01

The integration of genetic information with ecological and phenotypic data constitutes an effective approach to gain insight into the mechanisms determining interpopulation variability and the evolutionary processes underlying local adaptation and incipient speciation. Here, we use the Pyrenean Morales grasshopper (Chorthippus saulcyi moralesi) as study system to (i) analyse the relative role of genetic drift and selection in range-wide patterns of phenotypic differentiation and (ii) identify the potential selective agents (environment, elevation) responsible for variation. We also test the hypothesis that (iii) the development of dispersal-related traits is associated with different parameters related to population persistence/turnover, including habitat suitability stability over the last 120 000 years, distance to the species distribution core and population genetic variability. Our results indicate that selection shaped phenotypic differentiation across all the studied morphological traits (body size, forewing length and shape). Subsequent analyses revealed that among-population differentiation in forewing length was significantly explained by a temperature gradient, suggesting an adaptive response to thermoregulation or flight performance under contrasting temperature regimes. We found support for our hypothesis predicting a positive association between the distance to the species distribution core and the development of dispersal-related morphology, which suggests an increased dispersal capability in populations located at range edges that, in turn, exhibit lower levels of genetic variability. Overall, our results indicate that range-wide patterns of phenotypic variation are partially explained by adaptation in response to local environmental conditions and differences in habitat persistence between core and peripheral populations. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary

Common Distribution Patterns of Marsupials Related to Physiographical Diversity in Venezuela

Science.gov (United States)

Ventura, Jacint; Bagaria, Guillem; Sans-Fuentes, Maria Assumpció; Pérez-Hernández, Roger

2014-01-01

The aim of this study is to identify significant biotic regions (groups of areas with similar biotas) and biotic elements (groups of taxa with similar distributions) for the marsupial fauna in a part of northern South America using physiographical areas as Operational Geographical Units (OGUs). We considered Venezuela a good model to elucidate this issue because of its high diversity in landscapes and the relatively vast amount of information available on the geographical distribution of marsupial species. Based on the presence-absence of 33 species in 15 physiographical sub-regions (OGUs) we identified Operational Biogeographical Units (OBUs) and chorotypes using a quantitative analysis that tested statistical significance of the resulting groups. Altitudinal and/or climatic trends in the OBUs and chorotypes were studied using a redundancy analysis. The classification method revealed four OBUs. Strong biotic boundaries separated: i) the xerophytic zone of the Continental coast (OBU I); ii) the sub-regions north of the Orinoco River (OBU III and IV); and those south to the river (OBU II). Eleven chorotypes were identified, four of which included a single species with a restricted geographic distribution. As for the other chorotypes, three main common distribution patterns have been inferred: i) species from the Llanos and/or distributed south of the Orinoco River; ii) species exclusively from the Andes; and iii) species that either occur exclusively north of the Orinoco River or that show a wide distribution throughout Venezuela. Mean altitude, evapotranspiration and precipitation of the driest month, and temperature range allowed us to characterize environmentally most of the OBUs and chorotypes obtained. PMID:24806452

Common distribution patterns of marsupials related to physiographical diversity in Venezuela.

Directory of Open Access Journals (Sweden)

Jacint Ventura

Full Text Available The aim of this study is to identify significant biotic regions (groups of areas with similar biotas and biotic elements (groups of taxa with similar distributions for the marsupial fauna in a part of northern South America using physiographical areas as Operational Geographical Units (OGUs. We considered Venezuela a good model to elucidate this issue because of its high diversity in landscapes and the relatively vast amount of information available on the geographical distribution of marsupial species. Based on the presence-absence of 33 species in 15 physiographical sub-regions (OGUs we identified Operational Biogeographical Units (OBUs and chorotypes using a quantitative analysis that tested statistical significance of the resulting groups. Altitudinal and/or climatic trends in the OBUs and chorotypes were studied using a redundancy analysis. The classification method revealed four OBUs. Strong biotic boundaries separated: i the xerophytic zone of the Continental coast (OBU I; ii the sub-regions north of the Orinoco River (OBU III and IV; and those south to the river (OBU II. Eleven chorotypes were identified, four of which included a single species with a restricted geographic distribution. As for the other chorotypes, three main common distribution patterns have been inferred: i species from the Llanos and/or distributed south of the Orinoco River; ii species exclusively from the Andes; and iii species that either occur exclusively north of the Orinoco River or that show a wide distribution throughout Venezuela. Mean altitude, evapotranspiration and precipitation of the driest month, and temperature range allowed us to characterize environmentally most of the OBUs and chorotypes obtained.

Modeling geo-homopholy in online social networks for population distribution projection

Directory of Open Access Journals (Sweden)

Yuanxing Zhang

2017-09-01

Full Text Available Purpose – Projecting the population distribution in geographical regions is important for many applications such as launching marketing campaigns or enhancing the public safety in certain densely populated areas. Conventional studies require the collection of people’s trajectory data through offline means, which is limited in terms of cost and data availability. The wide use of online social network (OSN apps over smartphones has provided the opportunities of devising a lightweight approach of conducting the study using the online data of smartphone apps. This paper aims to reveal the relationship between the online social networks and the offline communities, as well as to project the population distribution by modeling geo-homophily in the online social networks. Design/methodology/approach – In this paper, the authors propose the concept of geo-homophily in OSNs to determine how much the data of an OSN can help project the population distribution in a given division of geographical regions. Specifically, the authors establish a three-layered theoretic framework that first maps the online message diffusion among friends in the OSN to the offline population distribution over a given division of regions via a Dirichlet process and then projects the floating population across the regions. Findings – By experiments over large-scale OSN data sets, the authors show that the proposed prediction models have a high prediction accuracy in characterizing the process of how the population distribution forms and how the floating population changes over time. Originality/value – This paper tries to project population distribution by modeling geo-homophily in OSNs.

Genome-wide mapping reveals single-origin chromosome replication in Leishmania, a eukaryotic microbe.

Science.gov (United States)

Marques, Catarina A; Dickens, Nicholas J; Paape, Daniel; Campbell, Samantha J; McCulloch, Richard

2015-10-19

DNA replication initiates on defined genome sites, termed origins. Origin usage appears to follow common rules in the eukaryotic organisms examined to date: all chromosomes are replicated from multiple origins, which display variations in firing efficiency and are selected from a larger pool of potential origins. To ask if these features of DNA replication are true of all eukaryotes, we describe genome-wide origin mapping in the parasite Leishmania. Origin mapping in Leishmania suggests a striking divergence in origin usage relative to characterized eukaryotes, since each chromosome appears to be replicated from a single origin. By comparing two species of Leishmania, we find evidence that such origin singularity is maintained in the face of chromosome fusion or fission events during evolution. Mapping Leishmania origins suggests that all origins fire with equal efficiency, and that the genomic sites occupied by origins differ from related non-origins sites. Finally, we provide evidence that origin location in Leishmania displays striking conservation with Trypanosoma brucei, despite the latter parasite replicating its chromosomes from multiple, variable strength origins. The demonstration of chromosome replication for a single origin in Leishmania, a microbial eukaryote, has implications for the evolution of origin multiplicity and associated controls, and may explain the pervasive aneuploidy that characterizes Leishmania chromosome architecture.

Equilibrium distribution function in collisionless systems

International Nuclear Information System (INIS)

Pergamenshchik, V.M.

1988-01-01

Collisionless systems of a large number of N particles interacting by Coulomb forces are widely spread in cosmic and laboratory plasma. A statistical theory of equilibrium state of collisionless Coulomb systems which evolution obeys Vlasov equation is proposed. The developed formalism permits a sequential consideration of such distributed in one-particle six-dimensional phase space of a system and to obtain a simple result: equilibrium distribution function has the form of Fermi-Dirac distribution and doesn't depend on initial state factors

Fuel flow distribution in SOFC stacks revealed by impedance spectroscopy

DEFF Research Database (Denmark)

Mosbæk, Rasmus Rode; Hjelm, Johan; Barfod, Rasmus

2014-01-01

As SOFC technology is moving closer to a commercial break through, methods to measure the “state-of-health” of operating stacks are becoming of increasing interest. This requires application of advanced methods for detailed electrical and electrochemical characterization during operation. An oper......As SOFC technology is moving closer to a commercial break through, methods to measure the “state-of-health” of operating stacks are becoming of increasing interest. This requires application of advanced methods for detailed electrical and electrochemical characterization during operation...... utilizations. The fuel flow distribution provides important information about the operating limits of the stack when high electrical efficiency is required....

Genome-wide classification and expression analysis of MYB transcription factor families in rice and Arabidopsis

Science.gov (United States)

2012-01-01

Background The MYB gene family comprises one of the richest groups of transcription factors in plants. Plant MYB proteins are characterized by a highly conserved MYB DNA-binding domain. MYB proteins are classified into four major groups namely, 1R-MYB, 2R-MYB, 3R-MYB and 4R-MYB based on the number and position of MYB repeats. MYB transcription factors are involved in plant development, secondary metabolism, hormone signal transduction, disease resistance and abiotic stress tolerance. A comparative analysis of MYB family genes in rice and Arabidopsis will help reveal the evolution and function of MYB genes in plants. Results A genome-wide analysis identified at least 155 and 197 MYB genes in rice and Arabidopsis, respectively. Gene structure analysis revealed that MYB family genes possess relatively more number of introns in the middle as compared with C- and N-terminal regions of the predicted genes. Intronless MYB-genes are highly conserved both in rice and Arabidopsis. MYB genes encoding R2R3 repeat MYB proteins retained conserved gene structure with three exons and two introns, whereas genes encoding R1R2R3 repeat containing proteins consist of six exons and five introns. The splicing pattern is similar among R1R2R3 MYB genes in Arabidopsis. In contrast, variation in splicing pattern was observed among R1R2R3 MYB members of rice. Consensus motif analysis of 1kb upstream region (5′ to translation initiation codon) of MYB gene ORFs led to the identification of conserved and over-represented cis-motifs in both rice and Arabidopsis. Real-time quantitative RT-PCR analysis showed that several members of MYBs are up-regulated by various abiotic stresses both in rice and Arabidopsis. Conclusion A comprehensive genome-wide analysis of chromosomal distribution, tandem repeats and phylogenetic relationship of MYB family genes in rice and Arabidopsis suggested their evolution via duplication. Genome-wide comparative analysis of MYB genes and their expression analysis

Live-cell and super-resolution imaging reveal that the distribution of wall-associated protein A is correlated with the cell chain integrity of Streptococcus mutans.

Science.gov (United States)

Li, Y; Liu, Z; Zhang, Y; Su, Q P; Xue, B; Shao, S; Zhu, Y; Xu, X; Wei, S; Sun, Y

2015-10-01

Streptococcus mutans is a primary pathogen responsible for dental caries. It has an outstanding ability to form biofilm, which is vital for virulence. Previous studies have shown that knockout of Wall-associated protein A (WapA) affects cell chain and biofilm formation of S. mutans. As a surface protein, the distribution of WapA remains unknown, but it is important to understand the mechanism underlying the function of WapA. This study applied the fluorescence protein mCherry as a reporter gene to characterize the dynamic distribution of WapA in S. mutans via time-lapse and super-resolution fluorescence imaging. The results revealed interesting subcellular distribution patterns of WapA in single, dividing and long chains of S. mutans cells. It appears at the middle of the cell and moves to the poles as the cell grows and divides. In a cell chain, after each round of cell division, such dynamic relocation results in WapA distribution at the previous cell division sites, resulting in a pattern where WapA is located at the boundary of two adjacent cell pairs. This WapA distribution pattern corresponds to the breaking segmentation of wapA deletion cell chains. The dynamic relocation of WapA through the cell cycle increases our understanding of the mechanism of WapA in maintaining cell chain integrity and biofilm formation. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Ecology and distribution of Lycopodiaceae Mirbel in Malaysia

NARCIS (Netherlands)

Rusea, G.; Claysius, K.; Runi, S.; Joanes, U.; Haja Maideen, K.M.; Latiff, A.

2009-01-01

This paper is the first account to discuss the distribution, ecology and habitats of the Lycopodiaceae in Malaysia. Lycopodiaceae are widely distributed throughout Malaysia with respect to altitudes and environmental conditions but most abundantly found in hill forest and lower montane forest,

GeoCENS: A Geospatial Cyberinfrastructure for the World-Wide Sensor Web

Directory of Open Access Journals (Sweden)

Steve H.L. Liang

2013-10-01

Full Text Available The world-wide sensor web has become a very useful technique for monitoring the physical world at spatial and temporal scales that were previously impossible. Yet we believe that the full potential of sensor web has thus far not been revealed. In order to harvest the world-wide sensor web’s full potential, a geospatial cyberinfrastructure is needed to store, process, and deliver large amount of sensor data collected worldwide. In this paper, we first define the issue of the sensor web long tail followed by our view of the world-wide sensor web architecture. Then, we introduce the Geospatial Cyberinfrastructure for Environmental Sensing (GeoCENS architecture and explain each of its components. Finally, with demonstration of three real-world powered-by-GeoCENS sensor web applications, we believe that the GeoCENS architecture can successfully address the sensor web long tail issue and consequently realize the world-wide sensor web vision.

Using Power-Law Degree Distribution to Accelerate PageRank

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Zhaoyan Jin

2012-12-01

Full Text Available The PageRank vector of a network is very important, for it can reflect the importance of a Web page in the World Wide Web, or of a people in a social network. However, with the growth of the World Wide Web and social networks, it needs more and more time to compute the PageRank vector of a network. In many real-world applications, the degree and PageRank distributions of these complex networks conform to the Power-Law distribution. This paper utilizes the degree distribution of a network to initialize its PageRank vector, and presents a Power-Law degree distribution accelerating algorithm of PageRank computation. Experiments on four real-world datasets show that the proposed algorithm converges more quickly than the original PageRank algorithm.

Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress.

Science.gov (United States)

Huang, Xiaosan; Li, Kongqing; Xu, Xiaoyong; Yao, Zhenghong; Jin, Cong; Zhang, Shaoling

2015-12-24

WRKY transcription factors (TFs) constitute one of the largest protein families in higher plants, and its members contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. WRKY proteins play significant roles in plant development, and in responses to biotic and abiotic stresses. Pear (Pyrus bretschneideri) is one of the most important fruit crops in the world and is frequently threatened by abiotic stress, such as drought, affecting growth, development and productivity. Although the pear genome sequence has been released, little is known about the WRKY TFs in pear, especially in respond to drought stress at the genome-wide level. We identified a total of 103 WRKY TFs in the pear genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the pear WRKY (PbWRKY) family was classified into seven groups (Groups 1, 2a-e, and 3). The microsyteny analysis indicated that 33 (32%) PbWRKY genes were tandemly duplicated and 57 genes (55.3%) were segmentally duplicated. RNA-seq experiment data and quantitative real-time reverse transcription PCR revealed that PbWRKY genes in different groups were induced by drought stress, and Group 2a and 3 were mainly involved in the biological pathways in response to drought stress. Furthermore, adaptive evolution analysis detected a significant positive selection for Pbr001425 in Group 3, and its expression pattern differed from that of other members in this group. The present study provides a solid foundation for further functional dissection and molecular evolution of WRKY TFs in pear, especially for improving the water-deficient resistance of pear through manipulation of the PbWRKYs.

Algorithms and ordering heuristics for distributed constraint satisfaction problems

CERN Document Server

Wahbi , Mohamed

2013-01-01

DisCSP (Distributed Constraint Satisfaction Problem) is a general framework for solving distributed problems arising in Distributed Artificial Intelligence.A wide variety of problems in artificial intelligence are solved using the constraint satisfaction problem paradigm. However, there are several applications in multi-agent coordination that are of a distributed nature. In this type of application, the knowledge about the problem, that is, variables and constraints, may be logically or geographically distributed among physical distributed agents. This distribution is mainly due to p

Not to put too fine a point on it - does increasing precision of geographic referencing improve species distribution models for a wide-ranging migratory bat?

Science.gov (United States)

Hayes, Mark A.; Ozenberger, Katharine; Cryan, Paul M.; Wunder, Michael B.

2015-01-01

Bat specimens held in natural history museum collections can provide insights into the distribution of species. However, there are several important sources of spatial error associated with natural history specimens that may influence the analysis and mapping of bat species distributions. We analyzed the importance of geographic referencing and error correction in species distribution modeling (SDM) using occurrence records of hoary bats (Lasiurus cinereus). This species is known to migrate long distances and is a species of increasing concern due to fatalities documented at wind energy facilities in North America. We used 3,215 museum occurrence records collected from 1950–2000 for hoary bats in North America. We compared SDM performance using five approaches: generalized linear models, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy models. We evaluated results using three SDM performance metrics (AUC, sensitivity, and specificity) and two data sets: one comprised of the original occurrence data, and a second data set consisting of these same records after the locations were adjusted to correct for identifiable spatial errors. The increase in precision improved the mean estimated spatial error associated with hoary bat records from 5.11 km to 1.58 km, and this reduction in error resulted in a slight increase in all three SDM performance metrics. These results provide insights into the importance of geographic referencing and the value of correcting spatial errors in modeling the distribution of a wide-ranging bat species. We conclude that the considerable time and effort invested in carefully increasing the precision of the occurrence locations in this data set was not worth the marginal gains in improved SDM performance, and it seems likely that gains would be similar for other bat species that range across large areas of the continent, migrate, and are habitat generalists.

Structure functions and parton distributions

International Nuclear Information System (INIS)

Martin, A.D.; Stirling, W.J.; Roberts, R.G.

1995-01-01

The MRS parton distribution analysis is described. The latest sets are shown to give an excellent description of a wide range of deep-inelastic and other hard scattering data. Two important theoretical issues-the behavior of the distributions at small x and the flavor structure of the quark sea-are discussed in detail. A comparison with the new structure function data from HERA is made, and the outlook for the future is discussed

Barium distributions in teeth reveal early-life dietary transitions in primates.

Science.gov (United States)

Austin, Christine; Smith, Tanya M; Bradman, Asa; Hinde, Katie; Joannes-Boyau, Renaud; Bishop, David; Hare, Dominic J; Doble, Philip; Eskenazi, Brenda; Arora, Manish

2013-06-13

Early-life dietary transitions reflect fundamental aspects of primate evolution and are important determinants of health in contemporary human populations. Weaning is critical to developmental and reproductive rates; early weaning can have detrimental health effects but enables shorter inter-birth intervals, which influences population growth. Uncovering early-life dietary history in fossils is hampered by the absence of prospectively validated biomarkers that are not modified during fossilization. Here we show that large dietary shifts in early life manifest as compositional variations in dental tissues. Teeth from human children and captive macaques, with prospectively recorded diet histories, demonstrate that barium (Ba) distributions accurately reflect dietary transitions from the introduction of mother's milk through the weaning process. We also document dietary transitions in a Middle Palaeolithic juvenile Neanderthal, which shows a pattern of exclusive breastfeeding for seven months, followed by seven months of supplementation. After this point, Ba levels in enamel returned to baseline prenatal levels, indicating an abrupt cessation of breastfeeding at 1.2 years of age. Integration of Ba spatial distributions and histological mapping of tooth formation enables novel studies of the evolution of human life history, dietary ontogeny in wild primates, and human health investigations through accurate reconstructions of breastfeeding history.

Barium distributions in teeth reveal early life dietary transitions in primates

Science.gov (United States)

Austin, Christine; Smith, Tanya M.; Bradman, Asa; Hinde, Katie; Joannes-Boyau, Renaud; Bishop, David; Hare, Dominic J.; Doble, Philip; Eskenazi, Brenda; Arora, Manish

2013-01-01

Early life dietary transitions reflect fundamental aspects of primate evolution and are important determinants of health in contemporary human populations1,2. Weaning is critical to developmental and reproductive rates; early weaning can have detrimental health effects but enables shorter inter-birth intervals, which influences population growth3. Uncovering early life dietary history in fossils is hampered by the absence of prospectively-validated biomarkers that are not modified during fossilisation4. Here we show that major dietary shifts in early life manifest as compositional variations in dental tissues. Teeth from human children and captive macaques, with prospectively-recorded diet histories, demonstrate that barium (Ba) distributions accurately reflect dietary transitions from the introduction of mother’s milk and through the weaning process. We also document transitions in a Middle Palaeolithic juvenile Neanderthal, which shows a pattern of exclusive breastfeeding for seven months, followed by seven months of supplementation. After this point, Ba levels in enamel returned to baseline prenatal levels, suggesting an abrupt cessation of breastfeeding at 1.2 years of age. Integration of Ba spatial distributions and histological mapping of tooth formation enables novel studies of the evolution of human life history, dietary ontogeny in wild primates, and human health investigations through accurate reconstructions of breastfeeding history. PMID:23698370

Plant 115-kDa actin-filament bundling protein, P-115-ABP, is a homologue of plant villin and is widely distributed in cells.

Science.gov (United States)

Yokota, Etsuo; Vidali, Luis; Tominaga, Motoki; Tahara, Hiroshi; Orii, Hidefumi; Morizane, Yosuke; Hepler, Peter K; Shimmen, Teruo

2003-10-01

In many cases, actin filaments are arranged into bundles and serve as tracks for cytoplasmic streaming in plant cells. We have isolated an actin-filament bundling protein, which is composed of 115-kDa polypeptide (P-115-ABP), from the germinating pollen of lily, Lilium longiflorum [Nakayasu et al. (1998) BIOCHEM: Biophys. Res. Commun. 249: 61]. P-115-ABP shared similar antigenicity with a plant 135-kDa actin-filament bundling protein (P-135-ABP), a plant homologue of villin. A full-length cDNA clone (ABP115; accession no. AB097407) was isolated from an expression cDNA library of lily pollen by immuno-screening using antisera against P-115-ABP and P-135-ABP. The amino acid sequence of P-115-ABP deduced from this clone showed high homology with those of P-135-ABP and four villin isoforms of Arabidopsis thaliana (AtVLN1, AtVLN2, AtVLN3 and AtVLN4), especially AtVLN4, indicating that P-115-ABP can also be classified as a plant villin. The P-115-ABP isolated biochemically from the germinating lily pollen was able to arrange F-actin filaments with uniform polarity into bundles and this bundling activity was suppressed by Ca2+-calmodulin (CaM), similar to the actin-filament bundling properties of P-135-ABP. The P-115-ABP type of plant villin was widely distributed in plant cells, from algae to land plants. In root hair cells of Hydrocharis dubia, this type of plant villin was co-localized with actin-filament bundles in the transvacuolar strands and the sub-cortical regions. Microinjection of the antiserum against P-115-ABP into living root hair cells caused the disappearance of transvaculor strands and alteration of the route of cytoplasmic streaming. In internodal cells of Chara corallina in which the P-135-ABP type of plant villin is lacking, the P-115-ABP type showed co-localization with actin-filament cables anchored on the intracellular surface of chloroplasts. These results indicated that plant villins are widely distributed and involved in the organization of actin

Autonomous control of distributed storages in microgrids

DEFF Research Database (Denmark)

Loh, Poh Chiang; Blaabjerg, Frede

2011-01-01

Operation of distributed generators in microgrids has widely been discussed, but would not be fully autonomous, if distributed storages are not considered. Storages in general are important, since they provide energy buffering to load changes, energy leveling to source variations and ride......-through enhancement to the overall microgrids. Recognizing their importance, this paper presents a scheme for sharing power among multiple distributed storages, in coordination with the distributed sources and loads. The scheme prompts the storages to autonomously sense for system conditions, requesting for maximum...

Genome-Wide Identification, Phylogenetic and Expression Analyses of the Ubiquitin-Conjugating Enzyme Gene Family in Maize

Science.gov (United States)

Jue, Dengwei; Sang, Xuelian; Lu, Shengqiao; Dong, Chen; Zhao, Qiufang; Chen, Hongliang; Jia, Liqiang

2015-01-01

Background Ubiquitination is a post-translation modification where ubiquitin is attached to a substrate. Ubiquitin-conjugating enzymes (E2s) play a major role in the ubiquitin transfer pathway, as well as a variety of functions in plant biological processes. To date, no genome-wide characterization of this gene family has been conducted in maize (Zea mays). Methodology/Principal Findings In the present study, a total of 75 putative ZmUBC genes have been identified and located in the maize genome. Phylogenetic analysis revealed that ZmUBC proteins could be divided into 15 subfamilies, which include 13 ubiquitin-conjugating enzymes (ZmE2s) and two independent ubiquitin-conjugating enzyme variant (UEV) groups. The predicted ZmUBC genes were distributed across 10 chromosomes at different densities. In addition, analysis of exon-intron junctions and sequence motifs in each candidate gene has revealed high levels of conservation within and between phylogenetic groups. Tissue expression analysis indicated that most ZmUBC genes were expressed in at least one of the tissues, indicating that these are involved in various physiological and developmental processes in maize. Moreover, expression profile analyses of ZmUBC genes under different stress treatments (4°C, 20% PEG6000, and 200 mM NaCl) and various expression patterns indicated that these may play crucial roles in the response of plants to stress. Conclusions Genome-wide identification, chromosome organization, gene structure, evolutionary and expression analyses of ZmUBC genes have facilitated in the characterization of this gene family, as well as determined its potential involvement in growth, development, and stress responses. This study provides valuable information for better understanding the classification and putative functions of the UBC-encoding genes of maize. PMID:26606743

Genome-wide characterization of the SiDof gene family in foxtail millet (Setaria italica).

Science.gov (United States)

Zhang, Li; Liu, Baoling; Zheng, Gewen; Zhang, Aiying; Li, Runzhi

2017-01-01

Dof (DNA binding with one finger) proteins, which constitute a class of transcription factors found exclusively in plants, are involved in numerous physiological and biochemical reactions affecting growth and development. A genome-wide analysis of SiDof genes was performed in this study. Thirty five SiDof genes were identified and those genes were unevenly distributed across nine chromosomes in the Seteria italica genome. Protein lengths, molecular weights, and theoretical isoelectric points of SiDofs all vary greatly. Gene structure analysis demonstrated that most SiDof genes lack introns. Phylogenetic analysis of SiDof proteins and Dof proteins from Arabidopsis thaliana, rice, sorghum, and Setaria viridis revealed six major groups. Analysis of RNA-Seq data indicated that SiDof gene expression levels varied across roots, stems, leaves, and spike. In addition, expression profiling of SiDof genes in response to stress suggested that SiDof 7 and SiDof 15 are involved in drought stress signalling. Overall, this study could provide novel information on SiDofs for further investigation in foxtail millet. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile.

Science.gov (United States)

Huang, Yen-Tsung; Hsu, Thomas; Christiani, David C

2014-01-01

The effects of copy number alterations make up a significant part of the tumor genome profile, but pathway analyses of these alterations are still not well established. We proposed a novel method to analyze multiple copy numbers of genes within a pathway, termed Test for the Effect of a Gene Set with Copy Number data (TEGS-CN). TEGS-CN was adapted from TEGS, a method that we previously developed for gene expression data using a variance component score test. With additional development, we extend the method to analyze DNA copy number data, accounting for different sizes and thus various numbers of copy number probes in genes. The test statistic follows a mixture of X (2) distributions that can be obtained using permutation with scaled X (2) approximation. We conducted simulation studies to evaluate the size and the power of TEGS-CN and to compare its performance with TEGS. We analyzed a genome-wide copy number data from 264 patients of non-small-cell lung cancer. With the Molecular Signatures Database (MSigDB) pathway database, the genome-wide copy number data can be classified into 1814 biological pathways or gene sets. We investigated associations of the copy number profile of the 1814 gene sets with pack-years of cigarette smoking. Our analysis revealed five pathways with significant P values after Bonferroni adjustment (number data, and causal mechanisms of the five pathways require further study.

Magneto-transport study of quantum phases in wide GaAs quantum wells

Science.gov (United States)

Liu, Yang

In this thesis we study several quantum phases in very high quality two-dimensional electron systems (2DESs) confined to GaAs single wide quantum wells (QWs). In these systems typically two electric subbands are occupied. By controlling the electron density as well as the QW symmetry, we can fine tune the cyclotron and subband separation energies, so that Landau levels (LLs) belonging to different subbands cross at the Fermi energy EF. The additional subband degree of freedom enables us to study different quantum phases. Magneto-transport measurements at fixed electron density n and various QW symmetries reveal a remarkable pattern for the appearance and disappearance of fractional quantum Hall (FQH) states at LL filling factors nu = 10/3, 11/3, 13/3, 14/3, 16/3, and 17/3. These q/3 states are stable and strong as long as EF lies in a ground-state (N = 0) LL, regardless of whether that level belongs to the symmetric or the anti-symmetric subband. We also observe subtle and distinct evolutions near filling factors nu = 5/2 and 7/2, as we change the density n, or the symmetry of the charge distribution. The even-denominator FQH states are observed at nu = 5/2, 7/2, 9/2 and 11/2 when EF lies in the N= 1 LLs of the symmetric subband (the S1 levels). As we increase n, the nu = 5/2 FQH state suddenly disappears and turns into a compressible state once EF moves to the spin-up, N = 0, anti-symmetric LL (the A0 ↑ level). The sharpness of this disappearance suggests a first-order transition from a FQH to a compressible state. Moreover, thanks to the renormalization of the susbband energy separation in a well with asymmetric change distribution, two LLs can get pinned to each other when they are crossing at E F. We observe a remarkable consequence of such pinning: There is a developing FQH state when the LL filling factor of the symmetric subband nuS equals 5/2 while the antisymmetric subband has filling 1 < nuA <2. Next, we study the evolution of the nu=5/2 and 7/2 FQH

REVEAL: Software Documentation and Platform Migration

Science.gov (United States)

Wilson, Michael A.; Veibell, Victoir T.

2011-01-01

The Research Environment for Vehicle Embedded Analysis on Linux (REVEAL) is reconfigurable data acquisition software designed for network-distributed test and measurement applications. In development since 2001, it has been successfully demonstrated in support of a number of actual missions within NASA's Suborbital Science Program. Improvements to software configuration control were needed to properly support both an ongoing transition to operational status and continued evolution of REVEAL capabilities. For this reason the project described in this report targets REVEAL software source documentation and deployment of the software on a small set of hardware platforms different from what is currently used in the baseline system implementation. This presentation specifically describes the actions taken over a ten week period by two undergraduate student interns and serves as an overview of the content of the final report for that internship.

How Cyanobacterial Distributions Reveal Flow and Irradiance Conditions of Photosynthetic Biofilm Formation

Science.gov (United States)

Prufert-Bebout, Lee

2001-01-01

Microbial life on Earth is enormously abundant at sediment-water interfaces. The fossil record in fact contains abundant evidence of the preservation of life on such surfaces. It is therefore critical to our interpretation of early Earth history, and potentially to history of life on other planets, to be able to recognize life forms at these interfaces. On Earth this life often occurs as organized structures of microbes and their extracellular exudates known as biofilms. When such biofilms occur in areas receiving sunlight photosynthetic biofilms are the dominant form in natural ecosystems due to selective advantage inherent in their ability to utilize solar energy. Cyanobacteria are the dominant phototrophic microbes in most modern and ancient photosynthetic biofilms, microbial mats and stromatolites. Due to their long (3.5 billion year) evolutionary history, this group has extensively diversified resulting in an enormous array of morphologies and physiological abilities. This enormous diversity and specialization results in very specific selection for a particular cyanobacterium in each available photosynthetic niche. Furthermore these organisms can alter their spatial orientation, cell morphology, pigmentation and associations with heterotrophic organisms in order to fine tune their optimization to a given micro-niche. These adaptations can be detected, and if adequate knowledge of the interaction between environmental conditions and organism response is available, the detectable organism response can be used to infer the environmental conditions causing that response. This presentation will detail two specific examples which illustrate this point. Light and water are essential to photosynthesis in cyanobacteria and these organisms have specific detectable behavioral responses to these parameters. We will present cyanobacterial responses to quantified flow and irradiance to demonstrate the interpretative power of distribution and orientation information. This

On the Truncated Pareto Distribution with applications

OpenAIRE

Zaninetti, Lorenzo; Ferraro, Mario

2008-01-01

The Pareto probability distribution is widely applied in different fields such us finance, physics, hydrology, geology and astronomy. This note deals with an application of the Pareto distribution to astrophysics and more precisely to the statistical analysis of mass of stars and of diameters of asteroids. In particular a comparison between the usual Pareto distribution and its truncated version is presented. Finally a possible physical mechanism that produces Pareto tails for the distributio...

Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium.

Science.gov (United States)

Walworth, Nathan G; Lee, Michael D; Suffridge, Christopher; Qu, Pingping; Fu, Fei-Xue; Saito, Mak A; Webb, Eric A; Sañudo-Wilhelmy, Sergio A; Hutchins, David A

2018-01-01

Only select prokaryotes can biosynthesize vitamin B 12 (i.e., cobalamins), but these organic co-enzymes are required by all microbial life and can be vanishingly scarce across extensive ocean biomes. Although global ocean genome data suggest cyanobacteria to be a major euphotic source of cobalamins, recent studies have highlighted that >95% of cyanobacteria can only produce a cobalamin analog, pseudo-B 12 , due to the absence of the BluB protein that synthesizes the α ligand 5,6-dimethylbenzimidizole (DMB) required to biosynthesize cobalamins. Pseudo-B 12 is substantially less bioavailable to eukaryotic algae, as only certain taxa can intracellularly remodel it to one of the cobalamins. Here we present phylogenetic, metagenomic, transcriptomic, proteomic, and chemical analyses providing multiple lines of evidence that the nitrogen-fixing cyanobacterium Trichodesmium transcribes and translates the biosynthetic, cobalamin-requiring BluB enzyme. Phylogenetic evidence suggests that the Trichodesmium DMB biosynthesis gene, bluB , is of ancient origin, which could have aided in its ecological differentiation from other nitrogen-fixing cyanobacteria. Additionally, orthologue analyses reveal two genes encoding iron-dependent B 12 biosynthetic enzymes (cbiX and isiB), suggesting that iron availability may be linked not only to new nitrogen supplies from nitrogen fixation, but also to B 12 inputs by Trichodesmium . These analyses suggest that Trichodesmium contains the genus-wide genomic potential for a previously unrecognized role as a source of cobalamins, which may prove to considerably impact marine biogeochemical cycles.

Temperature profile and other data collected using bottle and CTD casts from the PARRAMATTA and other platforms in a world-wide distribution during the California Cooperative Fisheries Investigation (CALCOFI) project, 04 October 1903 to 19 December 1963 (NODC Accession 6300000)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Oceanographic Station Data, temperature, and other data were collected using CTD and bottle casts from PARRAMATTA and other platforms in a world-wide distribution...

The Three-Dimensional Velocity Distribution of Wide Gap Taylor-Couette Flow Modelled by CFD

Directory of Open Access Journals (Sweden)

David Shina Adebayo

2016-01-01

Full Text Available A numerical investigation is conducted for the flow between two concentric cylinders with a wide gap, relevant to bearing chamber applications. This wide gap configuration has received comparatively less attention than narrow gap journal bearing type geometries. The flow in the gap between an inner rotating cylinder and an outer stationary cylinder has been modelled as an incompressible flow using an implicit finite volume RANS scheme with the realisable k-ε model. The model flow is above the critical Taylor number at which axisymmetric counterrotating Taylor vortices are formed. The tangential velocity profiles at all axial locations are different from typical journal bearing applications, where the velocity profiles are quasilinear. The predicted results led to two significant findings of impact in rotating machinery operations. Firstly, the axial variation of the tangential velocity gradient induces an axially varying shear stress, resulting in local bands of enhanced work input to the working fluid. This is likely to cause unwanted heat transfer on the surface in high torque turbomachinery applications. Secondly, the radial inflow at the axial end-wall boundaries is likely to promote the transport of debris to the junction between the end-collar and the rotating cylinder, causing the build-up of fouling in the seal.

Distributional impacts of climate change mitigation in Indian electricity: The influence of governance

International Nuclear Information System (INIS)

Rao, Narasimha D.

2013-01-01

Studies that examine the distributional impacts of climate change mitigation policies often neglect the influence of institutions that implement these policies. This study examines the short-term consumption-side distributional impacts of expanding low-carbon electric supply in the state of Maharashtra, India with a focus on the influence of regulatory discretion in pricing. Households' welfare impacts from economy-wide electricity price shocks are simulated against a baseline that is calibrated to actual household economic and electricity service conditions, including actual electricity budgets, block tier prices and supply rationing. Industrial price impacts are propagated to households using a Leontief input–output analysis. Regulatory pricing decisions are evaluated based on social welfare metrics for economic efficiency and income inequality. The analysis reveals new linkages between climate change mitigation, electricity policy and income distribution. Low-income households can be shielded from mitigation impacts without losses in aggregate welfare to the extent that regulators can recover mitigation costs through industrial price increases. Regulators' flexibility to distribute costs across households is constrained by industrial customers' migration off the grid. Reduced supply interruptions to the rural poor from the resulting demand contraction are a potential co-benefit of mitigation. Distributional impacts, therefore, depend on other electricity policies that are driven by the political economy of the sector. - Highlights: • Indirect price increases harm most households less than residential price increases. • Regulators have flexibility to distribute mitigation costs across income groups. • Reduced supply interruptions are a potential co-benefit of mitigation

Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

Science.gov (United States)

Dong, Yan; Liu, Jindong; Zhang, Yan; Geng, Hongwei; Rasheed, Awais; Xiao, Yonggui; Cao, Shuanghe; Fu, Luping; Yan, Jun; Wen, Weie; Zhang, Yong; Jing, Ruilian; Xia, Xianchun; He, Zhonghu

2016-01-01

Water soluble carbohydrates (WSC) in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS) using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs) distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs), and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content) and unfavorable alleles (decreasing WSC), indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars.

Genome-Wide Association of Stem Water Soluble Carbohydrates in Bread Wheat.

Directory of Open Access Journals (Sweden)

Yan Dong

Full Text Available Water soluble carbohydrates (WSC in stems play an important role in buffering grain yield in wheat against biotic and abiotic stresses; however, knowledge of genes controlling WSC is very limited. We conducted a genome-wide association study (GWAS using a high-density 90K SNP array to better understand the genetic basis underlying WSC, and to explore marker-based breeding approaches. WSC was evaluated in an association panel comprising 166 Chinese bread wheat cultivars planted in four environments. Fifty two marker-trait associations (MTAs distributed across 23 loci were identified for phenotypic best linear unbiased estimates (BLUEs, and 11 MTAs were identified in two or more environments. Liner regression showed a clear dependence of WSC BLUE scores on numbers of favorable (increasing WSC content and unfavorable alleles (decreasing WSC, indicating that genotypes with higher numbers of favorable or lower numbers of unfavorable alleles had higher WSC content. In silico analysis of flanking sequences of trait-associated SNPs revealed eight candidate genes related to WSC content grouped into two categories based on the type of encoding proteins, namely, defense response proteins and proteins triggered by environmental stresses. The identified SNPs and candidate genes related to WSC provide opportunities for breeding higher WSC wheat cultivars.

Wide Field Radio Transient Surveys

Science.gov (United States)

Bower, Geoffrey

2011-04-01

The time domain of the radio wavelength sky has been only sparsely explored. Nevertheless, serendipitous discovery and results from limited surveys indicate that there is much to be found on timescales from nanoseconds to years and at wavelengths from meters to millimeters. These observations have revealed unexpected phenomena such as rotating radio transients and coherent pulses from brown dwarfs. Additionally, archival studies have revealed an unknown class of radio transients without radio, optical, or high-energy hosts. The new generation of centimeter-wave radio telescopes such as the Allen Telescope Array (ATA) will exploit wide fields of view and flexible digital signal processing to systematically explore radio transient parameter space, as well as lay the scientific and technical foundation for the Square Kilometer Array. Known unknowns that will be the target of future transient surveys include orphan gamma-ray burst afterglows, radio supernovae, tidally-disrupted stars, flare stars, and magnetars. While probing the variable sky, these surveys will also provide unprecedented information on the static radio sky. I will present results from three large ATA surveys (the Fly's Eye survey, the ATA Twenty CM Survey (ATATS), and the Pi GHz Survey (PiGSS)) and several small ATA transient searches. Finally, I will discuss the landscape and opportunities for future instruments at centimeter wavelengths.

Distribution of the a2, a3, and a5 nicotinic acetylcholine receptor subunits in the chick brain

Directory of Open Access Journals (Sweden)

Torrão A.S.

1997-01-01

Full Text Available Nicotinic acetylcholine receptors (nAChRs are ionotropic receptors comprised of a and ß subunits. These receptors are widely distributed in the central nervous system, and previous studies have revealed specific patterns of localization for some nAChR subunits in the vertebrate brain. In the present study we used immunohistochemical methods and monoclonal antibodies to localize the a2, a3, and a5 nAChR subunits in the chick mesencephalon and diencephalon. We observed a differential distribution of these three subunits in the chick brain, and showed that the somata and neuropil of many central structures contain the a5 nAChR subunit. The a2 and a3 subunits, on the other hand, exhibited a more restricted distribution than a5 and other subunits previously studied, namely a7, a8 and ß2. The patterns of distribution of the different nAChR subunits suggest that neurons in many brain structures may contain several subtypes of nAChRs and that in a few regions one particular subtype may determine the cholinergic nicotinic responses

Distribution of transuranic elements in bone.

Science.gov (United States)

Durbin, P W

1992-01-01

The transport, retention, and excretion of transuranic elements from the body have been widely studied for many years. A summary of the results is given with an emphasis on the distribution of these elements in bone. Implications of these studies for understanding the relationships between lead in blood and lead in bone are presented. The expected distribution of lead at various bone sites is also considered.

A basic R and D for an analysis framework distributed on wide area network

International Nuclear Information System (INIS)

Ishino, M.; Kawabata, S.; Kawamoto, T.; Kobayashi, T.; Manabe, A.; Mashimo, T.; Matsumoto, H.; Morita, Y.; Sakamoto, H.; Sasaki, T.; Sato, H.; Tanaka, J.; Ueda, I.; Watase, Y.

2004-01-01

Present status is reported on several R and D issues related to world-wide analysis for forthcoming high-energy collider experiments. This study includes (1) high-density computer farm with effective configuration and management capability (2) high throughput data storage mechanisms covering disk arrays and hierarchical storage architecture, and (3) high-performance massive data transfer techniques on large latency WAN. Understanding these basic technologies is necessary for the deployment of developing data grid computing

A novel statistic for genome-wide interaction analysis.

Directory of Open Access Journals (Sweden)

Xuesen Wu

2010-09-01

Full Text Available Although great progress in genome-wide association studies (GWAS has been made, the significant SNP associations identified by GWAS account for only a few percent of the genetic variance, leading many to question where and how we can find the missing heritability. There is increasing interest in genome-wide interaction analysis as a possible source of finding heritability unexplained by current GWAS. However, the existing statistics for testing interaction have low power for genome-wide interaction analysis. To meet challenges raised by genome-wide interactional analysis, we have developed a novel statistic for testing interaction between two loci (either linked or unlinked. The null distribution and the type I error rates of the new statistic for testing interaction are validated using simulations. Extensive power studies show that the developed statistic has much higher power to detect interaction than classical logistic regression. The results identified 44 and 211 pairs of SNPs showing significant evidence of interactions with FDR<0.001 and 0.001wide interaction analysis is a valuable tool for finding remaining missing heritability unexplained by the current GWAS, and the developed novel statistic is able to search significant interaction between SNPs across the genome. Real data analysis showed that the results of genome-wide interaction analysis can be replicated in two independent studies.

Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women

DEFF Research Database (Denmark)

Fox, Caroline S; Liu, Yongmei; White, Charles C

2012-01-01

of European ancestry. Subcutaneous and visceral fat were quantified in 5,560 women and 4,997 men from 4 population-based studies. Genome-wide genotyping was performed using standard arrays and imputed to ~2.5 million Hapmap SNPs. Each study performed a genome-wide association analysis of subcutaneous adipose...... tissue (SAT), visceral adipose tissue (VAT), VAT adjusted for body mass index, and VAT/SAT ratio (a metric of the propensity to store fat viscerally as compared to subcutaneously) in the overall sample and in women and men separately. A weighted z-score meta-analysis was conducted. For the VAT/SAT ratio......-specific analyses. Our most significant finding was for VAT in women, rs1659258 near THNSL2 (p = 1.6 × 10-08), but not men (p = 0.75). Validation of this SNP in the GIANT consortium data demonstrated a similar sex-specific pattern, with observed significance in women (p = 0.006) but not men (p = 0.24) for BMI...

Molecular Comparison and Evolutionary Analyses of VP1 Nucleotide Sequences of New African Human Enterovirus 71 Isolates Reveal a Wide Genetic Diversity

Science.gov (United States)

Nougairède, Antoine; Joffret, Marie-Line; Deshpande, Jagadish M.; Dubot-Pérès, Audrey; Héraud, Jean-Michel

2014-01-01

Most circulating strains of Human enterovirus 71 (EV-A71) have been classified primarily into three genogroups (A to C) on the basis of genetic divergence between the 1D gene, which encodes the VP1 capsid protein. The aim of the present study was to provide further insights into the diversity of the EV-A71 genogroups following the recent description of highly divergent isolates, in particular those from African countries, including Madagascar. We classified recent EV-A71 isolates by a large comparison of 3,346 VP1 nucleotidic sequences collected from GenBank. Analysis of genetic distances and phylogenetic investigations indicated that some recently-reported isolates did not fall into the genogroups A-C and clustered into three additional genogroups, including one Indian genogroup (genogroup D) and 2 African ones (E and F). Our Bayesian phylogenetic analysis provided consistent data showing that the genogroup D isolates share a recent common ancestor with the members of genogroup E, while the isolates of genogroup F evolved from a recent common ancestor shared with the members of the genogroup B. Our results reveal the wide diversity that exists among EV-A71 isolates and suggest that the number of circulating genogroups is probably underestimated, particularly in developing countries where EV-A71 epidemiology has been poorly studied. PMID:24598878

A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study.

Science.gov (United States)

Bengtsson, Therése; Åhman, Inger; Manninen, Outi; Reitan, Lars; Christerson, Therese; Due Jensen, Jens; Krusell, Lene; Jahoor, Ahmed; Orabi, Jihad

2017-01-01

The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley ( Hordeum vulgare L. ssp. vulgare ) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis . The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.

Temperature profile and other data collected using bottle and CTD casts from the HMAS DERWENT and other platforms from a world-wide distribution during the California Cooperative Fisheries Investigation (CALCOFI) project, 03 August 1904 to 31 December 1964 (NODC Accession 6400000)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Oceanographic Station Data, temperature, and other data were collected using CTD and bottle casts from HMAS DERWENT and other platforms in a world-wide distribution...

Temperature profile and other data collected using bottle and CTD casts from the A. AGASSIZ and other platforms from a world-wide distribution during the California Cooperative Fisheries Investigation (CALCOFI) project, 06 January 1969 to 27 July 1977 (NODC Accession 8000006)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Oceanographic Station Data, temperature, and other data were collected using CTD and bottle casts from A. AGASSIZ and other platforms in a world-wide distribution...

ATLAS Distributed Computing Automation

CERN Document Server

Schovancova, J; The ATLAS collaboration; Borrego, C; Campana, S; Di Girolamo, A; Elmsheuser, J; Hejbal, J; Kouba, T; Legger, F; Magradze, E; Medrano Llamas, R; Negri, G; Rinaldi, L; Sciacca, G; Serfon, C; Van Der Ster, D C

2012-01-01

The ATLAS Experiment benefits from computing resources distributed worldwide at more than 100 WLCG sites. The ATLAS Grid sites provide over 100k CPU job slots, over 100 PB of storage space on disk or tape. Monitoring of status of such a complex infrastructure is essential. The ATLAS Grid infrastructure is monitored 24/7 by two teams of shifters distributed world-wide, by the ATLAS Distributed Computing experts, and by site administrators. In this paper we summarize automation efforts performed within the ATLAS Distributed Computing team in order to reduce manpower costs and improve the reliability of the system. Different aspects of the automation process are described: from the ATLAS Grid site topology provided by the ATLAS Grid Information System, via automatic site testing by the HammerCloud, to automatic exclusion from production or analysis activities.

Malaria transmission in Tripura: Disease distribution & determinants.

Science.gov (United States)

Dev, Vas; Adak, Tridibes; Singh, Om P; Nanda, Nutan; Baidya, Bimal K

2015-12-01

Malaria is a major public health problem in Tripura and focal disease outbreaks are of frequent occurrence. The state is co-endemic for both Plasmodium falciparum and P. vivax and transmission is perennial and persistent. The present study was aimed to review data on disease distribution to prioritize high-risk districts, and to study seasonal prevalence of disease vectors and their bionomical characteristics to help formulate vector species-specific interventions for malaria control. Data on malaria morbidity in the State were reviewed retrospectively (2008-2012) for understanding disease distribution and transmission dynamics. Cross-sectional mass blood surveys were conducted in malaria endemic villages of South Tripura district to ascertain the prevalence of malaria and proportions of parasite species. Mosquito collections were made in human dwellings of malaria endemic villages aiming at vector incrimination and to study relative abundance, resting and feeding preferences, and their present susceptibility status to DDT. The study showed that malaria was widely prevalent and P. falciparum was the predominant infection (>90%), the remaining were P. vivax cases. The disease distribution, however, was uneven with large concentration of cases in districts of South Tripura and Dhalai coinciding with vast forest cover and tribal populations. Both Anopheles minimus s.s. and An. baimaii were recorded to be prevalent and observed to be highly anthropophagic and susceptible to DDT. Of these, An. minimus was incriminated (sporozoite infection rate 4.92%), and its bionomical characteristics revealed this species to be largely indoor resting and endophagic. For effective control of malaria in the state, it is recommended that diseases surveillance should be robust, and vector control interventions including DDT spray coverage, mass distribution of insecticide-treated nets/ long-lasting insecticidal nets should be intensified prioritizing population groups most at risk to

Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

Science.gov (United States)

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide...

The wide-spread presence of rib-like patterns in basal shear of ice streams detected by surface data inversion

Science.gov (United States)

Sergienko, O. V.

2013-12-01

The direct observations of the basal conditions under continental-scale ice sheets are logistically impossible. A possible approach to estimate conditions at the ice - bed interface is from surface observations by means of inverse methods. The recent advances in remote and ground-based observations have allowed to acquire a wealth observations from Greenland and Antarctic ice sheets. Using high-resolution data sets of ice surface and bed elevations and surface velocities, inversions for basal conditions have been performed for several ice streams in Greenland and Antarctica. The inversion results reveal the wide-spread presence of rib-like spatial structures in basal shear. The analysis of the hydraulic potential distribution shows that these rib-like structures co-locate with highs of the gradient of hydraulic potential. This suggests that subglacial water plays a role in the development and evolution of the basal shear ribs.

The absolute magnitude distribution of Kuiper Belt objects

Energy Technology Data Exchange (ETDEWEB)

Fraser, Wesley C. [Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Brown, Michael E. [Division of Geological and Planetary Sciences, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Morbidelli, Alessandro [Laboratoire Lagrange, UMR7293, Université de Nice Sophia-Antipolis, CNRS, Observatoire de la Côte d' Azur, BP 4229, F-06304 Nice (France); Parker, Alex [Department of Astronomy, University of California at Berkeley, Berkeley, CA 94720 (United States); Batygin, Konstantin, E-mail: wesley.fraser@nrc.ca [Institute for Theory and Computation, Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MS 51, Cambridge, MA 02138 (United States)

2014-02-20

Here we measure the absolute magnitude distributions (H-distribution) of the dynamically excited and quiescent (hot and cold) Kuiper Belt objects (KBOs), and test if they share the same H-distribution as the Jupiter Trojans. From a compilation of all useable ecliptic surveys, we find that the KBO H-distributions are well described by broken power laws. The cold population has a bright-end slope, α{sub 1}=1.5{sub −0.2}{sup +0.4}, and break magnitude, H{sub B}=6.9{sub −0.2}{sup +0.1} (r'-band). The hot population has a shallower bright-end slope of, α{sub 1}=0.87{sub −0.2}{sup +0.07}, and break magnitude H{sub B}=7.7{sub −0.5}{sup +1.0}. Both populations share similar faint-end slopes of α{sub 2} ∼ 0.2. We estimate the masses of the hot and cold populations are ∼0.01 and ∼3 × 10{sup –4} M {sub ⊕}. The broken power-law fit to the Trojan H-distribution has α{sub 1} = 1.0 ± 0.2, α{sub 2} = 0.36 ± 0.01, and H {sub B} = 8.3. The Kolmogorov-Smirnov test reveals that the probability that the Trojans and cold KBOs share the same parent H-distribution is less than 1 in 1000. When the bimodal albedo distribution of the hot objects is accounted for, there is no evidence that the H-distributions of the Trojans and hot KBOs differ. Our findings are in agreement with the predictions of the Nice model in terms of both mass and H-distribution of the hot and Trojan populations. Wide-field survey data suggest that the brightest few hot objects, with H{sub r{sup ′}}≲3, do not fall on the steep power-law slope of fainter hot objects. Under the standard hierarchical model of planetesimal formation, it is difficult to account for the similar break diameters of the hot and cold populations given the low mass of the cold belt.

Distributed processing and analysis of ATLAS experimental data

CERN Document Server

Barberis, D; The ATLAS collaboration

2011-01-01

The ATLAS experiment is taking data steadily since Autumn 2009, collecting close to 1 fb-1 of data (several petabytes of raw and reconstructed data per year of data-taking). Data are calibrated, reconstructed, distributed and analysed at over 100 different sites using the World-wide LHC Computing Grid and the tools produced by the ATLAS Distributed Computing project. In addition to event data, ATLAS produces a wealth of information on detector status, luminosity, calibrations, alignments, and data processing conditions. This information is stored in relational databases, online and offline, and made transparently available to analysers of ATLAS data world-wide through an infrastructure consisting of distributed database replicas and web servers that exploit caching technologies. This paper reports on the experience of using this distributed computing infrastructure with real data and in real time, on the evolution of the computing model driven by this experience, and on the system performance during the first...

Distributed processing and analysis of ATLAS experimental data

CERN Document Server

Barberis, D; The ATLAS collaboration

2011-01-01

The ATLAS experiment is taking data steadily since Autumn 2009, and collected so far over 5 fb-1 of data (several petabytes of raw and reconstructed data per year of data-taking). Data are calibrated, reconstructed, distributed and analysed at over 100 different sites using the World-wide LHC Computing Grid and the tools produced by the ATLAS Distributed Computing project. In addition to event data, ATLAS produces a wealth of information on detector status, luminosity, calibrations, alignments, and data processing conditions. This information is stored in relational databases, online and offline, and made transparently available to analysers of ATLAS data world-wide through an infrastructure consisting of distributed database replicas and web servers that exploit caching technologies. This paper reports on the experience of using this distributed computing infrastructure with real data and in real time, on the evolution of the computing model driven by this experience, and on the system performance during the...

Firm-size distribution and price-cost margins in Dutch manufacturing

NARCIS (Netherlands)

Y.M. Prince (Yvonne); A.R. Thurik (Roy)

1993-01-01

textabstractIndustrial economists surmise a relation between the size distribution of firms and performance. Usually, attention is focused on the high end of the size distribution. The widely used 4-firm seller concentration, C4, ignores what happens at the low end of the size distribution. An

Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.).

Science.gov (United States)

Liu, Pu; Zhang, Chao; Ma, Jin-Qi; Zhang, Li-Yuan; Yang, Bo; Tang, Xin-Yu; Huang, Ling; Zhou, Xin-Tong; Lu, Kun; Li, Jia-Na

2018-03-16

Cytokinin oxidase/dehydrogenases (CKXs) play a critical role in the irreversible degradation of cytokinins, thereby regulating plant growth and development. Brassica napus is one of the most widely cultivated oilseed crops worldwide. With the completion of whole-genome sequencing of B. napus , genome-wide identification and expression analysis of the BnCKX gene family has become technically feasible. In this study, we identified 23 BnCKX genes and analyzed their phylogenetic relationships, gene structures, conserved motifs, protein subcellular localizations, and other properties. We also analyzed the expression of the 23 BnCKX genes in the B. napus cultivar Zhong Shuang 11 ('ZS11') by quantitative reverse-transcription polymerase chain reaction (qRT-PCR), revealing their diverse expression patterns. We selected four BnCKX genes based on the results of RNA-sequencing and qRT-PCR and compared their expression in cultivated varieties with extremely long versus short siliques. The expression levels of BnCKX5-1 , 5-2 , 6-1 , and 7-1 significantly differed between the two lines and changed during pod development, suggesting they might play roles in determining silique length and in pod development. Finally, we investigated the effects of treatment with the synthetic cytokinin 6-benzylaminopurine (6-BA) and the auxin indole-3-acetic acid (IAA) on the expression of the four selected BnCKX genes. Our results suggest that regulating BnCKX expression is a promising way to enhance the harvest index and stress resistance in plants.

Genome-Wide Identification and Evolution of HECT Genes in Soybean

Directory of Open Access Journals (Sweden)

Xianwen Meng

2015-04-01

Full Text Available Proteins containing domains homologous to the E6-associated protein (E6-AP carboxyl terminus (HECT are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.

Complex conjugate poles and parton distributions

International Nuclear Information System (INIS)

Tiburzi, B.C.; Detmold, W.; Miller, G.A.

2003-01-01

We calculate parton and generalized parton distributions in Minkowski space using a scalar propagator with a pair of complex conjugate poles. Correct spectral and support properties are obtained only after careful analytic continuation from Euclidean space. Alternately the quark distribution function can be calculated from modified cutting rules, which put the intermediate state on its complex mass shells. Distribution functions agree with those resulting from the model's Euclidean space double distribution which we calculate via nondiagonal matrix elements of twist-two operators. Thus one can use a wide class of analytic parametrizations of the quark propagator to connect Euclidean space Green functions to light-cone dominated amplitudes

Adiponectin Concentrations: A Genome-wide Association Study

Science.gov (United States)

Jee, Sun Ha; Sull, Jae Woong; Lee, Jong-Eun; Shin, Chol; Park, Jongkeun; Kimm, Heejin; Cho, Eun-Young; Shin, Eun-Soon; Yun, Ji Eun; Park, Ji Wan; Kim, Sang Yeun; Lee, Sun Ju; Jee, Eun Jung; Baik, Inkyung; Kao, Linda; Yoon, Sungjoo Kim; Jang, Yangsoo; Beaty, Terri H.

2010-01-01

Adiponectin is associated with obesity and insulin resistance. To date, there has been no genome-wide association study (GWAS) of adiponectin levels in Asians. Here we present a GWAS of a cohort of Korean volunteers. A total of 4,001 subjects were genotyped by using a genome-wide marker panel in a two-stage design (979 subjects initially and 3,022 in a second stage). Another 2,304 subjects were used for follow-up replication studies with selected markers. In the discovery phase, the top SNP associated with mean log adiponectin was rs3865188 in CDH13 on chromosome 16 (p = 1.69 × 10−15 in the initial sample, p = 6.58 × 10−39 in the second genome-wide sample, and p = 2.12 × 10−32 in the replication sample). The meta-analysis p value for rs3865188 in all 6,305 individuals was 2.82 × 10−83. The association of rs3865188 with high-molecular-weight adiponectin (p = 7.36 × 10−58) was even stronger in the third sample. A reporter assay that evaluated the effects of a CDH13 promoter SNP in complete linkage disequilibrium with rs3865188 revealed that the major allele increased expression 2.2-fold. This study clearly shows that genetic variants in CDH13 influence adiponectin levels in Korean adults. PMID:20887962

Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

KAUST Repository

Bagchi, Samik; Lamendella, Regina; Strutt, Steven; Van Loosdrecht, Mark C. M.; Saikaly, Pascal

2016-01-01

to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all

An appraisal of precipitation distribution in the high-altitude catchments of the Indus basin.

Science.gov (United States)

Dahri, Zakir Hussain; Ludwig, Fulco; Moors, Eddy; Ahmad, Bashir; Khan, Asif; Kabat, Pavel

2016-04-01

Scarcity of in-situ observations coupled with high orographic influences has prevented a comprehensive assessment of precipitation distribution in the high-altitude catchments of Indus basin. Available data are generally fragmented and scattered with different organizations and mostly cover the valleys. Here, we combine most of the available station data with the indirect precipitation estimates at the accumulation zones of major glaciers to analyse altitudinal dependency of precipitation in the high-altitude Indus basin. The available observations signified the importance of orography in each sub-hydrological basin but could not infer an accurate distribution of precipitation with altitude. We used Kriging with External Drift (KED) interpolation scheme with elevation as a predictor to appraise spatiotemporal distribution of mean monthly, seasonal and annual precipitation for the period of 1998-2012. The KED-based annual precipitation estimates are verified by the corresponding basin-wide observed specific runoffs, which show good agreement. In contrast to earlier studies, our estimates reveal substantially higher precipitation in most of the sub-basins indicating two distinct rainfall maxima; 1st along southern and lower most slopes of Chenab, Jhelum, Indus main and Swat basins, and 2nd around north-west corner of Shyok basin in the central Karakoram. The study demonstrated that the selected gridded precipitation products covering this region are prone to significant errors. In terms of quantitative estimates, ERA-Interim is relatively close to the observations followed by WFDEI and TRMM, while APHRODITE gives highly underestimated precipitation estimates in the study area. Basin-wide seasonal and annual correction factors introduced for each gridded dataset can be useful for lumped hydrological modelling studies, while the estimated precipitation distribution can serve as a basis for bias correction of any gridded precipitation products for the study area

Context Dependency of a Marine Defensive Symbiosis over a Wide Geographic Distribution

Science.gov (United States)

Lopanik, N.; Linneman, J.; Mathew, M.

2016-02-01

The invasive, temperate marine bryozoan Bugula neritina possesses an uncultured, vertically-transmitted bacterial symbiont that produces natural products known as bryostatins. These unpalatable polyketides protect the host larvae from predation. In the western Atlantic, two host genotypes were thought to be restricted to differing latitudes based on the presence of the defensive symbiont: undefended aposymbiotic Type N animals were found at high latitudes, while defended symbiotic Type S colonies were found at low latitudes, where predation pressure is higher. We found that the host genotypes are more widespread than previously thought, but that the symbiont appeared to be restricted to hosts at lower latitudes, regardless of host phylotype, leading to the question of what factors are involved in restricting the symbiont's range. We performed reciprocal transplant experiments of symbiotic and antibiotic-cured hosts, and measured host growth, a proxy for fitness. Our data indicate that possession of the symbiont appears to present a physiological cost to the host. This cost may be more pronounced at higher latitudes where the benefit of symbiosis is less apparent. In addition, preliminary evidence suggests that symbiont titer in a Type S colony from North Carolina transplanted to Virginia is reduced over a period of nearly 4 months. Taken together, these results suggest that a combination of factors may play a role in the distribution of the defensive symbiont: (i) hosts that possess the symbiont are outcompeted by aposymbiotic conspecifics at high latitude and reduced levels of predation pressure; and (ii) symbiont growth may be inhibited or sanctioned by the host at high latitudes. As defensive symbiosis is an important trait in marine habitats, understanding factors that affect the distribution of both the host and symbiont are necessary to fully appreciate the ecological impact of symbiosis.

Genome-wide analysis of tandem repeats in plants and green algae

Science.gov (United States)

Zhixin Zhao; Cheng Guo; Sreeskandarajan Sutharzan; Pei Li; Craig Echt; Jie Zhang; Chun Liang

2014-01-01

Tandem repeats (TRs) extensively exist in the genomes of prokaryotes and eukaryotes. Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 (http://www.phytozome.net/), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. Among...

A Review of Multivariate Distributions for Count Data Derived from the Poisson Distribution.

Science.gov (United States)

Inouye, David; Yang, Eunho; Allen, Genevera; Ravikumar, Pradeep

2017-01-01

The Poisson distribution has been widely studied and used for modeling univariate count-valued data. Multivariate generalizations of the Poisson distribution that permit dependencies, however, have been far less popular. Yet, real-world high-dimensional count-valued data found in word counts, genomics, and crime statistics, for example, exhibit rich dependencies, and motivate the need for multivariate distributions that can appropriately model this data. We review multivariate distributions derived from the univariate Poisson, categorizing these models into three main classes: 1) where the marginal distributions are Poisson, 2) where the joint distribution is a mixture of independent multivariate Poisson distributions, and 3) where the node-conditional distributions are derived from the Poisson. We discuss the development of multiple instances of these classes and compare the models in terms of interpretability and theory. Then, we empirically compare multiple models from each class on three real-world datasets that have varying data characteristics from different domains, namely traffic accident data, biological next generation sequencing data, and text data. These empirical experiments develop intuition about the comparative advantages and disadvantages of each class of multivariate distribution that was derived from the Poisson. Finally, we suggest new research directions as explored in the subsequent discussion section.

We'll meet again: revealing distributional and temporal patterns of social contact.

Directory of Open Access Journals (Sweden)

Thorsten Pachur

Full Text Available What are the dynamics and regularities underlying social contact, and how can contact with the people in one's social network be predicted? In order to characterize distributional and temporal patterns underlying contact probability, we asked 40 participants to keep a diary of their social contacts for 100 consecutive days. Using a memory framework previously used to study environmental regularities, we predicted that the probability of future contact would follow in systematic ways from the frequency, recency, and spacing of previous contact. The distribution of contact probability across the members of a person's social network was highly skewed, following an exponential function. As predicted, it emerged that future contact scaled linearly with frequency of past contact, proportionally to a power function with recency of past contact, and differentially according to the spacing of past contact. These relations emerged across different contact media and irrespective of whether the participant initiated or received contact. We discuss how the identification of these regularities might inspire more realistic analyses of behavior in social networks (e.g., attitude formation, cooperation.

Genetic differences among Haplorchis taichui populations in Indochina revealed by mitochondrial COX1 sequences.

Science.gov (United States)

Thaenkham, U; Phuphisut, O; Nuamtanong, S; Yoonuan, T; Sa-Nguankiat, S; Vonghachack, Y; Belizario, V Y; Dung, D T; Dekumyoy, P; Waikagul, J

2017-09-01

Haplorchis taichui is an intestinal heterophyid fluke that is pathogenic to humans. It is widely distributed in Asia, with a particularly high prevalence in Indochina. Previous work revealed that the lack of gene flow between three distinct populations of Vietnamese H. taichui can be attributed to their geographic isolation with no interconnected river basins. To test the hypothesis that interconnected river basins allow gene flow between otherwise isolated populations of H. taichui, as previously demonstrated for another trematode, Opisthorchis viverrini, we compared the genetic structures of seven populations of H. taichui from various localities in the lower Mekong Basin, in Thailand and Laos, with those in Vietnam, using the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene. To determine the gene flow between these H. taichui populations, we calculated their phylogenetic relationships, genetic distances and haplotype diversity. Each population showed very low nucleotide diversity at this locus. However, high levels of genetic differentiation between the populations indicated very little gene flow. A phylogenetic analysis divided the populations into four clusters that correlated with the country of origin. The negligible gene flow between the Thai and Laos populations, despite sharing the Mekong Basin, caused us to reject our hypothesis. Our data suggest that the distribution of H. taichui populations was incidentally associated with national borders.

Range-wide network of priority areas for greater sage-grouse - a design for conserving connected distributions or isolating individual zoos?

Science.gov (United States)

Crist, Michele R.; Knick, Steven T.; Hanser, Steven E.

2015-09-08

The network of areas delineated in 11 Western States for prioritizing management of greater sage-grouse (Centrocercus urophasianus) represents a grand experiment in conservation biology and reserve design. We used centrality metrics from social network theory to gain insights into how this priority area network might function. The network was highly centralized. Twenty of 188 priority areas accounted for 80 percent of the total centrality scores. These priority areas, characterized by large size and a central location in the range-wide distribution, are strongholds for greater sage-grouse populations and also might function as sources. Mid-ranking priority areas may serve as stepping stones because of their location between large central and smaller peripheral priority areas. The current network design and conservation strategy has risks. The contribution of almost one-half (n = 93) of the priority areas combined for less than 1 percent of the cumulative centrality scores for the network. These priority areas individually are likely too small to support viable sage-grouse populations within their boundary. Without habitat corridors to connect small priority areas either to larger priority areas or as a clustered group within the network, their isolation could lead to loss of sage-grouse within these regions of the network. 

Genome-Wide Association Study Reveals Greater Polygenic Loading for Schizophrenia in Cases With a Family History of Illness

Science.gov (United States)

Bigdeli, Tim B.; Ripke, Stephan; Bacanu, Silviu-Alin; Lee, Sang Hong; Wray, Naomi R.; Gejman, Pablo V.; Rietschel, Marcella; Cichon, Sven; St Clair, David; Corvin, Aiden; Kirov, George; McQuillin, Andrew; Gurling, Hugh; Rujescu, Dan; Andreassen, Ole A.; Werge, Thomas; Blackwood, Douglas H.R.; Pato, Carlos N.; Pato, Michele T.; Malhotra, Anil K.; O’Donovan, Michael C.; Kendler, Kenneth S.; Fanous, Ayman H.

2018-01-01

Genome-wide association studies (GWAS) of schizophrenia have yielded more than 100 common susceptibility variants, and strongly support a substantial polygenic contribution of a large number of small allelic effects. It has been hypothesized that familial schizophrenia is largely a consequence of inherited rather than environmental factors. We investigated the extent to which familiality of schizophrenia is associated with enrichment for common risk variants detectable in a large GWAS. We analyzed single nucleotide polymorphism (SNP) data for cases reporting a family history of psychotic illness (N = 978), cases reporting no such family history (N = 4,503), and unscreened controls (N = 8,285) from the Psychiatric Genomics Consortium (PGC1) study of schizophrenia. We used a multinomial logistic regression approach with model-fitting to detect allelic effects specific to either family history subgroup. We also considered a polygenic model, in which we tested whether family history positive subjects carried more schizophrenia risk alleles than family history negative subjects, on average. Several individual SNPs attained suggestive but not genome-wide significant association with either family history subgroup. Comparison of genome-wide polygenic risk scores based on GWAS summary statistics indicated a significant enrichment for SNP effects among family history positive compared to family history negative cases (Nagelkerke’s R2 = 0.0021; P = 0.00331; P-value threshold history positive compared to family history negative cases (0.32 and 0.22, respectively; P = 0.031).We found suggestive evidence of allelic effects detectable in large GWAS of schizophrenia that might be specific to particular family history subgroups. However, consideration of a polygenic risk score indicated a significant enrichment among family history positive cases for common allelic effects. Familial illness might, therefore, represent a more heritable form of schizophrenia, as suggested by

Extensive translational regulation during seed germination revealed by polysomal profiling

NARCIS (Netherlands)

Bai, Bing; Peviani, Alessia; Horst, van der Sjors; Gamm, Magdalena; Snel, Berend; Bentsink, Leónie; Hanson, Johannes

2017-01-01

This work investigates the extent of translational regulation during seed germination. The polysome occupancy of each gene is determined by genome-wide profiling of total mRNA and polysome-associated mRNA. This reveals extensive translational regulation during Arabidopsis thaliana seed

Genome-Wide Characterization and Expression Analysis of Major Intrinsic Proteins during Abiotic and Biotic Stresses in Sweet Orange (Citrus sinensis L. Osb.).

Science.gov (United States)

Martins, Cristina de Paula Santos; Pedrosa, Andresa Muniz; Du, Dongliang; Gonçalves, Luana Pereira; Yu, Qibin; Gmitter, Frederick G; Costa, Marcio Gilberto Cardoso

2015-01-01

The family of aquaporins (AQPs), or major intrinsic proteins (MIPs), includes integral membrane proteins that function as transmembrane channels for water and other small molecules of physiological significance. MIPs are classified into five subfamilies in higher plants, including plasma membrane (PIPs), tonoplast (TIPs), NOD26-like (NIPs), small basic (SIPs) and unclassified X (XIPs) intrinsic proteins. This study reports a genome-wide survey of MIP encoding genes in sweet orange (Citrus sinensis L. Osb.), the most widely cultivated Citrus spp. A total of 34 different genes encoding C. sinensis MIPs (CsMIPs) were identified and assigned into five subfamilies (CsPIPs, CsTIPs, CsNIPs, CsSIPs and CsXIPs) based on sequence analysis and also on their phylogenetic relationships with clearly classified MIPs of Arabidopsis thaliana. Analysis of key amino acid residues allowed the assessment of the substrate specificity of each CsMIP. Gene structure analysis revealed that the CsMIPs possess an exon-intron organization that is highly conserved within each subfamily. CsMIP loci were precisely mapped on every sweet orange chromosome, indicating a wide distribution of the gene family in the sweet orange genome. Investigation of their expression patterns in different tissues and upon drought and salt stress treatments, as well as with 'Candidatus Liberibacter asiaticus' infection, revealed a tissue-specific and coordinated regulation of the different CsMIP isoforms, consistent with the organization of the stress-responsive cis-acting regulatory elements observed in their promoter regions. A special role in regulating the flow of water and nutrients is proposed for CsTIPs and CsXIPs during drought stress, and for most CsMIPs during salt stress and the development of HLB disease. These results provide a valuable reference for further exploration of the CsMIPs functions and applications to the genetic improvement of both abiotic and biotic stress tolerance in citrus.

Genome-Wide Characterization and Expression Analysis of Major Intrinsic Proteins during Abiotic and Biotic Stresses in Sweet Orange (Citrus sinensis L. Osb..

Directory of Open Access Journals (Sweden)

Cristina de Paula Santos Martins

Full Text Available The family of aquaporins (AQPs, or major intrinsic proteins (MIPs, includes integral membrane proteins that function as transmembrane channels for water and other small molecules of physiological significance. MIPs are classified into five subfamilies in higher plants, including plasma membrane (PIPs, tonoplast (TIPs, NOD26-like (NIPs, small basic (SIPs and unclassified X (XIPs intrinsic proteins. This study reports a genome-wide survey of MIP encoding genes in sweet orange (Citrus sinensis L. Osb., the most widely cultivated Citrus spp. A total of 34 different genes encoding C. sinensis MIPs (CsMIPs were identified and assigned into five subfamilies (CsPIPs, CsTIPs, CsNIPs, CsSIPs and CsXIPs based on sequence analysis and also on their phylogenetic relationships with clearly classified MIPs of Arabidopsis thaliana. Analysis of key amino acid residues allowed the assessment of the substrate specificity of each CsMIP. Gene structure analysis revealed that the CsMIPs possess an exon-intron organization that is highly conserved within each subfamily. CsMIP loci were precisely mapped on every sweet orange chromosome, indicating a wide distribution of the gene family in the sweet orange genome. Investigation of their expression patterns in different tissues and upon drought and salt stress treatments, as well as with 'Candidatus Liberibacter asiaticus' infection, revealed a tissue-specific and coordinated regulation of the different CsMIP isoforms, consistent with the organization of the stress-responsive cis-acting regulatory elements observed in their promoter regions. A special role in regulating the flow of water and nutrients is proposed for CsTIPs and CsXIPs during drought stress, and for most CsMIPs during salt stress and the development of HLB disease. These results provide a valuable reference for further exploration of the CsMIPs functions and applications to the genetic improvement of both abiotic and biotic stress tolerance in citrus.

Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species

Science.gov (United States)

Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

2016-01-01

Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

Mitochondrial DNA haplotype distribution patterns in Pinus ponderosa (Pinaceae): range-wide evolutionary history and implications for conservation.

Science.gov (United States)

Potter, Kevin M; Hipkins, Valerie D; Mahalovich, Mary F; Means, Robert E

2013-08-01

Ponderosa pine (Pinus ponderosa Douglas ex P. Lawson & C. Lawson) exhibits complicated patterns of morphological and genetic variation across its range in western North America. This study aims to clarify P. ponderosa evolutionary history and phylogeography using a highly polymorphic mitochondrial DNA marker, with results offering insights into how geographical and climatological processes drove the modern evolutionary structure of tree species in the region. We amplified the mtDNA nad1 second intron minisatellite region for 3,100 trees representing 104 populations, and sequenced all length variants. We estimated population-level haplotypic diversity and determined diversity partitioning among varieties, races and populations. After aligning sequences of minisatellite repeat motifs, we evaluated evolutionary relationships among haplotypes. The geographical structuring of the 10 haplotypes corresponded with division between Pacific and Rocky Mountain varieties. Pacific haplotypes clustered with high bootstrap support, and appear to have descended from Rocky Mountain haplotypes. A greater proportion of diversity was partitioned between Rocky Mountain races than between Pacific races. Areas of highest haplotypic diversity were the southern Sierra Nevada mountain range in California, northwestern California, and southern Nevada. Pinus ponderosa haplotype distribution patterns suggest a complex phylogeographic history not revealed by other genetic and morphological data, or by the sparse paleoecological record. The results appear consistent with long-term divergence between the Pacific and Rocky Mountain varieties, along with more recent divergences not well-associated with race. Pleistocene refugia may have existed in areas of high haplotypic diversity, as well as the Great Basin, Southwestern United States/northern Mexico, and the High Plains.

Status of research reactor spent fuel world-wide

International Nuclear Information System (INIS)

Ritchie, I.G.

2004-01-01

Results compiled in the research reactor spent fuel database are used to assess the status of research reactor spent fuel world-wide. Fuel assemblies, their types, enrichment, origin of enrichment and geological distribution among the industrialised and developed countries of the world are discussed. Fuel management practices in wet and dry storage facilities and the concerns of reactor operators about long-term storage of their spent fuel are presented and some of the activities carried out by the International Atomic Energy Agency to address the issues associated with research reactor spent fuel are outlined. (author)

RBAC administration in distributed systems

NARCIS (Netherlands)

Dekker, M.A.C.; Crampton, J.; Etalle, Sandro; Li, N.

Large and distributed access control systems are increasingly common, for example in health care. In such settings, access control policies may become very complex, thus complicating correct and efficient adminstration of the access control system. Despite being one of the most widely used access

Genome-wide association studies on HIV susceptibility, pathogenesis and pharmacogenomics

Directory of Open Access Journals (Sweden)

van Manen Daniëlle

2012-08-01

Full Text Available Abstract Susceptibility to HIV-1 and the clinical course after infection show a substantial heterogeneity between individuals. Part of this variability can be attributed to host genetic variation. Initial candidate gene studies have revealed interesting host factors that influence HIV infection, replication and pathogenesis. Recently, genome-wide association studies (GWAS were utilized for unbiased searches at a genome-wide level to discover novel genetic factors and pathways involved in HIV-1 infection. This review gives an overview of findings from the GWAS performed on HIV infection, within different cohorts, with variable patient and phenotype selection. Furthermore, novel techniques and strategies in research that might contribute to the complete understanding of virus-host interactions and its role on the pathogenesis of HIV infection are discussed.

Compilation of a soil map for Nigeria: a nation-wide soil resource ...

African Journals Online (AJOL)

This paper presents the results of a nation-wide soil and land form inventory of Nigeria. The data compilation was conducted in the framework of two projects with the objective to calculate agricultural production potential under different input levels and assess the water erosion hazard. The information on spatial distribution ...

A Review of Power Distribution Test Feeders in the United States and the Need for Synthetic Representative Networks

Directory of Open Access Journals (Sweden)

Fernando E. Postigo Marcos

2017-11-01

Full Text Available Under the increasing penetration of distributed energy resources and new smart network technologies, distribution utilities face new challenges and opportunities to ensure reliable operations, manage service quality, and reduce operational and investment costs. Simultaneously, the research community is developing algorithms for advanced controls and distribution automation that can help to address some of these challenges. However, there is a shortage of realistic test systems that are publically available for development, testing, and evaluation of such new algorithms. Concerns around revealing critical infrastructure details and customer privacy have severely limited the number of actual networks published and that are available for testing. In recent decades, several distribution test feeders and US-featured representative networks have been published, but the scale, complexity, and control data vary widely. This paper presents a first-of-a-kind structured literature review of published distribution test networks with a special emphasis on classifying their main characteristics and identifying the types of studies for which they have been used. This both aids researchers in choosing suitable test networks for their needs and highlights the opportunities and directions for further test system development. In particular, we highlight the need for building large-scale synthetic networks to overcome the identified drawbacks of current distribution test feeders.